null Tue 25 Dec 19:27:58 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hx1-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:06 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-2.1-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1161 and 0 Target number of residues in the AU: 1161 Target solvent content: 0.4702 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-2.1-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.50 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 93.753 2.100 Wilson plot Bfac: 17.81 70128 reflections ( 99.92 % complete ) and 0 restraints for refining 10099 atoms. Observations/parameters ratio is 1.74 ------------------------------------------------------ Starting model: R = 0.3415 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2908 (Rfree = 0.000) for 10099 atoms. Found 301 (301 requested) and removed 161 (150 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.99 2.04 NCS extension: 0 residues added, 10239 seeds are put forward Round 1: 852 peptides, 98 chains. Longest chain 33 peptides. Score 0.712 Round 2: 976 peptides, 59 chains. Longest chain 78 peptides. Score 0.874 Round 3: 1049 peptides, 36 chains. Longest chain 87 peptides. Score 0.929 Round 4: 1055 peptides, 35 chains. Longest chain 87 peptides. Score 0.931 Round 5: 1064 peptides, 38 chains. Longest chain 94 peptides. Score 0.929 Taking the results from Round 4 Chains 40, Residues 1020, Estimated correctness of the model 99.4 % 20 chains (878 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 21 A and 24 A Built loop between residues 73 A and 78 A Built loop between residues 253 A and 256 A Built loop between residues 44 C and 48 C Built loop between residues 44 B and 48 B Built loop between residues 111 B and 117 B Built loop between residues 254 B and 257 B Built loop between residues 202 D and 207 D 29 chains (1041 residues) following loop building 12 chains (903 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10999 restraints for refining 9494 atoms. 3346 conditional restraints added. Observations/parameters ratio is 1.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3083 (Rfree = 0.000) for 9494 atoms. Found 283 (283 requested) and removed 159 (141 requested) atoms. Cycle 2: After refmac, R = 0.2898 (Rfree = 0.000) for 9581 atoms. Found 198 (280 requested) and removed 127 (143 requested) atoms. Cycle 3: After refmac, R = 0.2776 (Rfree = 0.000) for 9618 atoms. Found 161 (276 requested) and removed 39 (143 requested) atoms. Cycle 4: After refmac, R = 0.2687 (Rfree = 0.000) for 9723 atoms. Found 121 (278 requested) and removed 31 (145 requested) atoms. Cycle 5: After refmac, R = 0.2604 (Rfree = 0.000) for 9787 atoms. Found 104 (280 requested) and removed 25 (146 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.96 2.01 NCS extension: 9 residues added (34 deleted due to clashes), 9882 seeds are put forward Round 1: 1078 peptides, 30 chains. Longest chain 88 peptides. Score 0.941 Round 2: 1094 peptides, 23 chains. Longest chain 111 peptides. Score 0.952 Round 3: 1084 peptides, 29 chains. Longest chain 111 peptides. Score 0.943 Round 4: 1085 peptides, 28 chains. Longest chain 113 peptides. Score 0.945 Round 5: 1090 peptides, 26 chains. Longest chain 111 peptides. Score 0.948 Taking the results from Round 2 Chains 27, Residues 1071, Estimated correctness of the model 99.7 % 15 chains (990 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 114 A and 119 A Built loop between residues 44 C and 47 C Built loop between residues 40 B and 43 B Built loop between residues 201 B and 207 B Built loop between residues 112 D and 118 D Built loop between residues 201 D and 207 D 19 chains (1089 residues) following loop building 9 chains (1013 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10292 restraints for refining 9785 atoms. 2026 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2700 (Rfree = 0.000) for 9785 atoms. Found 230 (279 requested) and removed 152 (145 requested) atoms. Cycle 7: After refmac, R = 0.2563 (Rfree = 0.000) for 9855 atoms. Found 128 (276 requested) and removed 50 (147 requested) atoms. Cycle 8: After refmac, R = 0.2468 (Rfree = 0.000) for 9918 atoms. Found 116 (278 requested) and removed 19 (148 requested) atoms. Cycle 9: After refmac, R = 0.2335 (Rfree = 0.000) for 9997 atoms. Found 104 (280 requested) and removed 22 (149 requested) atoms. Cycle 10: After refmac, R = 0.2296 (Rfree = 0.000) for 10049 atoms. Found 114 (282 requested) and removed 17 (150 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.95 2.00 NCS extension: 14 residues added (110 deleted due to clashes), 10169 seeds are put forward Round 1: 1098 peptides, 21 chains. Longest chain 112 peptides. Score 0.954 Round 2: 1106 peptides, 18 chains. Longest chain 111 peptides. Score 0.958 Round 3: 1095 peptides, 28 chains. Longest chain 159 peptides. Score 0.946 Round 4: 1102 peptides, 22 chains. Longest chain 203 peptides. Score 0.954 Round 5: 1096 peptides, 27 chains. Longest chain 105 peptides. Score 0.947 Taking the results from Round 2 Chains 20, Residues 1088, Estimated correctness of the model 99.7 % 16 chains (1065 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 116 A Built loop between residues 204 A and 207 A Built loop between residues 20 C and 23 C Built loop between residues 112 C and 117 C Built loop between residues 200 C and 207 C Built loop between residues 44 B and 47 B Built loop between residues 113 B and 116 B Built loop between residues 204 B and 207 B Built loop between residues 235 B and 238 B Built loop between residues 94 D and 98 D Built loop between residues 201 D and 207 D 8 chains (1118 residues) following loop building 5 chains (1098 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 9904 restraints for refining 10042 atoms. 1171 conditional restraints added. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2534 (Rfree = 0.000) for 10042 atoms. Found 244 (281 requested) and removed 162 (149 requested) atoms. Cycle 12: After refmac, R = 0.2414 (Rfree = 0.000) for 10110 atoms. Found 164 (277 requested) and removed 55 (150 requested) atoms. Cycle 13: After refmac, R = 0.2331 (Rfree = 0.000) for 10197 atoms. Found 121 (280 requested) and removed 40 (152 requested) atoms. Cycle 14: After refmac, R = 0.2272 (Rfree = 0.000) for 10262 atoms. Found 111 (282 requested) and removed 27 (153 requested) atoms. Cycle 15: After refmac, R = 0.2221 (Rfree = 0.000) for 10333 atoms. Found 78 (283 requested) and removed 26 (154 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.95 2.00 NCS extension: 49 residues added (294 deleted due to clashes), 10445 seeds are put forward Round 1: 1104 peptides, 20 chains. Longest chain 113 peptides. Score 0.956 Round 2: 1108 peptides, 18 chains. Longest chain 106 peptides. Score 0.959 Round 3: 1103 peptides, 23 chains. Longest chain 194 peptides. Score 0.953 Round 4: 1098 peptides, 25 chains. Longest chain 105 peptides. Score 0.950 Round 5: 1097 peptides, 25 chains. Longest chain 122 peptides. Score 0.950 Taking the results from Round 2 Chains 21, Residues 1090, Estimated correctness of the model 99.8 % 16 chains (1069 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 113 A and 117 A Built loop between residues 204 A and 207 A Built loop between residues 215 A and 222 A Built loop between residues 26 C and 36 C Built loop between residues 113 C and 117 C Built loop between residues 200 C and 206 C Built loop between residues 25 B and 28 B Built loop between residues 200 B and 207 B Built loop between residues 95 D and 99 D 8 chains (1120 residues) following loop building 6 chains (1110 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 9905 restraints for refining 10269 atoms. 1106 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2433 (Rfree = 0.000) for 10269 atoms. Found 236 (282 requested) and removed 168 (153 requested) atoms. Cycle 17: After refmac, R = 0.2309 (Rfree = 0.000) for 10320 atoms. Found 147 (277 requested) and removed 58 (154 requested) atoms. Cycle 18: After refmac, R = 0.2243 (Rfree = 0.000) for 10392 atoms. Found 100 (279 requested) and removed 35 (155 requested) atoms. Cycle 19: After refmac, R = 0.2180 (Rfree = 0.000) for 10447 atoms. Found 103 (280 requested) and removed 13 (155 requested) atoms. Cycle 20: After refmac, R = 0.2144 (Rfree = 0.000) for 10528 atoms. Found 84 (283 requested) and removed 33 (157 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.94 1.99 NCS extension: 41 residues added (153 deleted due to clashes), 10629 seeds are put forward Round 1: 1105 peptides, 18 chains. Longest chain 111 peptides. Score 0.958 Round 2: 1104 peptides, 20 chains. Longest chain 204 peptides. Score 0.956 Round 3: 1098 peptides, 26 chains. Longest chain 112 peptides. Score 0.949 Round 4: 1100 peptides, 23 chains. Longest chain 108 peptides. Score 0.952 Round 5: 1095 peptides, 26 chains. Longest chain 112 peptides. Score 0.949 Taking the results from Round 1 Chains 20, Residues 1087, Estimated correctness of the model 99.7 % 17 chains (1076 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 203 A and 206 A Built loop between residues 112 C and 117 C Built loop between residues 204 C and 207 C Built loop between residues 215 C and 223 C Built loop between residues 254 C and 257 C Built loop between residues 32 B and 35 B Built loop between residues 114 B and 117 B Built loop between residues 200 B and 206 B Built loop between residues 254 B and 257 B Built loop between residues 95 D and 99 D Built loop between residues 254 D and 257 D 9 chains (1120 residues) following loop building 6 chains (1109 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10051 restraints for refining 10396 atoms. 1249 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2331 (Rfree = 0.000) for 10396 atoms. Found 246 (278 requested) and removed 159 (154 requested) atoms. Cycle 22: After refmac, R = 0.2244 (Rfree = 0.000) for 10471 atoms. Found 142 (275 requested) and removed 48 (156 requested) atoms. Cycle 23: After refmac, R = 0.2133 (Rfree = 0.000) for 10550 atoms. Found 119 (276 requested) and removed 31 (157 requested) atoms. Cycle 24: After refmac, R = 0.2073 (Rfree = 0.000) for 10606 atoms. Found 124 (279 requested) and removed 46 (158 requested) atoms. Cycle 25: After refmac, R = 0.2030 (Rfree = 0.000) for 10663 atoms. Found 116 (280 requested) and removed 67 (159 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.94 1.99 NCS extension: 18 residues added (239 deleted due to clashes), 10736 seeds are put forward Round 1: 1103 peptides, 18 chains. Longest chain 114 peptides. Score 0.958 Round 2: 1106 peptides, 17 chains. Longest chain 170 peptides. Score 0.960 Round 3: 1104 peptides, 24 chains. Longest chain 107 peptides. Score 0.952 Round 4: 1102 peptides, 20 chains. Longest chain 159 peptides. Score 0.956 Round 5: 1093 peptides, 24 chains. Longest chain 106 peptides. Score 0.950 Taking the results from Round 2 Chains 19, Residues 1089, Estimated correctness of the model 99.8 % 14 chains (1062 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 204 A and 207 A Built loop between residues 204 C and 208 C Built loop between residues 231 C and 234 C Built loop between residues 33 B and 36 B Built loop between residues 204 B and 207 B Built loop between residues 112 D and 117 D Built loop between residues 204 D and 207 D Built loop between residues 217 D and 225 D 9 chains (1111 residues) following loop building 6 chains (1086 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10288 restraints for refining 10385 atoms. 1611 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2286 (Rfree = 0.000) for 10385 atoms. Found 266 (266 requested) and removed 165 (154 requested) atoms. Cycle 27: After refmac, R = 0.2131 (Rfree = 0.000) for 10471 atoms. Found 192 (262 requested) and removed 41 (156 requested) atoms. Cycle 28: After refmac, R = 0.2047 (Rfree = 0.000) for 10598 atoms. Found 144 (265 requested) and removed 45 (158 requested) atoms. Cycle 29: After refmac, R = 0.2002 (Rfree = 0.000) for 10680 atoms. Found 117 (267 requested) and removed 60 (159 requested) atoms. Cycle 30: After refmac, R = 0.1997 (Rfree = 0.000) for 10719 atoms. Found 149 (262 requested) and removed 44 (160 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.94 1.99 NCS extension: 37 residues added (353 deleted due to clashes), 10865 seeds are put forward Round 1: 1110 peptides, 17 chains. Longest chain 204 peptides. Score 0.960 Round 2: 1115 peptides, 16 chains. Longest chain 171 peptides. Score 0.962 Round 3: 1111 peptides, 20 chains. Longest chain 204 peptides. Score 0.957 Round 4: 1108 peptides, 19 chains. Longest chain 107 peptides. Score 0.958 Round 5: 1113 peptides, 19 chains. Longest chain 204 peptides. Score 0.958 Taking the results from Round 2 Chains 19, Residues 1099, Estimated correctness of the model 99.8 % 12 chains (1033 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 204 A and 207 A Built loop between residues 233 A and 239 A Built loop between residues 31 C and 35 C Built loop between residues 203 C and 207 C Built loop between residues 204 B and 207 B 12 chains (1111 residues) following loop building 7 chains (1048 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10536 restraints for refining 10409 atoms. 2000 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2297 (Rfree = 0.000) for 10409 atoms. Found 254 (254 requested) and removed 164 (155 requested) atoms. Cycle 32: After refmac, R = 0.2194 (Rfree = 0.000) for 10485 atoms. Found 194 (250 requested) and removed 38 (156 requested) atoms. Cycle 33: After refmac, R = 0.2143 (Rfree = 0.000) for 10633 atoms. Found 126 (254 requested) and removed 47 (158 requested) atoms. Cycle 34: After refmac, R = 0.2086 (Rfree = 0.000) for 10702 atoms. Found 131 (255 requested) and removed 40 (159 requested) atoms. Cycle 35: After refmac, R = 0.2053 (Rfree = 0.000) for 10785 atoms. Found 123 (257 requested) and removed 65 (160 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.93 1.98 NCS extension: 3 residues added (192 deleted due to clashes), 10850 seeds are put forward Round 1: 1110 peptides, 18 chains. Longest chain 113 peptides. Score 0.959 Round 2: 1116 peptides, 14 chains. Longest chain 204 peptides. Score 0.964 Round 3: 1103 peptides, 23 chains. Longest chain 107 peptides. Score 0.953 Round 4: 1111 peptides, 20 chains. Longest chain 114 peptides. Score 0.957 Round 5: 1098 peptides, 23 chains. Longest chain 95 peptides. Score 0.952 Taking the results from Round 2 Chains 14, Residues 1102, Estimated correctness of the model 99.8 % 13 chains (1095 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 117 A Built loop between residues 235 A and 238 A Built loop between residues 113 B and 117 B Built loop between residues 235 D and 238 D 10 chains (1112 residues) following loop building 9 chains (1105 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10211 restraints for refining 10525 atoms. 1462 conditional restraints added. Observations/parameters ratio is 1.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2238 (Rfree = 0.000) for 10525 atoms. Found 244 (244 requested) and removed 159 (156 requested) atoms. Cycle 37: After refmac, R = 0.2160 (Rfree = 0.000) for 10592 atoms. Found 175 (240 requested) and removed 49 (158 requested) atoms. Cycle 38: After refmac, R = 0.2096 (Rfree = 0.000) for 10706 atoms. Found 126 (242 requested) and removed 49 (159 requested) atoms. Cycle 39: After refmac, R = 0.2043 (Rfree = 0.000) for 10775 atoms. Found 119 (244 requested) and removed 47 (160 requested) atoms. Cycle 40: After refmac, R = 0.2017 (Rfree = 0.000) for 10837 atoms. Found 114 (245 requested) and removed 64 (161 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.94 1.99 NCS extension: 12 residues added (292 deleted due to clashes), 10899 seeds are put forward Round 1: 1112 peptides, 17 chains. Longest chain 204 peptides. Score 0.960 Round 2: 1116 peptides, 13 chains. Longest chain 121 peptides. Score 0.965 Round 3: 1106 peptides, 21 chains. Longest chain 204 peptides. Score 0.955 Round 4: 1110 peptides, 18 chains. Longest chain 121 peptides. Score 0.959 Round 5: 1104 peptides, 23 chains. Longest chain 121 peptides. Score 0.953 Taking the results from Round 2 Chains 15, Residues 1103, Estimated correctness of the model 99.8 % 13 chains (1098 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 117 A Built loop between residues 204 A and 207 A Built loop between residues 81 C and 84 C Built loop between residues 202 C and 207 C Built loop between residues 32 B and 36 B Built loop between residues 121 B and 124 B Built loop between residues 114 D and 117 D Built loop between residues 203 D and 206 D 6 chains (1122 residues) following loop building 5 chains (1118 residues) in sequence following loop building ------------------------------------------------------ 70128 reflections ( 99.92 % complete ) and 10140 restraints for refining 10583 atoms. 1304 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2133 (Rfree = 0.000) for 10583 atoms. Found 233 (233 requested) and removed 167 (157 requested) atoms. Cycle 42: After refmac, R = 0.2050 (Rfree = 0.000) for 10619 atoms. Found 197 (228 requested) and removed 66 (158 requested) atoms. Cycle 43: After refmac, R = 0.1995 (Rfree = 0.000) for 10732 atoms. Found 162 (230 requested) and removed 61 (160 requested) atoms. Cycle 44: After refmac, R = 0.1947 (Rfree = 0.000) for 10824 atoms. Found 151 (232 requested) and removed 69 (161 requested) atoms. Cycle 45: After refmac, R = 0.1924 (Rfree = 0.000) for 10890 atoms. Found 154 (234 requested) and removed 77 (162 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.93 1.98 NCS extension: 35 residues added (293 deleted due to clashes), 11005 seeds are put forward Round 1: 1112 peptides, 16 chains. Longest chain 139 peptides. Score 0.961 Round 2: 1112 peptides, 14 chains. Longest chain 153 peptides. Score 0.963 Round 3: 1102 peptides, 21 chains. Longest chain 111 peptides. Score 0.955 Round 4: 1112 peptides, 15 chains. Longest chain 167 peptides. Score 0.962 Round 5: 1101 peptides, 22 chains. Longest chain 113 peptides. Score 0.954 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 1098, Estimated correctness of the model 99.8 % 12 chains (1073 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 113 A and 116 A Built loop between residues 219 A and 225 A Built loop between residues 202 C and 207 C Built loop between residues 113 B and 117 B Built loop between residues 128 B and 131 B Built loop between residues 113 D and 117 D 10 chains (1116 residues) following loop building 6 chains (1092 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 70128 reflections ( 99.92 % complete ) and 8718 restraints for refining 8579 atoms. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2739 (Rfree = 0.000) for 8579 atoms. Found 168 (184 requested) and removed 0 (184 requested) atoms. Cycle 47: After refmac, R = 0.2535 (Rfree = 0.000) for 8579 atoms. Found 86 (187 requested) and removed 3 (130 requested) atoms. Cycle 48: After refmac, R = 0.2431 (Rfree = 0.000) for 8579 atoms. Found 41 (189 requested) and removed 7 (131 requested) atoms. Cycle 49: After refmac, R = 0.2396 (Rfree = 0.000) for 8579 atoms. Found 22 (190 requested) and removed 7 (132 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:13:08 GMT 2018 Job finished. TimeTaking 165.18 Used memory is bytes: 26649576