Mon 24 Dec 08:06:04 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p7i-1.7-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p7i-1.7-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p7i-1.7-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 08:06:09 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/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-1.7-parrot-noncs/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 502 and 0 Target number of residues in the AU: 502 Target solvent content: 0.5030 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-1.7-parrot-noncs.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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-1.7-parrot-noncs.fasta_lf Building free atoms model in initial map for 4000 target number of atoms Had to go as low as 0.30 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: 94.045 1.740 Wilson plot Bfac: 23.93 56831 reflections ( 99.96 % complete ) and 0 restraints for refining 4416 atoms. Observations/parameters ratio is 3.22 ------------------------------------------------------ Starting model: R = 0.3190 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2655 (Rfree = 0.000) for 4416 atoms. Found 143 (224 requested) and removed 128 (112 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.02 2.02 NCS extension: 0 residues added, 4431 seeds are put forward Round 1: 353 peptides, 31 chains. Longest chain 45 peptides. Score 0.753 Round 2: 383 peptides, 17 chains. Longest chain 106 peptides. Score 0.867 Round 3: 403 peptides, 16 chains. Longest chain 76 peptides. Score 0.887 Round 4: 414 peptides, 11 chains. Longest chain 117 peptides. Score 0.914 Round 5: 414 peptides, 13 chains. Longest chain 112 peptides. Score 0.906 Taking the results from Round 4 Chains 13, Residues 403, Estimated correctness of the model 99.5 % 9 chains (373 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 78 B and 88 B Built loop between residues 165 B and 168 B Built loop between residues 211 B and 220 B 8 chains (423 residues) following loop building 5 chains (394 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4205 restraints for refining 3969 atoms. 856 conditional restraints added. Observations/parameters ratio is 3.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2783 (Rfree = 0.000) for 3969 atoms. Found 131 (202 requested) and removed 74 (101 requested) atoms. Cycle 2: After refmac, R = 0.2367 (Rfree = 0.000) for 4016 atoms. Found 107 (201 requested) and removed 31 (102 requested) atoms. Cycle 3: After refmac, R = 0.2168 (Rfree = 0.000) for 4079 atoms. Found 86 (204 requested) and removed 20 (104 requested) atoms. Cycle 4: After refmac, R = 0.2050 (Rfree = 0.000) for 4127 atoms. Found 63 (207 requested) and removed 21 (105 requested) atoms. Cycle 5: After refmac, R = 0.1965 (Rfree = 0.000) for 4146 atoms. Found 75 (208 requested) and removed 19 (106 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.96 1.96 NCS extension: 39 residues added (141 deleted due to clashes), 4245 seeds are put forward Round 1: 435 peptides, 8 chains. Longest chain 114 peptides. Score 0.934 Round 2: 436 peptides, 8 chains. Longest chain 157 peptides. Score 0.935 Round 3: 433 peptides, 11 chains. Longest chain 84 peptides. Score 0.924 Round 4: 430 peptides, 10 chains. Longest chain 120 peptides. Score 0.925 Round 5: 440 peptides, 9 chains. Longest chain 96 peptides. Score 0.933 Taking the results from Round 2 Chains 10, Residues 428, Estimated correctness of the model 99.7 % 7 chains (415 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 102 A Built loop between residues 165 A and 168 A Built loop between residues 206 A and 217 A Built loop between residues 84 B and 90 B 5 chains (440 residues) following loop building 3 chains (435 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4134 restraints for refining 4126 atoms. 546 conditional restraints added. Observations/parameters ratio is 3.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2150 (Rfree = 0.000) for 4126 atoms. Found 118 (206 requested) and removed 86 (105 requested) atoms. Cycle 7: After refmac, R = 0.1989 (Rfree = 0.000) for 4148 atoms. Found 79 (203 requested) and removed 47 (105 requested) atoms. Cycle 8: After refmac, R = 0.1902 (Rfree = 0.000) for 4171 atoms. Found 60 (199 requested) and removed 31 (106 requested) atoms. Cycle 9: After refmac, R = 0.1847 (Rfree = 0.000) for 4190 atoms. Found 76 (196 requested) and removed 32 (106 requested) atoms. Cycle 10: After refmac, R = 0.1794 (Rfree = 0.000) for 4229 atoms. Found 66 (198 requested) and removed 39 (107 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.96 1.96 NCS extension: 29 residues added (209 deleted due to clashes), 4292 seeds are put forward Round 1: 439 peptides, 8 chains. Longest chain 114 peptides. Score 0.936 Round 2: 442 peptides, 7 chains. Longest chain 165 peptides. Score 0.940 Round 3: 447 peptides, 6 chains. Longest chain 175 peptides. Score 0.945 Round 4: 442 peptides, 9 chains. Longest chain 104 peptides. Score 0.934 Round 5: 442 peptides, 9 chains. Longest chain 128 peptides. Score 0.934 Taking the results from Round 3 Chains 6, Residues 441, Estimated correctness of the model 99.8 % 4 chains (386 residues) have been docked in sequence Building loops using Loopy2018 6 chains (441 residues) following loop building 4 chains (386 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4425 restraints for refining 4092 atoms. 1059 conditional restraints added. Observations/parameters ratio is 3.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2063 (Rfree = 0.000) for 4092 atoms. Found 103 (187 requested) and removed 55 (104 requested) atoms. Cycle 12: After refmac, R = 0.1933 (Rfree = 0.000) for 4135 atoms. Found 67 (185 requested) and removed 37 (105 requested) atoms. Cycle 13: After refmac, R = 0.1855 (Rfree = 0.000) for 4156 atoms. Found 69 (182 requested) and removed 22 (106 requested) atoms. Cycle 14: After refmac, R = 0.1807 (Rfree = 0.000) for 4197 atoms. Found 53 (183 requested) and removed 38 (106 requested) atoms. Cycle 15: After refmac, R = 0.1779 (Rfree = 0.000) for 4208 atoms. Found 62 (180 requested) and removed 34 (107 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.96 1.96 NCS extension: 3 residues added (8 deleted due to clashes), 4243 seeds are put forward Round 1: 448 peptides, 5 chains. Longest chain 177 peptides. Score 0.948 Round 2: 448 peptides, 3 chains. Longest chain 224 peptides. Score 0.954 Round 3: 447 peptides, 6 chains. Longest chain 172 peptides. Score 0.945 Round 4: 443 peptides, 8 chains. Longest chain 214 peptides. Score 0.938 Round 5: 437 peptides, 12 chains. Longest chain 112 peptides. Score 0.922 Taking the results from Round 2 Chains 3, Residues 445, Estimated correctness of the model 99.8 % 3 chains (445 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 87 A 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 3990 restraints for refining 4155 atoms. 297 conditional restraints added. Observations/parameters ratio is 3.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2035 (Rfree = 0.000) for 4155 atoms. Found 131 (173 requested) and removed 92 (105 requested) atoms. Cycle 17: After refmac, R = 0.1914 (Rfree = 0.000) for 4192 atoms. Found 104 (170 requested) and removed 66 (106 requested) atoms. Cycle 18: After refmac, R = 0.1846 (Rfree = 0.000) for 4227 atoms. Found 113 (168 requested) and removed 65 (107 requested) atoms. Cycle 19: After refmac, R = 0.1826 (Rfree = 0.000) for 4269 atoms. Found 114 (165 requested) and removed 74 (108 requested) atoms. Cycle 20: After refmac, R = 0.1791 (Rfree = 0.000) for 4303 atoms. Found 104 (162 requested) and removed 60 (109 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.96 1.96 NCS extension: 60 residues added (172 deleted due to clashes), 4409 seeds are put forward Round 1: 446 peptides, 6 chains. Longest chain 114 peptides. Score 0.945 Round 2: 449 peptides, 4 chains. Longest chain 224 peptides. Score 0.951 Round 3: 441 peptides, 6 chains. Longest chain 166 peptides. Score 0.943 Round 4: 444 peptides, 7 chains. Longest chain 169 peptides. Score 0.941 Round 5: 443 peptides, 9 chains. Longest chain 154 peptides. Score 0.934 Taking the results from Round 2 Chains 5, Residues 445, Estimated correctness of the model 99.8 % 4 chains (443 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 B and 86 B Built loop between residues 214 B and 216 B 3 chains (450 residues) following loop building 2 chains (448 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4004 restraints for refining 4186 atoms. 321 conditional restraints added. Observations/parameters ratio is 3.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2033 (Rfree = 0.000) for 4186 atoms. Found 122 (153 requested) and removed 79 (106 requested) atoms. Cycle 22: After refmac, R = 0.1921 (Rfree = 0.000) for 4219 atoms. Found 107 (150 requested) and removed 53 (107 requested) atoms. Cycle 23: After refmac, R = 0.1850 (Rfree = 0.000) for 4270 atoms. Found 91 (152 requested) and removed 45 (108 requested) atoms. Cycle 24: After refmac, R = 0.1799 (Rfree = 0.000) for 4309 atoms. Found 86 (153 requested) and removed 59 (109 requested) atoms. Cycle 25: After refmac, R = 0.1772 (Rfree = 0.000) for 4331 atoms. Found 88 (150 requested) and removed 62 (110 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.95 1.95 NCS extension: 21 residues added (205 deleted due to clashes), 4382 seeds are put forward Round 1: 448 peptides, 5 chains. Longest chain 177 peptides. Score 0.948 Round 2: 449 peptides, 3 chains. Longest chain 224 peptides. Score 0.954 Round 3: 448 peptides, 5 chains. Longest chain 224 peptides. Score 0.948 Round 4: 440 peptides, 6 chains. Longest chain 104 peptides. Score 0.942 Round 5: 448 peptides, 6 chains. Longest chain 175 peptides. Score 0.945 Taking the results from Round 2 Chains 5, Residues 446, Estimated correctness of the model 99.8 % 3 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 B and 90 B 3 chains (450 residues) following loop building 2 chains (449 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4016 restraints for refining 4199 atoms. 329 conditional restraints added. Observations/parameters ratio is 3.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2016 (Rfree = 0.000) for 4199 atoms. Found 136 (141 requested) and removed 80 (106 requested) atoms. Cycle 27: After refmac, R = 0.1905 (Rfree = 0.000) for 4251 atoms. Found 101 (138 requested) and removed 54 (108 requested) atoms. Cycle 28: After refmac, R = 0.1827 (Rfree = 0.000) for 4291 atoms. Found 84 (135 requested) and removed 51 (109 requested) atoms. Cycle 29: After refmac, R = 0.1790 (Rfree = 0.000) for 4321 atoms. Found 72 (131 requested) and removed 52 (109 requested) atoms. Cycle 30: After refmac, R = 0.1763 (Rfree = 0.000) for 4336 atoms. Found 77 (128 requested) and removed 58 (110 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.95 1.95 NCS extension: 56 residues added (177 deleted due to clashes), 4415 seeds are put forward Round 1: 449 peptides, 5 chains. Longest chain 177 peptides. Score 0.949 Round 2: 452 peptides, 2 chains. Longest chain 228 peptides. Score 0.958 Round 3: 443 peptides, 6 chains. Longest chain 154 peptides. Score 0.943 Round 4: 447 peptides, 6 chains. Longest chain 188 peptides. Score 0.945 Round 5: 444 peptides, 7 chains. Longest chain 104 peptides. Score 0.941 Taking the results from Round 2 Chains 3, Residues 450, Estimated correctness of the model 99.9 % 2 chains (447 residues) have been docked in sequence Building loops using Loopy2018 3 chains (450 residues) following loop building 2 chains (447 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4032 restraints for refining 4206 atoms. 353 conditional restraints added. Observations/parameters ratio is 3.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1990 (Rfree = 0.000) for 4206 atoms. Found 120 (120 requested) and removed 79 (107 requested) atoms. Cycle 32: After refmac, R = 0.1887 (Rfree = 0.000) for 4242 atoms. Found 94 (117 requested) and removed 52 (108 requested) atoms. Cycle 33: After refmac, R = 0.1835 (Rfree = 0.000) for 4273 atoms. Found 92 (113 requested) and removed 46 (109 requested) atoms. Cycle 34: After refmac, R = 0.1801 (Rfree = 0.000) for 4313 atoms. Found 85 (114 requested) and removed 61 (109 requested) atoms. Cycle 35: After refmac, R = 0.1772 (Rfree = 0.000) for 4331 atoms. Found 94 (110 requested) and removed 51 (110 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.95 1.95 NCS extension: 25 residues added (200 deleted due to clashes), 4403 seeds are put forward Round 1: 444 peptides, 6 chains. Longest chain 177 peptides. Score 0.944 Round 2: 445 peptides, 5 chains. Longest chain 188 peptides. Score 0.947 Round 3: 445 peptides, 4 chains. Longest chain 188 peptides. Score 0.950 Round 4: 440 peptides, 6 chains. Longest chain 188 peptides. Score 0.942 Round 5: 438 peptides, 11 chains. Longest chain 85 peptides. Score 0.926 Taking the results from Round 3 Chains 5, Residues 441, Estimated correctness of the model 99.8 % 4 chains (439 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 87 A Built loop between residues 210 B and 217 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4036 restraints for refining 4217 atoms. 343 conditional restraints added. Observations/parameters ratio is 3.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2043 (Rfree = 0.000) for 4217 atoms. Found 107 (107 requested) and removed 80 (107 requested) atoms. Cycle 37: After refmac, R = 0.1915 (Rfree = 0.000) for 4234 atoms. Found 108 (108 requested) and removed 45 (108 requested) atoms. Cycle 38: After refmac, R = 0.1855 (Rfree = 0.000) for 4292 atoms. Found 84 (109 requested) and removed 55 (109 requested) atoms. Cycle 39: After refmac, R = 0.1813 (Rfree = 0.000) for 4320 atoms. Found 94 (109 requested) and removed 51 (109 requested) atoms. Cycle 40: After refmac, R = 0.1798 (Rfree = 0.000) for 4358 atoms. Found 84 (110 requested) and removed 74 (110 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.95 1.95 NCS extension: 30 residues added (202 deleted due to clashes), 4400 seeds are put forward Round 1: 442 peptides, 7 chains. Longest chain 114 peptides. Score 0.940 Round 2: 446 peptides, 5 chains. Longest chain 165 peptides. Score 0.948 Round 3: 451 peptides, 3 chains. Longest chain 224 peptides. Score 0.955 Round 4: 448 peptides, 4 chains. Longest chain 223 peptides. Score 0.951 Round 5: 446 peptides, 9 chains. Longest chain 114 peptides. Score 0.936 Taking the results from Round 3 Chains 3, Residues 448, Estimated correctness of the model 99.8 % 3 chains (448 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 B and 87 B 2 chains (450 residues) following loop building 2 chains (450 residues) in sequence following loop building ------------------------------------------------------ 56831 reflections ( 99.96 % complete ) and 4017 restraints for refining 4213 atoms. 324 conditional restraints added. Observations/parameters ratio is 3.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2000 (Rfree = 0.000) for 4213 atoms. Found 107 (107 requested) and removed 73 (107 requested) atoms. Cycle 42: After refmac, R = 0.1876 (Rfree = 0.000) for 4241 atoms. Found 102 (108 requested) and removed 31 (108 requested) atoms. Cycle 43: After refmac, R = 0.1824 (Rfree = 0.000) for 4307 atoms. Found 99 (109 requested) and removed 47 (109 requested) atoms. Cycle 44: After refmac, R = 0.1787 (Rfree = 0.000) for 4354 atoms. Found 96 (110 requested) and removed 65 (110 requested) atoms. Cycle 45: After refmac, R = 0.1773 (Rfree = 0.000) for 4376 atoms. Found 94 (111 requested) and removed 69 (111 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.95 1.95 NCS extension: 3 residues added (1 deleted due to clashes), 4405 seeds are put forward Round 1: 449 peptides, 5 chains. Longest chain 177 peptides. Score 0.949 Round 2: 447 peptides, 4 chains. Longest chain 164 peptides. Score 0.951 Round 3: 446 peptides, 7 chains. Longest chain 126 peptides. Score 0.942 Round 4: 445 peptides, 7 chains. Longest chain 120 peptides. Score 0.941 Round 5: 443 peptides, 10 chains. Longest chain 115 peptides. Score 0.931 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 443, Estimated correctness of the model 99.8 % 4 chains (439 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 84 A and 88 A Built loop between residues 84 B and 89 B 3 chains (450 residues) following loop building 2 chains (446 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 56831 reflections ( 99.96 % complete ) and 3679 restraints for refining 3596 atoms. Observations/parameters ratio is 3.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2565 (Rfree = 0.000) for 3596 atoms. Found 91 (91 requested) and removed 0 (91 requested) atoms. Cycle 47: After refmac, R = 0.2300 (Rfree = 0.000) for 3596 atoms. Found 89 (93 requested) and removed 0 (93 requested) atoms. Cycle 48: After refmac, R = 0.2063 (Rfree = 0.000) for 3596 atoms. Found 50 (96 requested) and removed 7 (96 requested) atoms. Cycle 49: After refmac, R = 0.1952 (Rfree = 0.000) for 3596 atoms. TimeTaking 73.88