null Sun 23 Dec 22:22:46 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 2hxv-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hxv-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-1.9-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/2hxv-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-1.9-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 ============================================================ Sun 23 Dec 22:22:56 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/2hxv-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hxv-1.9-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 364 and 0 Target number of residues in the AU: 364 Target solvent content: 0.5056 Checking the provided sequence file Detected sequence length: 360 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 360 Adjusted target solvent content: 0.51 Input MTZ file: 2hxv-1.9-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: 97 Cell parameters: 104.410 104.410 146.200 90.000 90.000 90.000 Input sequence file: 2hxv-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 2880 target number of atoms Had to go as low as 0.40 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 Loops will be built when appropriate and at the last cycle Resolution range: 84.967 1.900 Wilson plot Bfac: 24.63 32112 reflections ( 99.88 % complete ) and 0 restraints for refining 3199 atoms. Observations/parameters ratio is 2.51 ------------------------------------------------------ Starting model: R = 0.3189 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2734 (Rfree = 0.000) for 3199 atoms. Found 103 (126 requested) and removed 65 (63 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.04 2.01 Round 1: 299 peptides, 21 chains. Longest chain 39 peptides. Score 0.834 Round 2: 328 peptides, 14 chains. Longest chain 62 peptides. Score 0.904 Round 3: 333 peptides, 8 chains. Longest chain 100 peptides. Score 0.934 Round 4: 333 peptides, 9 chains. Longest chain 119 peptides. Score 0.930 Round 5: 335 peptides, 8 chains. Longest chain 115 peptides. Score 0.935 Taking the results from Round 5 Chains 10, Residues 327, Estimated correctness of the model 99.6 % 7 chains (317 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 35 A Built loop between residues 77 A and 80 A Built loop between residues 90 A and 95 A Built loop between residues 208 A and 211 A Built loop between residues 238 A and 242 A Built loop between residues 325 A and 328 A 3 chains (343 residues) following loop building 1 chains (334 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3169 restraints for refining 3070 atoms. 458 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2770 (Rfree = 0.000) for 3070 atoms. Found 96 (121 requested) and removed 62 (60 requested) atoms. Cycle 2: After refmac, R = 0.2427 (Rfree = 0.000) for 3094 atoms. Found 79 (121 requested) and removed 56 (61 requested) atoms. Cycle 3: After refmac, R = 0.2227 (Rfree = 0.000) for 3102 atoms. Found 84 (118 requested) and removed 30 (61 requested) atoms. Cycle 4: After refmac, R = 0.2098 (Rfree = 0.000) for 3141 atoms. Found 62 (120 requested) and removed 30 (62 requested) atoms. Cycle 5: After refmac, R = 0.2005 (Rfree = 0.000) for 3163 atoms. Found 58 (120 requested) and removed 29 (62 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.01 1.98 Round 1: 334 peptides, 6 chains. Longest chain 168 peptides. Score 0.942 Round 2: 338 peptides, 5 chains. Longest chain 236 peptides. Score 0.948 Round 3: 336 peptides, 6 chains. Longest chain 152 peptides. Score 0.944 Round 4: 339 peptides, 4 chains. Longest chain 254 peptides. Score 0.952 Round 5: 337 peptides, 5 chains. Longest chain 117 peptides. Score 0.948 Taking the results from Round 4 Chains 5, Residues 335, Estimated correctness of the model 99.8 % 3 chains (329 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 A and 34 A 4 chains (337 residues) following loop building 2 chains (331 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3200 restraints for refining 3074 atoms. 517 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2091 (Rfree = 0.000) for 3074 atoms. Found 80 (116 requested) and removed 64 (60 requested) atoms. Cycle 7: After refmac, R = 0.1949 (Rfree = 0.000) for 3083 atoms. Found 57 (115 requested) and removed 23 (61 requested) atoms. Cycle 8: After refmac, R = 0.1892 (Rfree = 0.000) for 3113 atoms. Found 52 (116 requested) and removed 19 (61 requested) atoms. Cycle 9: After refmac, R = 0.1840 (Rfree = 0.000) for 3140 atoms. Found 44 (117 requested) and removed 21 (62 requested) atoms. Cycle 10: After refmac, R = 0.1806 (Rfree = 0.000) for 3158 atoms. Found 40 (117 requested) and removed 24 (62 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.01 1.98 Round 1: 334 peptides, 6 chains. Longest chain 144 peptides. Score 0.942 Round 2: 336 peptides, 5 chains. Longest chain 147 peptides. Score 0.947 Round 3: 334 peptides, 7 chains. Longest chain 80 peptides. Score 0.939 Round 4: 336 peptides, 6 chains. Longest chain 152 peptides. Score 0.944 Round 5: 339 peptides, 5 chains. Longest chain 161 peptides. Score 0.949 Taking the results from Round 5 Chains 6, Residues 334, Estimated correctness of the model 99.7 % 5 chains (333 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 36 A Built loop between residues 91 A and 96 A Built loop between residues 255 A and 258 A Built loop between residues 318 A and 321 A 2 chains (344 residues) following loop building 1 chains (343 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3131 restraints for refining 3101 atoms. 374 conditional restraints added. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2009 (Rfree = 0.000) for 3101 atoms. Found 73 (112 requested) and removed 66 (61 requested) atoms. Cycle 12: After refmac, R = 0.1887 (Rfree = 0.000) for 3100 atoms. Found 57 (111 requested) and removed 35 (61 requested) atoms. Cycle 13: After refmac, R = 0.1830 (Rfree = 0.000) for 3121 atoms. Found 60 (108 requested) and removed 33 (61 requested) atoms. Cycle 14: After refmac, R = 0.1783 (Rfree = 0.000) for 3146 atoms. Found 50 (107 requested) and removed 27 (62 requested) atoms. Cycle 15: After refmac, R = 0.1760 (Rfree = 0.000) for 3165 atoms. Found 58 (105 requested) and removed 34 (62 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.01 1.98 Round 1: 337 peptides, 5 chains. Longest chain 144 peptides. Score 0.948 Round 2: 337 peptides, 5 chains. Longest chain 173 peptides. Score 0.948 Round 3: 340 peptides, 5 chains. Longest chain 145 peptides. Score 0.949 Round 4: 338 peptides, 5 chains. Longest chain 115 peptides. Score 0.948 Round 5: 338 peptides, 5 chains. Longest chain 231 peptides. Score 0.948 Taking the results from Round 3 Chains 6, Residues 335, Estimated correctness of the model 99.7 % 5 chains (334 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 91 A and 97 A Built loop between residues 139 A and 142 A Built loop between residues 210 A and 213 A 1 chains (345 residues) following loop building 1 chains (345 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3110 restraints for refining 3108 atoms. 336 conditional restraints added. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1984 (Rfree = 0.000) for 3108 atoms. Found 93 (101 requested) and removed 65 (61 requested) atoms. Cycle 17: After refmac, R = 0.1895 (Rfree = 0.000) for 3130 atoms. Found 42 (99 requested) and removed 44 (62 requested) atoms. Cycle 18: After refmac, R = 0.1803 (Rfree = 0.000) for 3127 atoms. Found 59 (96 requested) and removed 21 (61 requested) atoms. Cycle 19: After refmac, R = 0.1764 (Rfree = 0.000) for 3162 atoms. Found 45 (97 requested) and removed 32 (62 requested) atoms. Cycle 20: After refmac, R = 0.1745 (Rfree = 0.000) for 3169 atoms. Found 65 (95 requested) and removed 21 (62 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.01 1.98 Round 1: 337 peptides, 5 chains. Longest chain 196 peptides. Score 0.948 Round 2: 341 peptides, 3 chains. Longest chain 261 peptides. Score 0.957 Round 3: 336 peptides, 7 chains. Longest chain 107 peptides. Score 0.940 Round 4: 339 peptides, 5 chains. Longest chain 145 peptides. Score 0.949 Round 5: 336 peptides, 8 chains. Longest chain 154 peptides. Score 0.936 Taking the results from Round 2 Chains 3, Residues 338, Estimated correctness of the model 99.8 % 3 chains (338 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 91 A and 97 A 1 chains (345 residues) following loop building 1 chains (345 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3108 restraints for refining 3113 atoms. 334 conditional restraints added. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1937 (Rfree = 0.000) for 3113 atoms. Found 93 (93 requested) and removed 62 (61 requested) atoms. Cycle 22: After refmac, R = 0.1855 (Rfree = 0.000) for 3140 atoms. Found 52 (92 requested) and removed 45 (62 requested) atoms. Cycle 23: After refmac, R = 0.1790 (Rfree = 0.000) for 3145 atoms. Found 60 (89 requested) and removed 33 (62 requested) atoms. Cycle 24: After refmac, R = 0.1775 (Rfree = 0.000) for 3168 atoms. Found 53 (87 requested) and removed 29 (62 requested) atoms. Cycle 25: After refmac, R = 0.1749 (Rfree = 0.000) for 3184 atoms. Found 47 (86 requested) and removed 35 (63 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.02 1.99 Round 1: 339 peptides, 4 chains. Longest chain 197 peptides. Score 0.952 Round 2: 339 peptides, 5 chains. Longest chain 161 peptides. Score 0.949 Round 3: 335 peptides, 8 chains. Longest chain 72 peptides. Score 0.935 Round 4: 340 peptides, 5 chains. Longest chain 160 peptides. Score 0.949 Round 5: 341 peptides, 4 chains. Longest chain 250 peptides. Score 0.953 Taking the results from Round 5 Chains 4, Residues 337, Estimated correctness of the model 99.8 % 3 chains (328 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 92 A and 97 A 2 chains (343 residues) following loop building 1 chains (334 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3209 restraints for refining 3100 atoms. 493 conditional restraints added. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2004 (Rfree = 0.000) for 3100 atoms. Found 78 (81 requested) and removed 64 (61 requested) atoms. Cycle 27: After refmac, R = 0.1888 (Rfree = 0.000) for 3107 atoms. Found 67 (79 requested) and removed 26 (61 requested) atoms. Cycle 28: After refmac, R = 0.1837 (Rfree = 0.000) for 3144 atoms. Found 55 (79 requested) and removed 34 (62 requested) atoms. Cycle 29: After refmac, R = 0.1794 (Rfree = 0.000) for 3163 atoms. Found 57 (77 requested) and removed 29 (62 requested) atoms. Cycle 30: After refmac, R = 0.1763 (Rfree = 0.000) for 3190 atoms. Found 51 (76 requested) and removed 40 (63 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.01 1.98 Round 1: 338 peptides, 6 chains. Longest chain 161 peptides. Score 0.945 Round 2: 339 peptides, 5 chains. Longest chain 117 peptides. Score 0.949 Round 3: 338 peptides, 7 chains. Longest chain 153 peptides. Score 0.941 Round 4: 342 peptides, 4 chains. Longest chain 251 peptides. Score 0.954 Round 5: 337 peptides, 7 chains. Longest chain 108 peptides. Score 0.940 Taking the results from Round 4 Chains 4, Residues 338, Estimated correctness of the model 99.8 % 4 chains (338 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 91 A and 96 A Built loop between residues 345 A and 348 A 1 chains (346 residues) following loop building 1 chains (346 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3111 restraints for refining 3118 atoms. 327 conditional restraints added. Observations/parameters ratio is 2.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1968 (Rfree = 0.000) for 3118 atoms. Found 71 (71 requested) and removed 62 (61 requested) atoms. Cycle 32: After refmac, R = 0.1867 (Rfree = 0.000) for 3121 atoms. Found 59 (69 requested) and removed 37 (61 requested) atoms. Cycle 33: After refmac, R = 0.1809 (Rfree = 0.000) for 3142 atoms. Found 58 (67 requested) and removed 29 (62 requested) atoms. Cycle 34: After refmac, R = 0.1765 (Rfree = 0.000) for 3169 atoms. Found 53 (67 requested) and removed 36 (62 requested) atoms. Cycle 35: After refmac, R = 0.1744 (Rfree = 0.000) for 3184 atoms. Found 60 (66 requested) and removed 24 (63 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.02 1.99 Round 1: 339 peptides, 5 chains. Longest chain 160 peptides. Score 0.949 Round 2: 339 peptides, 6 chains. Longest chain 117 peptides. Score 0.945 Round 3: 340 peptides, 4 chains. Longest chain 197 peptides. Score 0.953 Round 4: 337 peptides, 8 chains. Longest chain 70 peptides. Score 0.936 Round 5: 340 peptides, 4 chains. Longest chain 197 peptides. Score 0.953 Taking the results from Round 5 Chains 4, Residues 336, Estimated correctness of the model 99.8 % 4 chains (336 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 35 A Built loop between residues 91 A and 97 A Built loop between residues 292 A and 296 A 1 chains (346 residues) following loop building 1 chains (346 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3124 restraints for refining 3106 atoms. 340 conditional restraints added. Observations/parameters ratio is 2.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1969 (Rfree = 0.000) for 3106 atoms. Found 64 (64 requested) and removed 61 (61 requested) atoms. Cycle 37: After refmac, R = 0.1864 (Rfree = 0.000) for 3105 atoms. Found 61 (61 requested) and removed 26 (61 requested) atoms. Cycle 38: After refmac, R = 0.1803 (Rfree = 0.000) for 3139 atoms. Found 49 (62 requested) and removed 25 (62 requested) atoms. Cycle 39: After refmac, R = 0.1763 (Rfree = 0.000) for 3163 atoms. Found 51 (62 requested) and removed 22 (62 requested) atoms. Cycle 40: After refmac, R = 0.1739 (Rfree = 0.000) for 3189 atoms. Found 45 (63 requested) and removed 36 (63 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.02 1.99 Round 1: 339 peptides, 7 chains. Longest chain 82 peptides. Score 0.941 Round 2: 340 peptides, 3 chains. Longest chain 161 peptides. Score 0.956 Round 3: 337 peptides, 7 chains. Longest chain 162 peptides. Score 0.940 Round 4: 339 peptides, 4 chains. Longest chain 116 peptides. Score 0.952 Round 5: 338 peptides, 7 chains. Longest chain 120 peptides. Score 0.941 Taking the results from Round 2 Chains 3, Residues 337, Estimated correctness of the model 99.8 % 3 chains (337 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 97 A Built loop between residues 256 A and 259 A 1 chains (346 residues) following loop building 1 chains (346 residues) in sequence following loop building ------------------------------------------------------ 32112 reflections ( 99.88 % complete ) and 3114 restraints for refining 3131 atoms. 330 conditional restraints added. Observations/parameters ratio is 2.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1979 (Rfree = 0.000) for 3131 atoms. Found 62 (62 requested) and removed 65 (62 requested) atoms. Cycle 42: After refmac, R = 0.1858 (Rfree = 0.000) for 3124 atoms. Found 61 (61 requested) and removed 29 (61 requested) atoms. Cycle 43: After refmac, R = 0.1800 (Rfree = 0.000) for 3152 atoms. Found 62 (62 requested) and removed 21 (62 requested) atoms. Cycle 44: After refmac, R = 0.1755 (Rfree = 0.000) for 3190 atoms. Found 41 (63 requested) and removed 27 (63 requested) atoms. Cycle 45: After refmac, R = 0.1725 (Rfree = 0.000) for 3202 atoms. Found 45 (63 requested) and removed 21 (63 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.02 1.99 Round 1: 338 peptides, 6 chains. Longest chain 161 peptides. Score 0.945 Round 2: 340 peptides, 5 chains. Longest chain 116 peptides. Score 0.949 Round 3: 341 peptides, 4 chains. Longest chain 161 peptides. Score 0.953 Round 4: 336 peptides, 7 chains. Longest chain 82 peptides. Score 0.940 Round 5: 339 peptides, 5 chains. Longest chain 160 peptides. Score 0.949 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 337, Estimated correctness of the model 99.8 % 4 chains (336 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 33 A and 36 A Built loop between residues 91 A and 97 A Built loop between residues 256 A and 259 A 2 chains (346 residues) following loop building 2 chains (346 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 32112 reflections ( 99.88 % complete ) and 2776 restraints for refining 2719 atoms. Observations/parameters ratio is 2.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2526 (Rfree = 0.000) for 2719 atoms. Found 52 (53 requested) and removed 0 (53 requested) atoms. Cycle 47: After refmac, R = 0.2334 (Rfree = 0.000) for 2719 atoms. Found 28 (54 requested) and removed 1 (54 requested) atoms. Cycle 48: After refmac, R = 0.2178 (Rfree = 0.000) for 2719 atoms. Found 8 (55 requested) and removed 2 (55 requested) atoms. Cycle 49: After refmac, R = 0.2139 (Rfree = 0.000) for 2719 atoms. Found 3 (55 requested) and removed 1 (55 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:33:53 GMT 2018 Job finished. TimeTaking 71.12 Used memory is bytes: 1929264