Sun 23 Dec 22:23:13 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 1vpb-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpb-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-1.8-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/1vpb-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-1.8-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 22:23:22 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/1vpb-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpb-1.8-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 586 and 0 Target number of residues in the AU: 586 Target solvent content: 0.4775 Checking the provided sequence file Detected sequence length: 451 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 451 Adjusted target solvent content: 0.60 Input MTZ file: 1vpb-1.8-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: 20 Cell parameters: 74.004 155.044 105.800 90.000 90.000 90.000 Input sequence file: 1vpb-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3608 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: 77.522 1.800 Wilson plot Bfac: 19.07 55749 reflections ( 98.38 % complete ) and 0 restraints for refining 3986 atoms. Observations/parameters ratio is 3.50 ------------------------------------------------------ Starting model: R = 0.3168 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2654 (Rfree = 0.000) for 3986 atoms. Found 184 (184 requested) and removed 95 (92 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.87 1.63 Round 1: 385 peptides, 19 chains. Longest chain 51 peptides. Score 0.833 Round 2: 399 peptides, 11 chains. Longest chain 128 peptides. Score 0.882 Round 3: 410 peptides, 12 chains. Longest chain 77 peptides. Score 0.885 Round 4: 414 peptides, 10 chains. Longest chain 84 peptides. Score 0.896 Round 5: 429 peptides, 6 chains. Longest chain 117 peptides. Score 0.919 Taking the results from Round 5 Chains 7, Residues 423, Estimated correctness of the model 99.5 % 6 chains (422 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 58 A Built loop between residues 83 A and 85 A Built loop between residues 200 A and 206 A Built loop between residues 251 A and 254 A Built loop between residues 368 A and 372 A 1 chains (436 residues) following loop building 1 chains (436 residues) in sequence following loop building ------------------------------------------------------ 55749 reflections ( 98.38 % complete ) and 3903 restraints for refining 3981 atoms. 471 conditional restraints added. Observations/parameters ratio is 3.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2725 (Rfree = 0.000) for 3981 atoms. Found 165 (184 requested) and removed 94 (92 requested) atoms. Cycle 2: After refmac, R = 0.2546 (Rfree = 0.000) for 4043 atoms. Found 116 (183 requested) and removed 39 (93 requested) atoms. Cycle 3: After refmac, R = 0.2287 (Rfree = 0.000) for 4109 atoms. Found 122 (186 requested) and removed 37 (95 requested) atoms. Cycle 4: After refmac, R = 0.2182 (Rfree = 0.000) for 4168 atoms. Found 111 (189 requested) and removed 42 (96 requested) atoms. Cycle 5: After refmac, R = 0.2105 (Rfree = 0.000) for 4227 atoms. Found 126 (191 requested) and removed 46 (97 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.81 1.58 Round 1: 428 peptides, 7 chains. Longest chain 178 peptides. Score 0.915 Round 2: 432 peptides, 4 chains. Longest chain 167 peptides. Score 0.927 Round 3: 430 peptides, 5 chains. Longest chain 196 peptides. Score 0.923 Round 4: 434 peptides, 2 chains. Longest chain 394 peptides. Score 0.935 Round 5: 427 peptides, 7 chains. Longest chain 165 peptides. Score 0.914 Taking the results from Round 4 Chains 4, Residues 432, Estimated correctness of the model 99.7 % 3 chains (422 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 56 A 3 chains (435 residues) following loop building 2 chains (425 residues) in sequence following loop building ------------------------------------------------------ 55749 reflections ( 98.38 % complete ) and 3929 restraints for refining 4075 atoms. 549 conditional restraints added. Observations/parameters ratio is 3.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2139 (Rfree = 0.000) for 4075 atoms. Found 177 (184 requested) and removed 68 (94 requested) atoms. Cycle 7: After refmac, R = 0.2074 (Rfree = 0.000) for 4176 atoms. Found 120 (189 requested) and removed 48 (96 requested) atoms. Cycle 8: After refmac, R = 0.2033 (Rfree = 0.000) for 4239 atoms. Found 109 (192 requested) and removed 56 (98 requested) atoms. Cycle 9: After refmac, R = 0.2000 (Rfree = 0.000) for 4283 atoms. Found 131 (190 requested) and removed 56 (99 requested) atoms. Cycle 10: After refmac, R = 0.1976 (Rfree = 0.000) for 4353 atoms. Found 106 (193 requested) and removed 66 (100 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.81 1.58 Round 1: 429 peptides, 7 chains. Longest chain 193 peptides. Score 0.915 Round 2: 433 peptides, 3 chains. Longest chain 246 peptides. Score 0.931 Round 3: 434 peptides, 4 chains. Longest chain 222 peptides. Score 0.928 Round 4: 436 peptides, 2 chains. Longest chain 432 peptides. Score 0.935 Round 5: 430 peptides, 3 chains. Longest chain 267 peptides. Score 0.930 Taking the results from Round 4 Chains 4, Residues 434, Estimated correctness of the model 99.7 % 2 chains (429 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 201 A and 203 A 3 chains (435 residues) following loop building 1 chains (430 residues) in sequence following loop building ------------------------------------------------------ 55749 reflections ( 98.38 % complete ) and 3955 restraints for refining 4166 atoms. 555 conditional restraints added. Observations/parameters ratio is 3.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2246 (Rfree = 0.000) for 4166 atoms. Found 167 (180 requested) and removed 86 (96 requested) atoms. Cycle 12: After refmac, R = 0.2075 (Rfree = 0.000) for 4244 atoms. Found 130 (180 requested) and removed 33 (98 requested) atoms. Cycle 13: After refmac, R = 0.2014 (Rfree = 0.000) for 4336 atoms. Found 107 (184 requested) and removed 45 (100 requested) atoms. Cycle 14: After refmac, R = 0.2015 (Rfree = 0.000) for 4388 atoms. Found 99 (187 requested) and removed 61 (101 requested) atoms. Cycle 15: After refmac, R = 0.1975 (Rfree = 0.000) for 4419 atoms. Found 105 (184 requested) and removed 54 (102 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.81 1.58 Round 1: 430 peptides, 5 chains. Longest chain 192 peptides. Score 0.923 Round 2: 435 peptides, 4 chains. Longest chain 248 peptides. Score 0.929 Round 3: 436 peptides, 3 chains. Longest chain 331 peptides. Score 0.932 Round 4: 428 peptides, 6 chains. Longest chain 248 peptides. Score 0.918 Round 5: 435 peptides, 3 chains. Longest chain 293 peptides. Score 0.932 Taking the results from Round 5 Chains 4, Residues 432, Estimated correctness of the model 99.6 % 3 chains (431 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 56 A Built loop between residues 347 A and 350 A 1 chains (437 residues) following loop building 1 chains (437 residues) in sequence following loop building ------------------------------------------------------ 55749 reflections ( 98.38 % complete ) and 4002 restraints for refining 4246 atoms. 562 conditional restraints added. Observations/parameters ratio is 3.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2242 (Rfree = 0.000) for 4246 atoms. Found 172 (172 requested) and removed 72 (98 requested) atoms. Cycle 17: After refmac, R = 0.2091 (Rfree = 0.000) for 4339 atoms. Found 120 (176 requested) and removed 36 (100 requested) atoms. Cycle 18: After refmac, R = 0.2044 (Rfree = 0.000) for 4413 atoms. Found 106 (180 requested) and removed 51 (102 requested) atoms. Cycle 19: After refmac, R = 0.2011 (Rfree = 0.000) for 4461 atoms. Found 107 (181 requested) and removed 67 (103 requested) atoms. Cycle 20: After refmac, R = 0.1992 (Rfree = 0.000) for 4491 atoms. Found 124 (179 requested) and removed 79 (104 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.80 1.57 Round 1: 428 peptides, 6 chains. Longest chain 176 peptides. Score 0.918 Round 2: 433 peptides, 3 chains. Longest chain 339 peptides. Score 0.931 Round 3: 430 peptides, 5 chains. Longest chain 176 peptides. Score 0.923 Round 4: 432 peptides, 3 chains. Longest chain 267 peptides. Score 0.930 Round 5: 427 peptides, 5 chains. Longest chain 176 peptides. Score 0.921 Taking the results from Round 2 Chains 5, Residues 430, Estimated correctness of the model 99.6 % 4 chains (425 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 56 A Built loop between residues 199 A and 206 A Built loop between residues 394 A and 397 A 1 chains (436 residues) following loop building 1 chains (436 residues) in sequence following loop building ------------------------------------------------------ 55749 reflections ( 98.38 % complete ) and 4001 restraints for refining 4249 atoms. 569 conditional restraints added. Observations/parameters ratio is 3.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2273 (Rfree = 0.000) for 4249 atoms. Found 165 (165 requested) and removed 84 (98 requested) atoms. Cycle 22: After refmac, R = 0.2101 (Rfree = 0.000) for 4325 atoms. Found 101 (164 requested) and removed 37 (100 requested) atoms. Cycle 23: After refmac, R = 0.2029 (Rfree = 0.000) for 4385 atoms. Found 94 (166 requested) and removed 45 (101 requested) atoms. Cycle 24: After refmac, R = 0.1997 (Rfree = 0.000) for 4424 atoms. Found 91 (168 requested) and removed 51 (102 requested) atoms. Cycle 25: After refmac, R = 0.1999 (Rfree = 0.000) for 4452 atoms. Found 99 (165 requested) and removed 60 (103 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.80 1.57 Round 1: 430 peptides, 4 chains. Longest chain 245 peptides. Score 0.926 Round 2: 432 peptides, 4 chains. Longest chain 199 peptides. Score 0.927 Round 3: 434 peptides, 4 chains. Longest chain 225 peptides. Score 0.928 Round 4: 436 peptides, 2 chains. Longest chain 395 peptides. Score 0.935 Round 5: 432 peptides, 2 chains. Longest chain 395 peptides. Score 0.934 Taking the results from Round 4 Chains 5, Residues 434, Estimated correctness of the model 99.7 % 3 chains (431 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 A and 56 A 3 chains (437 residues) following loop building 2 chains (435 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 55749 reflections ( 98.38 % complete ) and 4074 restraints for refining 4248 atoms. 651 conditional restraints added. Observations/parameters ratio is 3.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2077 (Rfree = 0.000) for 4248 atoms. Found 153 (153 requested) and removed 52 (98 requested) atoms. Cycle 27: After refmac, R = 0.2038 (Rfree = 0.000) for 4337 atoms. Found 115 (157 requested) and removed 36 (100 requested) atoms. Cycle 28: After refmac, R = 0.1994 (Rfree = 0.000) for 4412 atoms. Found 101 (159 requested) and removed 46 (102 requested) atoms. Cycle 29: After refmac, R = 0.1982 (Rfree = 0.000) for 4458 atoms. Found 105 (161 requested) and removed 66 (103 requested) atoms. Cycle 30: After refmac, R = 0.1959 (Rfree = 0.000) for 4482 atoms. Found 116 (157 requested) and removed 57 (103 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.81 1.58 Round 1: 426 peptides, 7 chains. Longest chain 173 peptides. Score 0.914 Round 2: 432 peptides, 6 chains. Longest chain 166 peptides. Score 0.920 Round 3: 432 peptides, 4 chains. Longest chain 173 peptides. Score 0.927 Round 4: 430 peptides, 4 chains. Longest chain 312 peptides. Score 0.926 Round 5: 430 peptides, 3 chains. Longest chain 322 peptides. Score 0.930 Taking the results from Round 5 Chains 6, Residues 427, Estimated correctness of the model 99.6 % 4 chains (420 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 56 A Built loop between residues 199 A and 206 A Built loop between residues 375 A and 381 A 2 chains (435 residues) following loop building 1 chains (434 residues) in sequence following loop building ------------------------------------------------------ 55749 reflections ( 98.38 % complete ) and 4033 restraints for refining 4251 atoms. 617 conditional restraints added. Observations/parameters ratio is 3.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2112 (Rfree = 0.000) for 4251 atoms. Found 149 (149 requested) and removed 79 (98 requested) atoms. Cycle 32: After refmac, R = 0.2039 (Rfree = 0.000) for 4316 atoms. Found 138 (147 requested) and removed 43 (99 requested) atoms. Cycle 33: After refmac, R = 0.2023 (Rfree = 0.000) for 4404 atoms. Found 110 (150 requested) and removed 68 (101 requested) atoms. Cycle 34: After refmac, R = 0.1986 (Rfree = 0.000) for 4437 atoms. Found 108 (148 requested) and removed 63 (102 requested) atoms. Cycle 35: After refmac, R = 0.1972 (Rfree = 0.000) for 4463 atoms. Found 97 (145 requested) and removed 71 (103 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.81 1.58 Round 1: 428 peptides, 6 chains. Longest chain 166 peptides. Score 0.918 Round 2: 433 peptides, 3 chains. Longest chain 246 peptides. Score 0.931 Round 3: 428 peptides, 3 chains. Longest chain 244 peptides. Score 0.929 Round 4: 431 peptides, 5 chains. Longest chain 246 peptides. Score 0.923 Round 5: 430 peptides, 4 chains. Longest chain 147 peptides. Score 0.926 Taking the results from Round 2 Chains 3, Residues 430, Estimated correctness of the model 99.6 % 3 chains (430 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 56 A Built loop between residues 201 A and 206 A 1 chains (437 residues) following loop building 1 chains (437 residues) in sequence following loop building ------------------------------------------------------ 55749 reflections ( 98.38 % complete ) and 4019 restraints for refining 4238 atoms. 583 conditional restraints added. Observations/parameters ratio is 3.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2090 (Rfree = 0.000) for 4238 atoms. Found 133 (133 requested) and removed 64 (98 requested) atoms. Cycle 37: After refmac, R = 0.2012 (Rfree = 0.000) for 4300 atoms. Found 107 (135 requested) and removed 33 (99 requested) atoms. Cycle 38: After refmac, R = 0.1957 (Rfree = 0.000) for 4371 atoms. Found 98 (137 requested) and removed 34 (101 requested) atoms. Cycle 39: After refmac, R = 0.1953 (Rfree = 0.000) for 4423 atoms. Found 89 (139 requested) and removed 54 (102 requested) atoms. Cycle 40: After refmac, R = 0.1926 (Rfree = 0.000) for 4450 atoms. Found 113 (136 requested) and removed 57 (103 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.80 1.57 Round 1: 432 peptides, 5 chains. Longest chain 193 peptides. Score 0.924 Round 2: 433 peptides, 4 chains. Longest chain 201 peptides. Score 0.928 Round 3: 435 peptides, 3 chains. Longest chain 271 peptides. Score 0.932 Round 4: 431 peptides, 3 chains. Longest chain 248 peptides. Score 0.930 Round 5: 427 peptides, 6 chains. Longest chain 248 peptides. Score 0.918 Taking the results from Round 3 Chains 3, Residues 432, Estimated correctness of the model 99.6 % 3 chains (432 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 56 A Built loop between residues 178 A and 181 A 1 chains (437 residues) following loop building 1 chains (437 residues) in sequence following loop building ------------------------------------------------------ 55749 reflections ( 98.38 % complete ) and 4023 restraints for refining 4260 atoms. 587 conditional restraints added. Observations/parameters ratio is 3.27 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2199 (Rfree = 0.000) for 4260 atoms. Found 126 (126 requested) and removed 72 (98 requested) atoms. Cycle 42: After refmac, R = 0.2041 (Rfree = 0.000) for 4309 atoms. Found 123 (123 requested) and removed 29 (99 requested) atoms. Cycle 43: After refmac, R = 0.1986 (Rfree = 0.000) for 4397 atoms. Found 117 (126 requested) and removed 56 (101 requested) atoms. Cycle 44: After refmac, R = 0.1969 (Rfree = 0.000) for 4450 atoms. Found 123 (128 requested) and removed 72 (103 requested) atoms. Cycle 45: After refmac, R = 0.1949 (Rfree = 0.000) for 4492 atoms. Found 125 (125 requested) and removed 71 (104 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.81 1.58 Round 1: 430 peptides, 5 chains. Longest chain 168 peptides. Score 0.923 Round 2: 430 peptides, 5 chains. Longest chain 192 peptides. Score 0.923 Round 3: 431 peptides, 4 chains. Longest chain 247 peptides. Score 0.927 Round 4: 430 peptides, 5 chains. Longest chain 247 peptides. Score 0.923 Round 5: 427 peptides, 7 chains. Longest chain 164 peptides. Score 0.914 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 427, Estimated correctness of the model 99.6 % 4 chains (427 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 52 A and 57 A Built loop between residues 179 A and 182 A Built loop between residues 200 A and 204 A 1 chains (436 residues) following loop building 1 chains (436 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 55749 reflections ( 98.38 % complete ) and 3432 restraints for refining 3378 atoms. Observations/parameters ratio is 4.13 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2833 (Rfree = 0.000) for 3378 atoms. Found 90 (90 requested) and removed 0 (90 requested) atoms. Cycle 47: After refmac, R = 0.2457 (Rfree = 0.000) for 3378 atoms. Found 93 (93 requested) and removed 0 (80 requested) atoms. Cycle 48: After refmac, R = 0.2269 (Rfree = 0.000) for 3378 atoms. Found 68 (95 requested) and removed 0 (82 requested) atoms. Cycle 49: After refmac, R = 0.2141 (Rfree = 0.000) for 3378 atoms. TimeTaking 84.75