Tue 25 Dec 19:27:56 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 1vlo-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-1.7-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/1vlo-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-1.7-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 19:28:11 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/1vlo-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-1.7-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 378 and 0 Target number of residues in the AU: 378 Target solvent content: 0.4195 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 381 Adjusted target solvent content: 0.41 Input MTZ file: 1vlo-1.7-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: 46.529 64.578 117.291 90.000 90.000 90.000 Input sequence file: 1vlo-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 3048 target number of atoms Had to go as low as 0.35 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: 43.415 1.700 Wilson plot Bfac: 10.24 38281 reflections ( 96.51 % complete ) and 0 restraints for refining 3376 atoms. Observations/parameters ratio is 2.83 ------------------------------------------------------ Starting model: R = 0.3335 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2848 (Rfree = 0.000) for 3376 atoms. Found 183 (183 requested) and removed 100 (91 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.55 1.75 Round 1: 320 peptides, 21 chains. Longest chain 47 peptides. Score 0.885 Round 2: 343 peptides, 13 chains. Longest chain 78 peptides. Score 0.937 Round 3: 346 peptides, 11 chains. Longest chain 78 peptides. Score 0.946 Round 4: 355 peptides, 6 chains. Longest chain 213 peptides. Score 0.966 Round 5: 350 peptides, 9 chains. Longest chain 101 peptides. Score 0.955 Taking the results from Round 4 Chains 6, Residues 349, Estimated correctness of the model 99.9 % 4 chains (335 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 59 A Built loop between residues 270 A and 281 A 3 chains (355 residues) following loop building 2 chains (348 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38281 reflections ( 96.51 % complete ) and 3231 restraints for refining 3191 atoms. 463 conditional restraints added. Observations/parameters ratio is 3.00 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2909 (Rfree = 0.000) for 3191 atoms. Found 164 (173 requested) and removed 74 (86 requested) atoms. Cycle 2: After refmac, R = 0.2699 (Rfree = 0.000) for 3276 atoms. Found 98 (178 requested) and removed 23 (89 requested) atoms. Cycle 3: After refmac, R = 0.2370 (Rfree = 0.000) for 3344 atoms. Found 107 (182 requested) and removed 22 (91 requested) atoms. Cycle 4: After refmac, R = 0.2186 (Rfree = 0.000) for 3418 atoms. Found 93 (186 requested) and removed 26 (93 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2105 (Rfree = 0.000) for 3475 atoms. Found 87 (189 requested) and removed 16 (94 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.53 1.73 Round 1: 357 peptides, 4 chains. Longest chain 198 peptides. Score 0.972 Round 2: 359 peptides, 3 chains. Longest chain 255 peptides. Score 0.975 Round 3: 357 peptides, 5 chains. Longest chain 154 peptides. Score 0.969 Round 4: 358 peptides, 4 chains. Longest chain 247 peptides. Score 0.972 Round 5: 359 peptides, 3 chains. Longest chain 255 peptides. Score 0.975 Taking the results from Round 5 Chains 3, Residues 356, Estimated correctness of the model 100.0 % 3 chains (356 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 270 A and 273 A Built loop between residues 353 A and 358 A 1 chains (362 residues) following loop building 1 chains (362 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38281 reflections ( 96.51 % complete ) and 3232 restraints for refining 3441 atoms. 371 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2379 (Rfree = 0.000) for 3441 atoms. Found 110 (187 requested) and removed 53 (93 requested) atoms. Cycle 7: After refmac, R = 0.2094 (Rfree = 0.000) for 3496 atoms. Found 104 (190 requested) and removed 11 (95 requested) atoms. Cycle 8: After refmac, R = 0.2016 (Rfree = 0.000) for 3582 atoms. Found 90 (195 requested) and removed 22 (97 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1953 (Rfree = 0.000) for 3639 atoms. Found 85 (198 requested) and removed 34 (99 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1900 (Rfree = 0.000) for 3684 atoms. Found 103 (200 requested) and removed 31 (100 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.53 1.73 Round 1: 360 peptides, 3 chains. Longest chain 255 peptides. Score 0.976 Round 2: 361 peptides, 2 chains. Longest chain 255 peptides. Score 0.979 Round 3: 358 peptides, 4 chains. Longest chain 255 peptides. Score 0.972 Round 4: 359 peptides, 4 chains. Longest chain 154 peptides. Score 0.973 Round 5: 358 peptides, 4 chains. Longest chain 186 peptides. Score 0.972 Taking the results from Round 2 Chains 2, Residues 359, Estimated correctness of the model 100.0 % 2 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 270 A and 273 A 1 chains (361 residues) following loop building 1 chains (361 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38281 reflections ( 96.51 % complete ) and 3360 restraints for refining 3546 atoms. 507 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2242 (Rfree = 0.000) for 3546 atoms. Found 134 (193 requested) and removed 49 (96 requested) atoms. Cycle 12: After refmac, R = 0.2000 (Rfree = 0.000) for 3627 atoms. Found 103 (197 requested) and removed 25 (98 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1936 (Rfree = 0.000) for 3697 atoms. Found 82 (201 requested) and removed 38 (100 requested) atoms. Cycle 14: After refmac, R = 0.1875 (Rfree = 0.000) for 3735 atoms. Found 98 (203 requested) and removed 29 (101 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1847 (Rfree = 0.000) for 3794 atoms. Found 90 (207 requested) and removed 51 (103 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.52 1.72 Round 1: 359 peptides, 3 chains. Longest chain 254 peptides. Score 0.975 Round 2: 360 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Round 3: 361 peptides, 3 chains. Longest chain 255 peptides. Score 0.976 Round 4: 359 peptides, 3 chains. Longest chain 255 peptides. Score 0.975 Round 5: 361 peptides, 3 chains. Longest chain 154 peptides. Score 0.976 Taking the results from Round 5 Chains 3, Residues 358, Estimated correctness of the model 100.0 % 3 chains (358 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 172 A Built loop between residues 269 A and 272 A 1 chains (362 residues) following loop building 1 chains (362 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38281 reflections ( 96.51 % complete ) and 3422 restraints for refining 3598 atoms. 561 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2232 (Rfree = 0.000) for 3598 atoms. Found 157 (191 requested) and removed 51 (97 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2009 (Rfree = 0.000) for 3698 atoms. Found 107 (197 requested) and removed 38 (100 requested) atoms. Cycle 18: After refmac, R = 0.1920 (Rfree = 0.000) for 3754 atoms. Found 97 (201 requested) and removed 37 (102 requested) atoms. Cycle 19: After refmac, R = 0.1872 (Rfree = 0.000) for 3807 atoms. Found 94 (203 requested) and removed 45 (103 requested) atoms. Cycle 20: After refmac, R = 0.1829 (Rfree = 0.000) for 3853 atoms. Found 86 (205 requested) and removed 50 (104 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.53 1.73 Round 1: 357 peptides, 4 chains. Longest chain 215 peptides. Score 0.972 Round 2: 360 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Round 3: 359 peptides, 5 chains. Longest chain 154 peptides. Score 0.970 Round 4: 361 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Round 5: 362 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Taking the results from Round 5 Chains 3, Residues 359, Estimated correctness of the model 100.0 % 3 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 269 A and 272 A Built loop between residues 284 A and 287 A 1 chains (363 residues) following loop building 1 chains (363 residues) in sequence following loop building ------------------------------------------------------ 38281 reflections ( 96.51 % complete ) and 3449 restraints for refining 3626 atoms. 582 conditional restraints added. Observations/parameters ratio is 2.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2224 (Rfree = 0.000) for 3626 atoms. Found 149 (189 requested) and removed 48 (98 requested) atoms. Cycle 22: After refmac, R = 0.1991 (Rfree = 0.000) for 3724 atoms. Found 90 (194 requested) and removed 35 (101 requested) atoms. Cycle 23: After refmac, R = 0.1915 (Rfree = 0.000) for 3766 atoms. Found 95 (197 requested) and removed 32 (102 requested) atoms. Cycle 24: After refmac, R = 0.1861 (Rfree = 0.000) for 3825 atoms. Found 89 (200 requested) and removed 42 (104 requested) atoms. Cycle 25: After refmac, R = 0.1814 (Rfree = 0.000) for 3867 atoms. Found 99 (202 requested) and removed 48 (105 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.52 1.72 Round 1: 359 peptides, 3 chains. Longest chain 254 peptides. Score 0.975 Round 2: 359 peptides, 3 chains. Longest chain 254 peptides. Score 0.975 Round 3: 358 peptides, 4 chains. Longest chain 255 peptides. Score 0.972 Round 4: 359 peptides, 3 chains. Longest chain 255 peptides. Score 0.975 Round 5: 358 peptides, 4 chains. Longest chain 255 peptides. Score 0.972 Taking the results from Round 4 Chains 4, Residues 356, Estimated correctness of the model 100.0 % 3 chains (355 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 270 A and 273 A Built loop between residues 352 A and 358 A 1 chains (362 residues) following loop building 1 chains (362 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38281 reflections ( 96.51 % complete ) and 3463 restraints for refining 3646 atoms. 602 conditional restraints added. Observations/parameters ratio is 2.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2209 (Rfree = 0.000) for 3646 atoms. Found 154 (190 requested) and removed 45 (99 requested) atoms. Cycle 27: After refmac, R = 0.2000 (Rfree = 0.000) for 3748 atoms. Found 115 (196 requested) and removed 36 (102 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1897 (Rfree = 0.000) for 3819 atoms. Found 108 (200 requested) and removed 41 (104 requested) atoms. Cycle 29: After refmac, R = 0.1872 (Rfree = 0.000) for 3877 atoms. Found 104 (203 requested) and removed 69 (105 requested) atoms. Cycle 30: After refmac, R = 0.1827 (Rfree = 0.000) for 3903 atoms. Found 123 (199 requested) and removed 61 (106 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.52 1.72 Round 1: 360 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Round 2: 362 peptides, 2 chains. Longest chain 255 peptides. Score 0.979 Round 3: 360 peptides, 4 chains. Longest chain 154 peptides. Score 0.973 Round 4: 360 peptides, 3 chains. Longest chain 255 peptides. Score 0.976 Round 5: 362 peptides, 2 chains. Longest chain 255 peptides. Score 0.979 Taking the results from Round 5 Chains 2, Residues 360, Estimated correctness of the model 100.0 % 2 chains (360 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 270 A and 273 A 1 chains (362 residues) following loop building 1 chains (362 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38281 reflections ( 96.51 % complete ) and 3511 restraints for refining 3670 atoms. 650 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2187 (Rfree = 0.000) for 3670 atoms. Found 153 (187 requested) and removed 35 (99 requested) atoms. Cycle 32: After refmac, R = 0.1947 (Rfree = 0.000) for 3785 atoms. Found 96 (194 requested) and removed 34 (103 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1883 (Rfree = 0.000) for 3836 atoms. Found 100 (196 requested) and removed 47 (104 requested) atoms. Cycle 34: After refmac, R = 0.1834 (Rfree = 0.000) for 3881 atoms. Found 96 (198 requested) and removed 52 (105 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1817 (Rfree = 0.000) for 3918 atoms. Found 104 (196 requested) and removed 59 (106 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.53 1.73 Round 1: 358 peptides, 5 chains. Longest chain 198 peptides. Score 0.969 Round 2: 360 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Round 3: 355 peptides, 7 chains. Longest chain 100 peptides. Score 0.963 Round 4: 360 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Round 5: 360 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Taking the results from Round 5 Chains 4, Residues 357, Estimated correctness of the model 100.0 % 3 chains (356 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 269 A and 272 A Built loop between residues 353 A and 358 A 1 chains (362 residues) following loop building 1 chains (362 residues) in sequence following loop building ------------------------------------------------------ 38281 reflections ( 96.51 % complete ) and 3511 restraints for refining 3667 atoms. 650 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2191 (Rfree = 0.000) for 3667 atoms. Found 160 (179 requested) and removed 38 (99 requested) atoms. Cycle 37: After refmac, R = 0.1974 (Rfree = 0.000) for 3782 atoms. Found 112 (185 requested) and removed 34 (103 requested) atoms. Cycle 38: After refmac, R = 0.1901 (Rfree = 0.000) for 3847 atoms. Found 113 (189 requested) and removed 46 (105 requested) atoms. Cycle 39: After refmac, R = 0.1859 (Rfree = 0.000) for 3911 atoms. Found 93 (192 requested) and removed 64 (106 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1820 (Rfree = 0.000) for 3930 atoms. Found 106 (188 requested) and removed 52 (107 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.53 1.73 Round 1: 358 peptides, 4 chains. Longest chain 216 peptides. Score 0.972 Round 2: 359 peptides, 3 chains. Longest chain 255 peptides. Score 0.975 Round 3: 358 peptides, 4 chains. Longest chain 255 peptides. Score 0.972 Round 4: 358 peptides, 4 chains. Longest chain 154 peptides. Score 0.972 Round 5: 359 peptides, 3 chains. Longest chain 255 peptides. Score 0.975 Taking the results from Round 5 Chains 4, Residues 356, Estimated correctness of the model 100.0 % 3 chains (355 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 270 A and 273 A Built loop between residues 352 A and 358 A 1 chains (362 residues) following loop building 1 chains (362 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 38281 reflections ( 96.51 % complete ) and 3535 restraints for refining 3680 atoms. 674 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2221 (Rfree = 0.000) for 3680 atoms. Found 171 (176 requested) and removed 47 (100 requested) atoms. Cycle 42: After refmac, R = 0.1992 (Rfree = 0.000) for 3801 atoms. Found 100 (182 requested) and removed 40 (103 requested) atoms. Cycle 43: After refmac, R = 0.1894 (Rfree = 0.000) for 3849 atoms. Found 104 (185 requested) and removed 24 (105 requested) atoms. Cycle 44: After refmac, R = 0.1862 (Rfree = 0.000) for 3922 atoms. Found 92 (187 requested) and removed 59 (106 requested) atoms. Cycle 45: After refmac, R = 0.1819 (Rfree = 0.000) for 3949 atoms. Found 113 (185 requested) and removed 67 (107 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.53 1.73 Round 1: 359 peptides, 3 chains. Longest chain 254 peptides. Score 0.975 Round 2: 360 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Round 3: 359 peptides, 4 chains. Longest chain 254 peptides. Score 0.973 Round 4: 359 peptides, 4 chains. Longest chain 154 peptides. Score 0.973 Round 5: 360 peptides, 3 chains. Longest chain 254 peptides. Score 0.976 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 357, Estimated correctness of the model 100.0 % 3 chains (356 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 269 A and 272 A Built loop between residues 353 A and 358 A 1 chains (362 residues) following loop building 1 chains (362 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 38281 reflections ( 96.51 % complete ) and 2861 restraints for refining 2804 atoms. Observations/parameters ratio is 3.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2852 (Rfree = 0.000) for 2804 atoms. Found 119 (128 requested) and removed 0 (128 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2403 (Rfree = 0.000) for 2804 atoms. Found 60 (134 requested) and removed 0 (79 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2222 (Rfree = 0.000) for 2804 atoms. Found 34 (136 requested) and removed 2 (81 requested) atoms. Cycle 49: After refmac, R = 0.2120 (Rfree = 0.000) for 2804 atoms. Found 27 (138 requested) and removed 0 (82 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:50:55 GMT 2018 Job finished. TimeTaking 82.98