Tue 25 Dec 19:27:57 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 1vp8-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.6-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/1vp8-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.6-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 19:28:07 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/1vp8-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.6-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 180 and 0 Target number of residues in the AU: 180 Target solvent content: 0.6339 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.59 Input MTZ file: 1vp8-3.6-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: 182 Cell parameters: 109.749 109.749 76.534 90.000 90.000 120.000 Input sequence file: 1vp8-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.75 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 3 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: 18.945 3.601 Wilson plot Bfac: 67.69 3410 reflections ( 98.93 % complete ) and 0 restraints for refining 1791 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3165 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2939 (Rfree = 0.000) for 1791 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.00 Search for helices and strands: 0 residues in 0 chains, 1816 seeds are put forward Round 1: 93 peptides, 17 chains. Longest chain 10 peptides. Score 0.344 Round 2: 123 peptides, 15 chains. Longest chain 14 peptides. Score 0.564 Round 3: 129 peptides, 18 chains. Longest chain 18 peptides. Score 0.527 Round 4: 140 peptides, 15 chains. Longest chain 16 peptides. Score 0.641 Round 5: 136 peptides, 15 chains. Longest chain 24 peptides. Score 0.624 Taking the results from Round 4 Chains 16, Residues 125, Estimated correctness of the model 29.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3410 reflections ( 98.93 % complete ) and 3001 restraints for refining 1457 atoms. 2477 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2521 (Rfree = 0.000) for 1457 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.2387 (Rfree = 0.000) for 1434 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 3: After refmac, R = 0.2392 (Rfree = 0.000) for 1427 atoms. Found 3 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2291 (Rfree = 0.000) for 1416 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2245 (Rfree = 0.000) for 1414 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.02 Search for helices and strands: 0 residues in 0 chains, 1457 seeds are put forward Round 1: 127 peptides, 18 chains. Longest chain 18 peptides. Score 0.517 Round 2: 141 peptides, 17 chains. Longest chain 18 peptides. Score 0.606 Round 3: 132 peptides, 14 chains. Longest chain 22 peptides. Score 0.627 Round 4: 134 peptides, 13 chains. Longest chain 22 peptides. Score 0.655 Round 5: 139 peptides, 15 chains. Longest chain 25 peptides. Score 0.637 Taking the results from Round 4 Chains 15, Residues 121, Estimated correctness of the model 34.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3410 reflections ( 98.93 % complete ) and 3162 restraints for refining 1449 atoms. 2662 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2574 (Rfree = 0.000) for 1449 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.2487 (Rfree = 0.000) for 1435 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2419 (Rfree = 0.000) for 1425 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2327 (Rfree = 0.000) for 1421 atoms. Found 6 (9 requested) and removed 12 (4 requested) atoms. Cycle 10: After refmac, R = 0.2195 (Rfree = 0.000) for 1412 atoms. Found 7 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 2.99 Search for helices and strands: 0 residues in 0 chains, 1475 seeds are put forward Round 1: 123 peptides, 17 chains. Longest chain 16 peptides. Score 0.519 Round 2: 128 peptides, 13 chains. Longest chain 17 peptides. Score 0.630 Round 3: 134 peptides, 14 chains. Longest chain 20 peptides. Score 0.635 Round 4: 137 peptides, 14 chains. Longest chain 26 peptides. Score 0.648 Round 5: 137 peptides, 12 chains. Longest chain 41 peptides. Score 0.685 Taking the results from Round 5 Chains 14, Residues 125, Estimated correctness of the model 44.8 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 3410 reflections ( 98.93 % complete ) and 2850 restraints for refining 1458 atoms. 2281 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2361 (Rfree = 0.000) for 1458 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2154 (Rfree = 0.000) for 1444 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2148 (Rfree = 0.000) for 1435 atoms. Found 8 (9 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2116 (Rfree = 0.000) for 1429 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2054 (Rfree = 0.000) for 1424 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.00 Search for helices and strands: 0 residues in 0 chains, 1473 seeds are put forward Round 1: 125 peptides, 17 chains. Longest chain 18 peptides. Score 0.529 Round 2: 127 peptides, 15 chains. Longest chain 20 peptides. Score 0.583 Round 3: 117 peptides, 12 chains. Longest chain 23 peptides. Score 0.602 Round 4: 126 peptides, 14 chains. Longest chain 24 peptides. Score 0.600 Round 5: 133 peptides, 13 chains. Longest chain 21 peptides. Score 0.651 Taking the results from Round 5 Chains 15, Residues 120, Estimated correctness of the model 33.4 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3410 reflections ( 98.93 % complete ) and 2863 restraints for refining 1458 atoms. 2304 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2356 (Rfree = 0.000) for 1458 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 17: After refmac, R = 0.2133 (Rfree = 0.000) for 1449 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 18: After refmac, R = 0.2151 (Rfree = 0.000) for 1445 atoms. Found 7 (9 requested) and removed 8 (4 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1959 (Rfree = 0.000) for 1441 atoms. Found 4 (9 requested) and removed 11 (4 requested) atoms. Cycle 20: After refmac, R = 0.1977 (Rfree = 0.000) for 1430 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.00 Search for helices and strands: 0 residues in 0 chains, 1483 seeds are put forward Round 1: 119 peptides, 13 chains. Longest chain 19 peptides. Score 0.589 Round 2: 120 peptides, 11 chains. Longest chain 20 peptides. Score 0.636 Round 3: 127 peptides, 11 chains. Longest chain 21 peptides. Score 0.665 Round 4: 130 peptides, 12 chains. Longest chain 22 peptides. Score 0.658 Round 5: 124 peptides, 12 chains. Longest chain 22 peptides. Score 0.633 Taking the results from Round 3 Chains 12, Residues 116, Estimated correctness of the model 38.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3410 reflections ( 98.93 % complete ) and 3065 restraints for refining 1458 atoms. 2583 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2181 (Rfree = 0.000) for 1458 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 22: After refmac, R = 0.2109 (Rfree = 0.000) for 1451 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 23: After refmac, R = 0.2041 (Rfree = 0.000) for 1449 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 24: After refmac, R = 0.2004 (Rfree = 0.000) for 1444 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.1893 (Rfree = 0.000) for 1444 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.97 Search for helices and strands: 0 residues in 0 chains, 1496 seeds are put forward Round 1: 129 peptides, 16 chains. Longest chain 21 peptides. Score 0.571 Round 2: 140 peptides, 14 chains. Longest chain 21 peptides. Score 0.660 Round 3: 130 peptides, 15 chains. Longest chain 21 peptides. Score 0.597 Round 4: 143 peptides, 15 chains. Longest chain 21 peptides. Score 0.653 Round 5: 144 peptides, 15 chains. Longest chain 21 peptides. Score 0.657 Taking the results from Round 2 Chains 14, Residues 126, Estimated correctness of the model 36.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3410 reflections ( 98.93 % complete ) and 3151 restraints for refining 1458 atoms. 2661 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2250 (Rfree = 0.000) for 1458 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 1450 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.2039 (Rfree = 0.000) for 1445 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.2045 (Rfree = 0.000) for 1445 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.1919 (Rfree = 0.000) for 1448 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 2.99 Search for helices and strands: 0 residues in 0 chains, 1505 seeds are put forward Round 1: 122 peptides, 15 chains. Longest chain 15 peptides. Score 0.559 Round 2: 136 peptides, 15 chains. Longest chain 21 peptides. Score 0.624 Round 3: 139 peptides, 14 chains. Longest chain 21 peptides. Score 0.656 Round 4: 145 peptides, 14 chains. Longest chain 22 peptides. Score 0.679 Round 5: 130 peptides, 15 chains. Longest chain 19 peptides. Score 0.597 Taking the results from Round 4 Chains 14, Residues 131, Estimated correctness of the model 42.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3410 reflections ( 98.93 % complete ) and 3019 restraints for refining 1437 atoms. 2509 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2180 (Rfree = 0.000) for 1437 atoms. Found 7 (9 requested) and removed 9 (4 requested) atoms. Cycle 32: After refmac, R = 0.1972 (Rfree = 0.000) for 1433 atoms. Found 1 (9 requested) and removed 7 (4 requested) atoms. Cycle 33: After refmac, R = 0.2504 (Rfree = 0.000) for 1424 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 34: After refmac, R = 0.2045 (Rfree = 0.000) for 1417 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.1885 (Rfree = 0.000) for 1412 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.99 Search for helices and strands: 0 residues in 0 chains, 1453 seeds are put forward Round 1: 102 peptides, 15 chains. Longest chain 15 peptides. Score 0.453 Round 2: 120 peptides, 11 chains. Longest chain 20 peptides. Score 0.636 Round 3: 125 peptides, 14 chains. Longest chain 26 peptides. Score 0.596 Round 4: 125 peptides, 12 chains. Longest chain 23 peptides. Score 0.637 Round 5: 138 peptides, 14 chains. Longest chain 20 peptides. Score 0.652 Taking the results from Round 5 Chains 18, Residues 124, Estimated correctness of the model 33.8 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 3410 reflections ( 98.93 % complete ) and 2938 restraints for refining 1457 atoms. 2384 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2399 (Rfree = 0.000) for 1457 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 37: After refmac, R = 0.2220 (Rfree = 0.000) for 1449 atoms. Found 5 (9 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.2084 (Rfree = 0.000) for 1440 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 39: After refmac, R = 0.1986 (Rfree = 0.000) for 1438 atoms. Found 5 (9 requested) and removed 12 (4 requested) atoms. Cycle 40: After refmac, R = 0.1864 (Rfree = 0.000) for 1429 atoms. Found 4 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.07 Search for helices and strands: 0 residues in 0 chains, 1480 seeds are put forward Round 1: 120 peptides, 18 chains. Longest chain 14 peptides. Score 0.479 Round 2: 125 peptides, 16 chains. Longest chain 21 peptides. Score 0.552 Round 3: 126 peptides, 16 chains. Longest chain 30 peptides. Score 0.557 Round 4: 125 peptides, 15 chains. Longest chain 24 peptides. Score 0.574 Round 5: 129 peptides, 16 chains. Longest chain 24 peptides. Score 0.571 Taking the results from Round 4 Chains 15, Residues 110, Estimated correctness of the model 4.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3410 reflections ( 98.93 % complete ) and 3293 restraints for refining 1458 atoms. 2868 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2286 (Rfree = 0.000) for 1458 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 42: After refmac, R = 0.2167 (Rfree = 0.000) for 1454 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2070 (Rfree = 0.000) for 1455 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1974 (Rfree = 0.000) for 1455 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1942 (Rfree = 0.000) for 1455 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.00 Search for helices and strands: 0 residues in 0 chains, 1515 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 11 peptides. Score 0.313 Round 2: 117 peptides, 17 chains. Longest chain 14 peptides. Score 0.487 Round 3: 118 peptides, 17 chains. Longest chain 13 peptides. Score 0.492 Round 4: 124 peptides, 14 chains. Longest chain 20 peptides. Score 0.591 Round 5: 115 peptides, 15 chains. Longest chain 16 peptides. Score 0.524 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 110, Estimated correctness of the model 11.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vp8-3_warpNtrace.pdb as input Building loops using Loopy2018 14 chains (110 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3410 reflections ( 98.93 % complete ) and 3187 restraints for refining 1458 atoms. 2731 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2221 (Rfree = 0.000) for 1458 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2085 (Rfree = 0.000) for 1451 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2022 (Rfree = 0.000) for 1446 atoms. Found 0 (9 requested) and removed 3 (4 requested) atoms. Cycle 49: After refmac, R = 0.1995 (Rfree = 0.000) for 1443 atoms. Found 0 (9 requested) and removed 2 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:11:17 GMT 2018 Job finished. TimeTaking 43.33