Tue 25 Dec 19:27:55 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 1vp8-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.4-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/1vp8-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.4-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 19:28:05 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/1vp8-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.4-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 184 and 0 Target number of residues in the AU: 184 Target solvent content: 0.6258 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: 1vp8-3.4-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: 1vp8-3.4-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 3.401 Wilson plot Bfac: 64.19 4023 reflections ( 99.09 % complete ) and 0 restraints for refining 1801 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3113 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2966 (Rfree = 0.000) for 1801 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.91 Search for helices and strands: 0 residues in 0 chains, 1830 seeds are put forward Round 1: 118 peptides, 17 chains. Longest chain 24 peptides. Score 0.492 Round 2: 146 peptides, 17 chains. Longest chain 29 peptides. Score 0.627 Round 3: 144 peptides, 14 chains. Longest chain 26 peptides. Score 0.676 Round 4: 150 peptides, 14 chains. Longest chain 32 peptides. Score 0.698 Round 5: 146 peptides, 14 chains. Longest chain 27 peptides. Score 0.683 Taking the results from Round 4 Chains 14, Residues 136, Estimated correctness of the model 57.3 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 99.09 % complete ) and 2926 restraints for refining 1460 atoms. 2347 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2981 (Rfree = 0.000) for 1460 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 2: After refmac, R = 0.2713 (Rfree = 0.000) for 1427 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 3: After refmac, R = 0.2503 (Rfree = 0.000) for 1416 atoms. Found 9 (10 requested) and removed 14 (5 requested) atoms. Cycle 4: After refmac, R = 0.2392 (Rfree = 0.000) for 1402 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2395 (Rfree = 0.000) for 1401 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 2.89 Search for helices and strands: 0 residues in 0 chains, 1442 seeds are put forward Round 1: 126 peptides, 14 chains. Longest chain 15 peptides. Score 0.600 Round 2: 133 peptides, 14 chains. Longest chain 18 peptides. Score 0.631 Round 3: 137 peptides, 14 chains. Longest chain 23 peptides. Score 0.648 Round 4: 143 peptides, 15 chains. Longest chain 17 peptides. Score 0.653 Round 5: 148 peptides, 13 chains. Longest chain 19 peptides. Score 0.708 Taking the results from Round 5 Chains 13, Residues 135, Estimated correctness of the model 59.9 % 2 chains (28 residues) have been docked in sequence Building loops using Loopy2018 13 chains (135 residues) following loop building 2 chains (28 residues) in sequence following loop building ------------------------------------------------------ 4023 reflections ( 99.09 % complete ) and 2874 restraints for refining 1462 atoms. 2255 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3165 (Rfree = 0.000) for 1462 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2719 (Rfree = 0.000) for 1438 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2669 (Rfree = 0.000) for 1432 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2658 (Rfree = 0.000) for 1430 atoms. Found 9 (9 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2522 (Rfree = 0.000) for 1426 atoms. Found 9 (9 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 2.81 Search for helices and strands: 0 residues in 0 chains, 1470 seeds are put forward Round 1: 148 peptides, 16 chains. Longest chain 29 peptides. Score 0.654 Round 2: 156 peptides, 16 chains. Longest chain 23 peptides. Score 0.685 Round 3: 147 peptides, 12 chains. Longest chain 24 peptides. Score 0.721 Round 4: 154 peptides, 14 chains. Longest chain 19 peptides. Score 0.712 Round 5: 153 peptides, 13 chains. Longest chain 21 peptides. Score 0.725 Taking the results from Round 5 Chains 13, Residues 140, Estimated correctness of the model 64.0 % 2 chains (33 residues) have been docked in sequence Building loops using Loopy2018 13 chains (140 residues) following loop building 2 chains (33 residues) in sequence following loop building ------------------------------------------------------ 4023 reflections ( 99.09 % complete ) and 2796 restraints for refining 1462 atoms. 2132 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2790 (Rfree = 0.000) for 1462 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.2575 (Rfree = 0.000) for 1441 atoms. Found 7 (10 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2475 (Rfree = 0.000) for 1437 atoms. Found 3 (9 requested) and removed 6 (5 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2310 (Rfree = 0.000) for 1433 atoms. Found 3 (8 requested) and removed 8 (5 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2335 (Rfree = 0.000) for 1426 atoms. Found 5 (8 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 2.90 Search for helices and strands: 0 residues in 0 chains, 1475 seeds are put forward Round 1: 141 peptides, 16 chains. Longest chain 18 peptides. Score 0.626 Round 2: 155 peptides, 14 chains. Longest chain 24 peptides. Score 0.715 Round 3: 155 peptides, 14 chains. Longest chain 20 peptides. Score 0.715 Round 4: 147 peptides, 16 chains. Longest chain 31 peptides. Score 0.650 Round 5: 137 peptides, 13 chains. Longest chain 20 peptides. Score 0.667 Taking the results from Round 3 Chains 15, Residues 141, Estimated correctness of the model 61.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4023 reflections ( 99.09 % complete ) and 3039 restraints for refining 1462 atoms. 2464 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2667 (Rfree = 0.000) for 1462 atoms. Found 9 (9 requested) and removed 15 (5 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2437 (Rfree = 0.000) for 1450 atoms. Found 8 (8 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.2401 (Rfree = 0.000) for 1447 atoms. Found 8 (8 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2302 (Rfree = 0.000) for 1444 atoms. Found 7 (7 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2348 (Rfree = 0.000) for 1440 atoms. Found 7 (7 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 2.88 Search for helices and strands: 0 residues in 0 chains, 1501 seeds are put forward Round 1: 138 peptides, 16 chains. Longest chain 16 peptides. Score 0.613 Round 2: 155 peptides, 13 chains. Longest chain 23 peptides. Score 0.731 Round 3: 151 peptides, 15 chains. Longest chain 21 peptides. Score 0.684 Round 4: 152 peptides, 16 chains. Longest chain 18 peptides. Score 0.670 Round 5: 159 peptides, 14 chains. Longest chain 21 peptides. Score 0.728 Taking the results from Round 2 Chains 15, Residues 142, Estimated correctness of the model 65.5 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4023 reflections ( 99.09 % complete ) and 3050 restraints for refining 1462 atoms. 2458 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2525 (Rfree = 0.000) for 1462 atoms. Found 8 (8 requested) and removed 9 (5 requested) atoms. Cycle 22: After refmac, R = 0.2461 (Rfree = 0.000) for 1453 atoms. Found 7 (7 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.2334 (Rfree = 0.000) for 1448 atoms. Found 7 (7 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.2322 (Rfree = 0.000) for 1445 atoms. Found 6 (6 requested) and removed 9 (5 requested) atoms. Cycle 25: After refmac, R = 0.2311 (Rfree = 0.000) for 1440 atoms. Found 6 (6 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 2.88 Search for helices and strands: 0 residues in 0 chains, 1470 seeds are put forward Round 1: 143 peptides, 18 chains. Longest chain 17 peptides. Score 0.594 Round 2: 144 peptides, 16 chains. Longest chain 18 peptides. Score 0.638 Round 3: 154 peptides, 15 chains. Longest chain 27 peptides. Score 0.695 Round 4: 142 peptides, 11 chains. Longest chain 24 peptides. Score 0.721 Round 5: 155 peptides, 14 chains. Longest chain 21 peptides. Score 0.715 Taking the results from Round 4 Chains 12, Residues 131, Estimated correctness of the model 63.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 99.09 % complete ) and 3176 restraints for refining 1462 atoms. 2632 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2648 (Rfree = 0.000) for 1462 atoms. Found 7 (7 requested) and removed 16 (5 requested) atoms. Cycle 27: After refmac, R = 0.2498 (Rfree = 0.000) for 1449 atoms. Found 6 (6 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2476 (Rfree = 0.000) for 1446 atoms. Found 6 (6 requested) and removed 8 (5 requested) atoms. Cycle 29: After refmac, R = 0.2365 (Rfree = 0.000) for 1444 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.2262 (Rfree = 0.000) for 1441 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 2.91 Search for helices and strands: 0 residues in 0 chains, 1480 seeds are put forward Round 1: 128 peptides, 12 chains. Longest chain 19 peptides. Score 0.650 Round 2: 133 peptides, 14 chains. Longest chain 15 peptides. Score 0.631 Round 3: 134 peptides, 14 chains. Longest chain 21 peptides. Score 0.635 Round 4: 139 peptides, 14 chains. Longest chain 21 peptides. Score 0.656 Round 5: 137 peptides, 15 chains. Longest chain 23 peptides. Score 0.628 Taking the results from Round 4 Chains 15, Residues 125, Estimated correctness of the model 45.8 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 99.09 % complete ) and 3130 restraints for refining 1462 atoms. 2593 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2448 (Rfree = 0.000) for 1462 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2245 (Rfree = 0.000) for 1457 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2263 (Rfree = 0.000) for 1453 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2218 (Rfree = 0.000) for 1448 atoms. Found 5 (5 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2024 (Rfree = 0.000) for 1443 atoms. Found 3 (5 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.90 Search for helices and strands: 0 residues in 0 chains, 1492 seeds are put forward Round 1: 120 peptides, 17 chains. Longest chain 14 peptides. Score 0.503 Round 2: 140 peptides, 15 chains. Longest chain 18 peptides. Score 0.641 Round 3: 135 peptides, 15 chains. Longest chain 18 peptides. Score 0.620 Round 4: 135 peptides, 12 chains. Longest chain 24 peptides. Score 0.678 Round 5: 137 peptides, 14 chains. Longest chain 18 peptides. Score 0.648 Taking the results from Round 4 Chains 13, Residues 123, Estimated correctness of the model 52.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4023 reflections ( 99.09 % complete ) and 3102 restraints for refining 1461 atoms. 2594 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2540 (Rfree = 0.000) for 1461 atoms. Found 5 (5 requested) and removed 13 (5 requested) atoms. Cycle 37: After refmac, R = 0.2445 (Rfree = 0.000) for 1446 atoms. Found 5 (5 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2339 (Rfree = 0.000) for 1438 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2272 (Rfree = 0.000) for 1434 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2303 (Rfree = 0.000) for 1430 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 2.90 Search for helices and strands: 0 residues in 0 chains, 1485 seeds are put forward Round 1: 120 peptides, 17 chains. Longest chain 18 peptides. Score 0.503 Round 2: 139 peptides, 18 chains. Longest chain 19 peptides. Score 0.576 Round 3: 142 peptides, 17 chains. Longest chain 22 peptides. Score 0.610 Round 4: 145 peptides, 16 chains. Longest chain 20 peptides. Score 0.642 Round 5: 147 peptides, 17 chains. Longest chain 18 peptides. Score 0.631 Taking the results from Round 4 Chains 16, Residues 129, Estimated correctness of the model 41.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4023 reflections ( 99.09 % complete ) and 3222 restraints for refining 1462 atoms. 2722 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2536 (Rfree = 0.000) for 1462 atoms. Found 5 (5 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2397 (Rfree = 0.000) for 1454 atoms. Found 5 (5 requested) and removed 12 (5 requested) atoms. Cycle 43: After refmac, R = 0.2262 (Rfree = 0.000) for 1446 atoms. Found 5 (5 requested) and removed 6 (5 requested) atoms. Cycle 44: After refmac, R = 0.2256 (Rfree = 0.000) for 1445 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2188 (Rfree = 0.000) for 1444 atoms. Found 5 (5 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 2.91 Search for helices and strands: 0 residues in 0 chains, 1496 seeds are put forward Round 1: 115 peptides, 18 chains. Longest chain 12 peptides. Score 0.451 Round 2: 126 peptides, 15 chains. Longest chain 16 peptides. Score 0.579 Round 3: 130 peptides, 14 chains. Longest chain 17 peptides. Score 0.618 Round 4: 126 peptides, 13 chains. Longest chain 16 peptides. Score 0.621 Round 5: 123 peptides, 13 chains. Longest chain 20 peptides. Score 0.608 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 113, Estimated correctness of the model 35.3 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vp8-3_warpNtrace.pdb as input ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 4023 reflections ( 99.09 % complete ) and 3213 restraints for refining 1462 atoms. 2749 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2459 (Rfree = 0.000) for 1462 atoms. Found 0 (5 requested) and removed 4 (5 requested) atoms. Cycle 47: After refmac, R = 0.2368 (Rfree = 0.000) for 1456 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2259 (Rfree = 0.000) for 1450 atoms. Found 0 (5 requested) and removed 2 (5 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2234 (Rfree = 0.000) for 1448 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:11:58 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 44.06