null 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 1vlo-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlo-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.8-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/1vlo-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.8-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 ============================================================ 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/1vlo-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlo-3.8-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 240 and 0 Target number of residues in the AU: 240 Target solvent content: 0.6315 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: 0.42 Input MTZ file: 1vlo-3.8-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: 19 Cell parameters: 46.529 64.578 117.291 90.000 90.000 90.000 Input sequence file: 1vlo-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3048 target number of atoms Had to go as low as 0.65 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: 43.415 3.801 Wilson plot Bfac: 67.02 3677 reflections ( 97.33 % complete ) and 0 restraints for refining 3360 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3469 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3257 (Rfree = 0.000) for 3360 atoms. Found 18 (18 requested) and removed 45 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.84 Search for helices and strands: 0 residues in 0 chains, 3393 seeds are put forward Round 1: 98 peptides, 22 chains. Longest chain 7 peptides. Score 0.224 Round 2: 125 peptides, 24 chains. Longest chain 14 peptides. Score 0.322 Round 3: 141 peptides, 24 chains. Longest chain 15 peptides. Score 0.398 Round 4: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.383 Round 5: 142 peptides, 22 chains. Longest chain 14 peptides. Score 0.442 Taking the results from Round 5 Chains 22, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6611 restraints for refining 2757 atoms. 6153 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2639 (Rfree = 0.000) for 2757 atoms. Found 13 (15 requested) and removed 26 (7 requested) atoms. Cycle 2: After refmac, R = 0.2265 (Rfree = 0.000) for 2713 atoms. Found 12 (15 requested) and removed 18 (7 requested) atoms. Cycle 3: After refmac, R = 0.2069 (Rfree = 0.000) for 2695 atoms. Found 10 (14 requested) and removed 14 (7 requested) atoms. Cycle 4: After refmac, R = 0.1567 (Rfree = 0.000) for 2683 atoms. Found 0 (14 requested) and removed 10 (7 requested) atoms. Cycle 5: After refmac, R = 0.1508 (Rfree = 0.000) for 2669 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.86 Search for helices and strands: 0 residues in 0 chains, 2746 seeds are put forward Round 1: 122 peptides, 26 chains. Longest chain 9 peptides. Score 0.264 Round 2: 150 peptides, 25 chains. Longest chain 18 peptides. Score 0.419 Round 3: 140 peptides, 24 chains. Longest chain 11 peptides. Score 0.394 Round 4: 154 peptides, 24 chains. Longest chain 11 peptides. Score 0.456 Round 5: 150 peptides, 21 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 5 Chains 21, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6584 restraints for refining 2750 atoms. 6089 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1946 (Rfree = 0.000) for 2750 atoms. Found 8 (15 requested) and removed 29 (7 requested) atoms. Cycle 7: After refmac, R = 0.1869 (Rfree = 0.000) for 2715 atoms. Found 6 (14 requested) and removed 27 (7 requested) atoms. Cycle 8: After refmac, R = 0.1715 (Rfree = 0.000) for 2683 atoms. Found 9 (14 requested) and removed 20 (7 requested) atoms. Cycle 9: After refmac, R = 0.1676 (Rfree = 0.000) for 2667 atoms. Found 9 (14 requested) and removed 19 (7 requested) atoms. Cycle 10: After refmac, R = 0.1633 (Rfree = 0.000) for 2655 atoms. Found 8 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.76 Search for helices and strands: 0 residues in 0 chains, 2730 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 8 peptides. Score 0.310 Round 2: 162 peptides, 29 chains. Longest chain 11 peptides. Score 0.396 Round 3: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.402 Round 4: 169 peptides, 29 chains. Longest chain 13 peptides. Score 0.427 Round 5: 154 peptides, 26 chains. Longest chain 18 peptides. Score 0.418 Taking the results from Round 4 Chains 29, Residues 140, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6431 restraints for refining 2756 atoms. 5870 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2086 (Rfree = 0.000) for 2756 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 12: After refmac, R = 0.1859 (Rfree = 0.000) for 2730 atoms. Found 8 (15 requested) and removed 20 (7 requested) atoms. Cycle 13: After refmac, R = 0.1759 (Rfree = 0.000) for 2712 atoms. Found 10 (14 requested) and removed 17 (7 requested) atoms. Cycle 14: After refmac, R = 0.1317 (Rfree = 0.000) for 2699 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 15: After refmac, R = 0.1336 (Rfree = 0.000) for 2692 atoms. Found 3 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.84 Search for helices and strands: 0 residues in 0 chains, 2751 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 7 peptides. Score 0.288 Round 2: 148 peptides, 26 chains. Longest chain 17 peptides. Score 0.391 Round 3: 141 peptides, 22 chains. Longest chain 13 peptides. Score 0.438 Round 4: 150 peptides, 26 chains. Longest chain 12 peptides. Score 0.400 Round 5: 139 peptides, 22 chains. Longest chain 17 peptides. Score 0.429 Taking the results from Round 3 Chains 22, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6569 restraints for refining 2756 atoms. 6115 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1694 (Rfree = 0.000) for 2756 atoms. Found 9 (15 requested) and removed 12 (7 requested) atoms. Cycle 17: After refmac, R = 0.1661 (Rfree = 0.000) for 2746 atoms. Found 7 (15 requested) and removed 14 (7 requested) atoms. Cycle 18: After refmac, R = 0.1661 (Rfree = 0.000) for 2737 atoms. Found 8 (15 requested) and removed 17 (7 requested) atoms. Cycle 19: After refmac, R = 0.1478 (Rfree = 0.000) for 2725 atoms. Found 13 (14 requested) and removed 14 (7 requested) atoms. Cycle 20: After refmac, R = 0.1447 (Rfree = 0.000) for 2720 atoms. Found 7 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.79 Search for helices and strands: 0 residues in 0 chains, 2789 seeds are put forward Round 1: 122 peptides, 25 chains. Longest chain 9 peptides. Score 0.286 Round 2: 153 peptides, 28 chains. Longest chain 10 peptides. Score 0.375 Round 3: 166 peptides, 28 chains. Longest chain 11 peptides. Score 0.433 Round 4: 163 peptides, 27 chains. Longest chain 12 peptides. Score 0.438 Round 5: 153 peptides, 27 chains. Longest chain 10 peptides. Score 0.394 Taking the results from Round 4 Chains 27, Residues 136, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6442 restraints for refining 2757 atoms. 5897 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2193 (Rfree = 0.000) for 2757 atoms. Found 7 (15 requested) and removed 20 (7 requested) atoms. Cycle 22: After refmac, R = 0.1838 (Rfree = 0.000) for 2728 atoms. Found 4 (15 requested) and removed 20 (7 requested) atoms. Cycle 23: After refmac, R = 0.1850 (Rfree = 0.000) for 2704 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 24: After refmac, R = 0.1631 (Rfree = 0.000) for 2692 atoms. Found 1 (14 requested) and removed 12 (7 requested) atoms. Cycle 25: After refmac, R = 0.1555 (Rfree = 0.000) for 2677 atoms. Found 3 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.81 Search for helices and strands: 0 residues in 0 chains, 2753 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 7 peptides. Score 0.251 Round 2: 128 peptides, 20 chains. Longest chain 12 peptides. Score 0.419 Round 3: 137 peptides, 23 chains. Longest chain 13 peptides. Score 0.400 Round 4: 139 peptides, 23 chains. Longest chain 13 peptides. Score 0.409 Round 5: 148 peptides, 22 chains. Longest chain 13 peptides. Score 0.468 Taking the results from Round 5 Chains 22, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6469 restraints for refining 2756 atoms. 5987 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1840 (Rfree = 0.000) for 2756 atoms. Found 11 (15 requested) and removed 18 (7 requested) atoms. Cycle 27: After refmac, R = 0.1787 (Rfree = 0.000) for 2736 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 28: After refmac, R = 0.1686 (Rfree = 0.000) for 2722 atoms. Found 11 (15 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.1788 (Rfree = 0.000) for 2711 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 30: After refmac, R = 0.1644 (Rfree = 0.000) for 2708 atoms. Found 11 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.81 Search for helices and strands: 0 residues in 0 chains, 2811 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 9 peptides. Score 0.270 Round 2: 150 peptides, 27 chains. Longest chain 11 peptides. Score 0.380 Round 3: 144 peptides, 25 chains. Longest chain 10 peptides. Score 0.392 Round 4: 157 peptides, 25 chains. Longest chain 10 peptides. Score 0.450 Round 5: 140 peptides, 22 chains. Longest chain 14 peptides. Score 0.433 Taking the results from Round 4 Chains 25, Residues 132, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6463 restraints for refining 2754 atoms. 5950 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2065 (Rfree = 0.000) for 2754 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 32: After refmac, R = 0.1885 (Rfree = 0.000) for 2719 atoms. Found 13 (15 requested) and removed 21 (7 requested) atoms. Cycle 33: After refmac, R = 0.1958 (Rfree = 0.000) for 2699 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 34: After refmac, R = 0.1848 (Rfree = 0.000) for 2692 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.1798 (Rfree = 0.000) for 2681 atoms. Found 9 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.77 Search for helices and strands: 0 residues in 0 chains, 2756 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 7 peptides. Score 0.234 Round 2: 119 peptides, 23 chains. Longest chain 11 peptides. Score 0.313 Round 3: 127 peptides, 26 chains. Longest chain 8 peptides. Score 0.290 Round 4: 124 peptides, 21 chains. Longest chain 13 peptides. Score 0.380 Round 5: 132 peptides, 24 chains. Longest chain 17 peptides. Score 0.356 Taking the results from Round 4 Chains 21, Residues 103, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6133 restraints for refining 2647 atoms. 5718 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2117 (Rfree = 0.000) for 2647 atoms. Found 14 (14 requested) and removed 28 (7 requested) atoms. Cycle 37: After refmac, R = 0.1825 (Rfree = 0.000) for 2624 atoms. Found 10 (14 requested) and removed 12 (7 requested) atoms. Cycle 38: After refmac, R = 0.1662 (Rfree = 0.000) for 2615 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 39: After refmac, R = 0.1565 (Rfree = 0.000) for 2615 atoms. Found 7 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.1579 (Rfree = 0.000) for 2608 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.80 Search for helices and strands: 0 residues in 0 chains, 2667 seeds are put forward Round 1: 99 peptides, 21 chains. Longest chain 7 peptides. Score 0.253 Round 2: 118 peptides, 19 chains. Longest chain 17 peptides. Score 0.393 Round 3: 112 peptides, 19 chains. Longest chain 15 peptides. Score 0.364 Round 4: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.330 Round 5: 111 peptides, 18 chains. Longest chain 15 peptides. Score 0.381 Taking the results from Round 2 Chains 19, Residues 99, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3677 reflections ( 97.33 % complete ) and 6077 restraints for refining 2639 atoms. 5661 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1692 (Rfree = 0.000) for 2639 atoms. Found 13 (14 requested) and removed 17 (7 requested) atoms. Cycle 42: After refmac, R = 0.1565 (Rfree = 0.000) for 2630 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 43: After refmac, R = 0.1571 (Rfree = 0.000) for 2624 atoms. Found 9 (14 requested) and removed 12 (7 requested) atoms. Cycle 44: After refmac, R = 0.1594 (Rfree = 0.000) for 2621 atoms. Found 13 (14 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.1345 (Rfree = 0.000) for 2619 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.79 Search for helices and strands: 0 residues in 0 chains, 2671 seeds are put forward Round 1: 90 peptides, 20 chains. Longest chain 6 peptides. Score 0.226 Round 2: 95 peptides, 18 chains. Longest chain 8 peptides. Score 0.300 Round 3: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.330 Round 4: 92 peptides, 17 chains. Longest chain 11 peptides. Score 0.307 Round 5: 95 peptides, 18 chains. Longest chain 10 peptides. Score 0.300 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 76, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 1vlo-3_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (76 residues) following loop building 4 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3677 reflections ( 97.33 % complete ) and 6307 restraints for refining 2685 atoms. 5967 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1513 (Rfree = 0.000) for 2685 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1606 (Rfree = 0.000) for 2674 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1545 (Rfree = 0.000) for 2664 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1318 (Rfree = 0.000) for 2654 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:15:44 GMT 2018 Job finished. TimeTaking 47.82 Used memory is bytes: 4770160