Mon 24 Dec 00:17:23 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fqp-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:17:28 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-parrot-mrncs/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 244 and 0 Target number of residues in the AU: 244 Target solvent content: 0.6100 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-3.4-parrot-mrncs.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: 4 Cell parameters: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.60 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 50.895 3.400 Wilson plot Bfac: 56.75 3849 reflections ( 82.76 % complete ) and 0 restraints for refining 3434 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3128 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2659 (Rfree = 0.000) for 3434 atoms. Found 19 (25 requested) and removed 126 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 3.64 Search for helices and strands: 0 residues in 0 chains, 3349 seeds are put forward NCS extension: 0 residues added, 3349 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 7 peptides. Score 0.238 Round 2: 130 peptides, 27 chains. Longest chain 8 peptides. Score 0.287 Round 3: 138 peptides, 27 chains. Longest chain 9 peptides. Score 0.328 Round 4: 141 peptides, 25 chains. Longest chain 14 peptides. Score 0.385 Round 5: 136 peptides, 26 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 4 Chains 25, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6712 restraints for refining 2822 atoms. 6273 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.1901 (Rfree = 0.000) for 2822 atoms. Found 10 (21 requested) and removed 19 (10 requested) atoms. Cycle 2: After refmac, R = 0.1930 (Rfree = 0.000) for 2774 atoms. Found 8 (21 requested) and removed 15 (10 requested) atoms. Cycle 3: After refmac, R = 0.1447 (Rfree = 0.000) for 2752 atoms. Found 4 (20 requested) and removed 11 (10 requested) atoms. Cycle 4: After refmac, R = 0.1372 (Rfree = 0.000) for 2726 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. Cycle 5: After refmac, R = 0.1334 (Rfree = 0.000) for 2713 atoms. Found 1 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.60 Search for helices and strands: 0 residues in 0 chains, 2768 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 2777 seeds are put forward Round 1: 107 peptides, 20 chains. Longest chain 13 peptides. Score 0.322 Round 2: 148 peptides, 30 chains. Longest chain 8 peptides. Score 0.315 Round 3: 138 peptides, 26 chains. Longest chain 9 peptides. Score 0.349 Round 4: 163 peptides, 29 chains. Longest chain 10 peptides. Score 0.408 Round 5: 160 peptides, 30 chains. Longest chain 10 peptides. Score 0.374 Taking the results from Round 4 Chains 29, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 5954 restraints for refining 2602 atoms. 5447 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1751 (Rfree = 0.000) for 2602 atoms. Found 13 (19 requested) and removed 10 (9 requested) atoms. Cycle 7: After refmac, R = 0.1676 (Rfree = 0.000) for 2590 atoms. Found 15 (19 requested) and removed 10 (9 requested) atoms. Cycle 8: After refmac, R = 0.1512 (Rfree = 0.000) for 2589 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. Cycle 9: After refmac, R = 0.1443 (Rfree = 0.000) for 2581 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.1605 (Rfree = 0.000) for 2577 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.63 Search for helices and strands: 0 residues in 0 chains, 2646 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2657 seeds are put forward Round 1: 132 peptides, 28 chains. Longest chain 8 peptides. Score 0.276 Round 2: 176 peptides, 34 chains. Longest chain 11 peptides. Score 0.370 Round 3: 193 peptides, 34 chains. Longest chain 14 peptides. Score 0.447 Round 4: 189 peptides, 34 chains. Longest chain 14 peptides. Score 0.430 Round 5: 175 peptides, 32 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 3 Chains 34, Residues 159, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 5663 restraints for refining 2585 atoms. 5046 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1868 (Rfree = 0.000) for 2585 atoms. Found 17 (19 requested) and removed 13 (9 requested) atoms. Cycle 12: After refmac, R = 0.1644 (Rfree = 0.000) for 2580 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 13: After refmac, R = 0.1596 (Rfree = 0.000) for 2571 atoms. Found 11 (19 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.1566 (Rfree = 0.000) for 2568 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.1491 (Rfree = 0.000) for 2560 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 3.59 Search for helices and strands: 0 residues in 0 chains, 2598 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2614 seeds are put forward Round 1: 154 peptides, 30 chains. Longest chain 9 peptides. Score 0.345 Round 2: 165 peptides, 27 chains. Longest chain 10 peptides. Score 0.455 Round 3: 171 peptides, 27 chains. Longest chain 15 peptides. Score 0.481 Round 4: 161 peptides, 25 chains. Longest chain 12 peptides. Score 0.476 Round 5: 179 peptides, 30 chains. Longest chain 11 peptides. Score 0.460 Taking the results from Round 3 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 5667 restraints for refining 2568 atoms. 5118 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1651 (Rfree = 0.000) for 2568 atoms. Found 15 (19 requested) and removed 12 (9 requested) atoms. Cycle 17: After refmac, R = 0.1529 (Rfree = 0.000) for 2569 atoms. Found 11 (19 requested) and removed 10 (9 requested) atoms. Cycle 18: After refmac, R = 0.1470 (Rfree = 0.000) for 2566 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.1447 (Rfree = 0.000) for 2558 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.1435 (Rfree = 0.000) for 2552 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.61 Search for helices and strands: 0 residues in 0 chains, 2566 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2578 seeds are put forward Round 1: 154 peptides, 30 chains. Longest chain 10 peptides. Score 0.345 Round 2: 164 peptides, 28 chains. Longest chain 11 peptides. Score 0.432 Round 3: 169 peptides, 29 chains. Longest chain 12 peptides. Score 0.435 Round 4: 177 peptides, 28 chains. Longest chain 14 peptides. Score 0.488 Round 5: 186 peptides, 28 chains. Longest chain 14 peptides. Score 0.525 Taking the results from Round 5 Chains 28, Residues 158, Estimated correctness of the model 2.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 5892 restraints for refining 2646 atoms. 5288 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1731 (Rfree = 0.000) for 2646 atoms. Found 18 (19 requested) and removed 11 (9 requested) atoms. Cycle 22: After refmac, R = 0.1587 (Rfree = 0.000) for 2649 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 23: After refmac, R = 0.1592 (Rfree = 0.000) for 2633 atoms. Found 12 (19 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.1476 (Rfree = 0.000) for 2632 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.1458 (Rfree = 0.000) for 2621 atoms. Found 1 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 3.58 Search for helices and strands: 0 residues in 0 chains, 2651 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2666 seeds are put forward Round 1: 146 peptides, 27 chains. Longest chain 10 peptides. Score 0.368 Round 2: 167 peptides, 31 chains. Longest chain 10 peptides. Score 0.387 Round 3: 168 peptides, 27 chains. Longest chain 13 peptides. Score 0.469 Round 4: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.447 Round 5: 163 peptides, 30 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 3 Chains 27, Residues 141, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6094 restraints for refining 2683 atoms. 5542 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1560 (Rfree = 0.000) for 2683 atoms. Found 10 (20 requested) and removed 14 (10 requested) atoms. Cycle 27: After refmac, R = 0.1396 (Rfree = 0.000) for 2673 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.1376 (Rfree = 0.000) for 2665 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.1366 (Rfree = 0.000) for 2665 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1355 (Rfree = 0.000) for 2659 atoms. Found 5 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.61 Search for helices and strands: 0 residues in 0 chains, 2681 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2695 seeds are put forward Round 1: 156 peptides, 31 chains. Longest chain 8 peptides. Score 0.334 Round 2: 160 peptides, 28 chains. Longest chain 9 peptides. Score 0.414 Round 3: 157 peptides, 28 chains. Longest chain 9 peptides. Score 0.400 Round 4: 165 peptides, 30 chains. Longest chain 12 peptides. Score 0.398 Round 5: 161 peptides, 26 chains. Longest chain 11 peptides. Score 0.457 Taking the results from Round 5 Chains 26, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6180 restraints for refining 2710 atoms. 5666 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1628 (Rfree = 0.000) for 2710 atoms. Found 17 (20 requested) and removed 13 (10 requested) atoms. Cycle 32: After refmac, R = 0.1466 (Rfree = 0.000) for 2706 atoms. Found 8 (20 requested) and removed 11 (10 requested) atoms. Cycle 33: After refmac, R = 0.1405 (Rfree = 0.000) for 2700 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.1388 (Rfree = 0.000) for 2690 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1369 (Rfree = 0.000) for 2685 atoms. Found 5 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 3.63 Search for helices and strands: 0 residues in 0 chains, 2731 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2746 seeds are put forward Round 1: 113 peptides, 24 chains. Longest chain 7 peptides. Score 0.263 Round 2: 120 peptides, 23 chains. Longest chain 10 peptides. Score 0.323 Round 3: 139 peptides, 26 chains. Longest chain 11 peptides. Score 0.354 Round 4: 134 peptides, 26 chains. Longest chain 12 peptides. Score 0.329 Round 5: 149 peptides, 29 chains. Longest chain 9 peptides. Score 0.341 Taking the results from Round 3 Chains 26, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6355 restraints for refining 2731 atoms. 5929 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1545 (Rfree = 0.000) for 2731 atoms. Found 9 (20 requested) and removed 14 (10 requested) atoms. Cycle 37: After refmac, R = 0.1465 (Rfree = 0.000) for 2724 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 38: After refmac, R = 0.1553 (Rfree = 0.000) for 2716 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1660 (Rfree = 0.000) for 2713 atoms. Found 19 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1257 (Rfree = 0.000) for 2717 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 3.63 Search for helices and strands: 0 residues in 0 chains, 2771 seeds are put forward NCS extension: 0 residues added, 2771 seeds are put forward Round 1: 125 peptides, 27 chains. Longest chain 9 peptides. Score 0.261 Round 2: 122 peptides, 23 chains. Longest chain 9 peptides. Score 0.333 Round 3: 134 peptides, 26 chains. Longest chain 8 peptides. Score 0.329 Round 4: 120 peptides, 23 chains. Longest chain 12 peptides. Score 0.323 Round 5: 121 peptides, 21 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 5 Chains 21, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6439 restraints for refining 2730 atoms. 6060 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1586 (Rfree = 0.000) for 2730 atoms. Found 9 (20 requested) and removed 13 (10 requested) atoms. Cycle 42: After refmac, R = 0.1366 (Rfree = 0.000) for 2720 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.1214 (Rfree = 0.000) for 2714 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. Cycle 44: After refmac, R = 0.1186 (Rfree = 0.000) for 2706 atoms. Found 9 (20 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.1414 (Rfree = 0.000) for 2699 atoms. Found 14 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.61 Search for helices and strands: 0 residues in 0 chains, 2736 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2749 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 8 peptides. Score 0.254 Round 2: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.322 Round 3: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.333 Round 4: 105 peptides, 20 chains. Longest chain 9 peptides. Score 0.311 Round 5: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fqp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3849 reflections ( 82.76 % complete ) and 6232 restraints for refining 2657 atoms. 5903 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1630 (Rfree = 0.000) for 2657 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2484 (Rfree = 0.000) for 2642 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2071 (Rfree = 0.000) for 2631 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1831 (Rfree = 0.000) for 2616 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. TimeTaking 36.65