Mon 24 Dec 00:56:23 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 2nyh-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.8-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/2nyh-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.8-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 00:56:28 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/2nyh-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.8-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6396 Checking the provided sequence file Detected sequence length: 117 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 234 Adjusted target solvent content: 0.54 Input MTZ file: 2nyh-3.8-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.80 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: 55.335 3.802 Wilson plot Bfac: 71.07 2851 reflections ( 97.87 % complete ) and 0 restraints for refining 2070 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3528 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3672 (Rfree = 0.000) for 2070 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 2087 seeds are put forward NCS extension: 0 residues added, 2087 seeds are put forward Round 1: 66 peptides, 14 chains. Longest chain 8 peptides. Score 0.244 Round 2: 95 peptides, 19 chains. Longest chain 8 peptides. Score 0.297 Round 3: 101 peptides, 20 chains. Longest chain 7 peptides. Score 0.309 Round 4: 110 peptides, 20 chains. Longest chain 8 peptides. Score 0.364 Round 5: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.406 Taking the results from Round 5 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3959 restraints for refining 1693 atoms. 3628 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3305 (Rfree = 0.000) for 1693 atoms. Found 8 (9 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.3242 (Rfree = 0.000) for 1664 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.3310 (Rfree = 0.000) for 1632 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 4: After refmac, R = 0.3185 (Rfree = 0.000) for 1619 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 5: After refmac, R = 0.3122 (Rfree = 0.000) for 1602 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1640 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 1651 seeds are put forward Round 1: 86 peptides, 17 chains. Longest chain 9 peptides. Score 0.294 Round 2: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.351 Round 3: 121 peptides, 19 chains. Longest chain 13 peptides. Score 0.452 Round 4: 117 peptides, 19 chains. Longest chain 11 peptides. Score 0.430 Round 5: 131 peptides, 21 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 5 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3548 restraints for refining 1623 atoms. 3129 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3053 (Rfree = 0.000) for 1623 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.3046 (Rfree = 0.000) for 1590 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 8: After refmac, R = 0.2913 (Rfree = 0.000) for 1573 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2766 (Rfree = 0.000) for 1564 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2938 (Rfree = 0.000) for 1555 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 1596 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1609 seeds are put forward Round 1: 88 peptides, 19 chains. Longest chain 8 peptides. Score 0.251 Round 2: 112 peptides, 19 chains. Longest chain 10 peptides. Score 0.402 Round 3: 117 peptides, 19 chains. Longest chain 14 peptides. Score 0.430 Round 4: 112 peptides, 18 chains. Longest chain 14 peptides. Score 0.427 Round 5: 111 peptides, 17 chains. Longest chain 15 peptides. Score 0.446 Taking the results from Round 5 Chains 17, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3694 restraints for refining 1648 atoms. 3335 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3023 (Rfree = 0.000) for 1648 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 12: After refmac, R = 0.3118 (Rfree = 0.000) for 1613 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 13: After refmac, R = 0.3024 (Rfree = 0.000) for 1593 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2827 (Rfree = 0.000) for 1584 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.3114 (Rfree = 0.000) for 1573 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 1605 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 1628 seeds are put forward Round 1: 108 peptides, 22 chains. Longest chain 8 peptides. Score 0.300 Round 2: 117 peptides, 22 chains. Longest chain 10 peptides. Score 0.355 Round 3: 121 peptides, 20 chains. Longest chain 17 peptides. Score 0.428 Round 4: 127 peptides, 20 chains. Longest chain 13 peptides. Score 0.461 Round 5: 129 peptides, 21 chains. Longest chain 12 peptides. Score 0.448 Taking the results from Round 4 Chains 20, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3858 restraints for refining 1693 atoms. 3450 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2994 (Rfree = 0.000) for 1693 atoms. Found 9 (9 requested) and removed 44 (4 requested) atoms. Cycle 17: After refmac, R = 0.2639 (Rfree = 0.000) for 1635 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 18: After refmac, R = 0.2649 (Rfree = 0.000) for 1620 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2764 (Rfree = 0.000) for 1614 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.2897 (Rfree = 0.000) for 1599 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1624 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1640 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 8 peptides. Score 0.277 Round 2: 96 peptides, 17 chains. Longest chain 17 peptides. Score 0.358 Round 3: 101 peptides, 19 chains. Longest chain 11 peptides. Score 0.336 Round 4: 100 peptides, 18 chains. Longest chain 14 peptides. Score 0.356 Round 5: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 5 Chains 19, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3845 restraints for refining 1693 atoms. 3496 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2956 (Rfree = 0.000) for 1693 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 22: After refmac, R = 0.2942 (Rfree = 0.000) for 1670 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.2841 (Rfree = 0.000) for 1653 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 24: After refmac, R = 0.2764 (Rfree = 0.000) for 1639 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2644 (Rfree = 0.000) for 1633 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 1666 seeds are put forward NCS extension: 0 residues added, 1666 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 8 peptides. Score 0.255 Round 2: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.279 Round 3: 83 peptides, 15 chains. Longest chain 8 peptides. Score 0.330 Round 4: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.345 Round 5: 94 peptides, 13 chains. Longest chain 14 peptides. Score 0.451 Taking the results from Round 5 Chains 13, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3769 restraints for refining 1657 atoms. 3458 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3001 (Rfree = 0.000) for 1657 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.2656 (Rfree = 0.000) for 1636 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 28: After refmac, R = 0.2961 (Rfree = 0.000) for 1623 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 29: After refmac, R = 0.2628 (Rfree = 0.000) for 1612 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.2865 (Rfree = 0.000) for 1606 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 1636 seeds are put forward NCS extension: 0 residues added, 1636 seeds are put forward Round 1: 68 peptides, 13 chains. Longest chain 8 peptides. Score 0.288 Round 2: 81 peptides, 14 chains. Longest chain 8 peptides. Score 0.346 Round 3: 83 peptides, 14 chains. Longest chain 11 peptides. Score 0.358 Round 4: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.346 Round 5: 85 peptides, 12 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 5 Chains 12, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3586 restraints for refining 1588 atoms. 3306 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3078 (Rfree = 0.000) for 1588 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 32: After refmac, R = 0.3079 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2858 (Rfree = 0.000) for 1553 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 34: After refmac, R = 0.2943 (Rfree = 0.000) for 1549 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2776 (Rfree = 0.000) for 1547 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 1565 seeds are put forward NCS extension: 0 residues added, 1565 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 7 peptides. Score 0.260 Round 2: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.286 Round 3: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.320 Round 4: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.313 Round 5: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.335 Taking the results from Round 5 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3427 restraints for refining 1492 atoms. 3218 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3240 (Rfree = 0.000) for 1492 atoms. Found 8 (8 requested) and removed 23 (4 requested) atoms. Cycle 37: After refmac, R = 0.2807 (Rfree = 0.000) for 1469 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 38: After refmac, R = 0.3117 (Rfree = 0.000) for 1463 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.3047 (Rfree = 0.000) for 1455 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.3134 (Rfree = 0.000) for 1449 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 1469 seeds are put forward NCS extension: 0 residues added, 1469 seeds are put forward Round 1: 64 peptides, 13 chains. Longest chain 10 peptides. Score 0.260 Round 2: 62 peptides, 11 chains. Longest chain 8 peptides. Score 0.307 Round 3: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.320 Round 4: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.293 Round 5: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.335 Taking the results from Round 5 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2851 reflections ( 97.87 % complete ) and 3039 restraints for refining 1392 atoms. 2830 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3246 (Rfree = 0.000) for 1392 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 42: After refmac, R = 0.3297 (Rfree = 0.000) for 1379 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 43: After refmac, R = 0.3152 (Rfree = 0.000) for 1370 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.3244 (Rfree = 0.000) for 1362 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2979 (Rfree = 0.000) for 1357 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 1376 seeds are put forward NCS extension: 0 residues added, 1376 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.254 Round 2: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.302 Round 3: 73 peptides, 13 chains. Longest chain 9 peptides. Score 0.322 Round 4: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.361 Round 5: 81 peptides, 14 chains. Longest chain 9 peptides. Score 0.346 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 66, 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 2nyh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2851 reflections ( 97.87 % complete ) and 2834 restraints for refining 1375 atoms. 2583 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3309 (Rfree = 0.000) for 1375 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3218 (Rfree = 0.000) for 1361 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3233 (Rfree = 0.000) for 1346 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2935 (Rfree = 0.000) for 1334 atoms. TimeTaking 25.25