Sun 23 Dec 23:45:07 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-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 ============================================================ Sun 23 Dec 23:45:12 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-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 191 and 0 Target number of residues in the AU: 191 Target solvent content: 0.6279 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-3.6-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-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1872 target number of atoms Had to go as low as 0.85 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 3.600 Wilson plot Bfac: 64.85 3363 reflections ( 98.05 % complete ) and 0 restraints for refining 2078 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3543 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2678 (Rfree = 0.000) for 2078 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 2096 seeds are put forward NCS extension: 0 residues added, 2096 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 8 peptides. Score 0.229 Round 2: 122 peptides, 23 chains. Longest chain 13 peptides. Score 0.360 Round 3: 137 peptides, 21 chains. Longest chain 19 peptides. Score 0.491 Round 4: 138 peptides, 20 chains. Longest chain 17 peptides. Score 0.518 Round 5: 128 peptides, 15 chains. Longest chain 22 peptides. Score 0.577 Taking the results from Round 5 Chains 15, Residues 113, Estimated correctness of the model 5.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3747 restraints for refining 1697 atoms. 3310 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2928 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 2: After refmac, R = 0.2739 (Rfree = 0.000) for 1696 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 3: After refmac, R = 0.2655 (Rfree = 0.000) for 1691 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.2608 (Rfree = 0.000) for 1686 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2619 (Rfree = 0.000) for 1675 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 1724 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1748 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.351 Round 2: 127 peptides, 16 chains. Longest chain 17 peptides. Score 0.551 Round 3: 127 peptides, 18 chains. Longest chain 17 peptides. Score 0.507 Round 4: 126 peptides, 15 chains. Longest chain 17 peptides. Score 0.568 Round 5: 123 peptides, 18 chains. Longest chain 16 peptides. Score 0.486 Taking the results from Round 4 Chains 15, Residues 111, Estimated correctness of the model 1.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3917 restraints for refining 1697 atoms. 3488 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2943 (Rfree = 0.000) for 1697 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 7: After refmac, R = 0.2761 (Rfree = 0.000) for 1697 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2654 (Rfree = 0.000) for 1694 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.2590 (Rfree = 0.000) for 1687 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2547 (Rfree = 0.000) for 1685 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 1722 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1741 seeds are put forward Round 1: 109 peptides, 18 chains. Longest chain 15 peptides. Score 0.409 Round 2: 117 peptides, 18 chains. Longest chain 19 peptides. Score 0.454 Round 3: 108 peptides, 13 chains. Longest chain 19 peptides. Score 0.526 Round 4: 116 peptides, 17 chains. Longest chain 12 peptides. Score 0.473 Round 5: 114 peptides, 18 chains. Longest chain 16 peptides. Score 0.438 Taking the results from Round 3 Chains 13, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3975 restraints for refining 1697 atoms. 3608 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2794 (Rfree = 0.000) for 1697 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 12: After refmac, R = 0.2620 (Rfree = 0.000) for 1697 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 13: After refmac, R = 0.2557 (Rfree = 0.000) for 1694 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2513 (Rfree = 0.000) for 1686 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2507 (Rfree = 0.000) for 1679 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 1705 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 1728 seeds are put forward Round 1: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.386 Round 2: 105 peptides, 17 chains. Longest chain 13 peptides. Score 0.412 Round 3: 113 peptides, 18 chains. Longest chain 13 peptides. Score 0.432 Round 4: 119 peptides, 18 chains. Longest chain 13 peptides. Score 0.465 Round 5: 113 peptides, 16 chains. Longest chain 15 peptides. Score 0.481 Taking the results from Round 5 Chains 16, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3983 restraints for refining 1697 atoms. 3611 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2880 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 17: After refmac, R = 0.2707 (Rfree = 0.000) for 1700 atoms. Found 3 (10 requested) and removed 6 (5 requested) atoms. Cycle 18: After refmac, R = 0.2638 (Rfree = 0.000) for 1696 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.2576 (Rfree = 0.000) for 1692 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2532 (Rfree = 0.000) for 1689 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1711 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 1725 seeds are put forward Round 1: 102 peptides, 16 chains. Longest chain 16 peptides. Score 0.420 Round 2: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.451 Round 3: 113 peptides, 15 chains. Longest chain 16 peptides. Score 0.504 Round 4: 113 peptides, 13 chains. Longest chain 15 peptides. Score 0.550 Round 5: 117 peptides, 17 chains. Longest chain 13 peptides. Score 0.478 Taking the results from Round 4 Chains 13, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3971 restraints for refining 1697 atoms. 3584 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2905 (Rfree = 0.000) for 1697 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.2757 (Rfree = 0.000) for 1699 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.2686 (Rfree = 0.000) for 1697 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2658 (Rfree = 0.000) for 1691 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 25: After refmac, R = 0.2626 (Rfree = 0.000) for 1685 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1715 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 1731 seeds are put forward Round 1: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.323 Round 2: 118 peptides, 20 chains. Longest chain 12 peptides. Score 0.411 Round 3: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.396 Round 4: 112 peptides, 19 chains. Longest chain 13 peptides. Score 0.402 Round 5: 120 peptides, 19 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 5 Chains 19, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3994 restraints for refining 1696 atoms. 3609 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2805 (Rfree = 0.000) for 1696 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2656 (Rfree = 0.000) for 1696 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2589 (Rfree = 0.000) for 1694 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2556 (Rfree = 0.000) for 1689 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 30: After refmac, R = 0.2517 (Rfree = 0.000) for 1686 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.19 Search for helices and strands: 0 residues in 0 chains, 1712 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 1730 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 8 peptides. Score 0.292 Round 2: 108 peptides, 18 chains. Longest chain 14 peptides. Score 0.404 Round 3: 119 peptides, 19 chains. Longest chain 11 peptides. Score 0.441 Round 4: 111 peptides, 18 chains. Longest chain 13 peptides. Score 0.421 Round 5: 111 peptides, 19 chains. Longest chain 13 peptides. Score 0.396 Taking the results from Round 3 Chains 19, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3980 restraints for refining 1697 atoms. 3599 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2724 (Rfree = 0.000) for 1697 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 32: After refmac, R = 0.2608 (Rfree = 0.000) for 1701 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2531 (Rfree = 0.000) for 1697 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2466 (Rfree = 0.000) for 1694 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2455 (Rfree = 0.000) for 1691 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 1710 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1724 seeds are put forward Round 1: 90 peptides, 17 chains. Longest chain 10 peptides. Score 0.320 Round 2: 99 peptides, 18 chains. Longest chain 12 peptides. Score 0.350 Round 3: 103 peptides, 16 chains. Longest chain 11 peptides. Score 0.425 Round 4: 105 peptides, 15 chains. Longest chain 15 peptides. Score 0.462 Round 5: 114 peptides, 18 chains. Longest chain 15 peptides. Score 0.438 Taking the results from Round 4 Chains 15, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 4051 restraints for refining 1697 atoms. 3706 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2636 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.2533 (Rfree = 0.000) for 1699 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2497 (Rfree = 0.000) for 1695 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2452 (Rfree = 0.000) for 1690 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 40: After refmac, R = 0.2421 (Rfree = 0.000) for 1686 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1715 seeds are put forward NCS extension: 0 residues added, 1715 seeds are put forward Round 1: 98 peptides, 16 chains. Longest chain 12 peptides. Score 0.396 Round 2: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.412 Round 3: 102 peptides, 18 chains. Longest chain 15 peptides. Score 0.368 Round 4: 111 peptides, 19 chains. Longest chain 8 peptides. Score 0.396 Round 5: 101 peptides, 15 chains. Longest chain 12 peptides. Score 0.439 Taking the results from Round 5 Chains 15, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 4024 restraints for refining 1697 atoms. 3695 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2696 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2582 (Rfree = 0.000) for 1700 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2512 (Rfree = 0.000) for 1702 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2455 (Rfree = 0.000) for 1698 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2424 (Rfree = 0.000) for 1694 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 1720 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 1734 seeds are put forward Round 1: 95 peptides, 18 chains. Longest chain 12 peptides. Score 0.325 Round 2: 106 peptides, 18 chains. Longest chain 12 peptides. Score 0.392 Round 3: 108 peptides, 15 chains. Longest chain 17 peptides. Score 0.478 Round 4: 112 peptides, 15 chains. Longest chain 18 peptides. Score 0.499 Round 5: 111 peptides, 16 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 97, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2nyh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3363 reflections ( 98.05 % complete ) and 3916 restraints for refining 1697 atoms. 3511 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2688 (Rfree = 0.000) for 1697 atoms. Found 0 (10 requested) and removed 3 (5 requested) atoms. Cycle 47: After refmac, R = 0.2596 (Rfree = 0.000) for 1693 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2531 (Rfree = 0.000) for 1688 atoms. Found 0 (10 requested) and removed 0 (5 requested) atoms. Cycle 49: After refmac, R = 0.2483 (Rfree = 0.000) for 1688 atoms. TimeTaking 28.82