Mon 24 Dec 00:26:32 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-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2nyh-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-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/2nyh-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-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 00:26:37 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-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2nyh-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 198 and 0 Target number of residues in the AU: 198 Target solvent content: 0.6142 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-3.4-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-3.4-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 3.400 Wilson plot Bfac: 58.28 3967 reflections ( 98.17 % complete ) and 0 restraints for refining 2076 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3545 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2639 (Rfree = 0.000) for 2076 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 2095 seeds are put forward NCS extension: 0 residues added, 2095 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.284 Round 2: 131 peptides, 25 chains. Longest chain 12 peptides. Score 0.363 Round 3: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.440 Round 4: 134 peptides, 22 chains. Longest chain 13 peptides. Score 0.452 Round 5: 137 peptides, 20 chains. Longest chain 14 peptides. Score 0.513 Taking the results from Round 5 Chains 21, Residues 117, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3748 restraints for refining 1702 atoms. 3268 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3144 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 2: After refmac, R = 0.2998 (Rfree = 0.000) for 1706 atoms. Found 8 (12 requested) and removed 6 (6 requested) atoms. Cycle 3: After refmac, R = 0.2906 (Rfree = 0.000) for 1705 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 4: After refmac, R = 0.2849 (Rfree = 0.000) for 1699 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.2820 (Rfree = 0.000) for 1693 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 1732 seeds are put forward NCS extension: 0 residues added, 1732 seeds are put forward Round 1: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.351 Round 2: 122 peptides, 19 chains. Longest chain 10 peptides. Score 0.458 Round 3: 133 peptides, 21 chains. Longest chain 11 peptides. Score 0.470 Round 4: 139 peptides, 19 chains. Longest chain 20 peptides. Score 0.544 Round 5: 128 peptides, 16 chains. Longest chain 14 peptides. Score 0.556 Taking the results from Round 5 Chains 16, Residues 112, Estimated correctness of the model 13.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3865 restraints for refining 1702 atoms. 3433 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2940 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 7: After refmac, R = 0.2776 (Rfree = 0.000) for 1708 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 8: After refmac, R = 0.2669 (Rfree = 0.000) for 1705 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2626 (Rfree = 0.000) for 1701 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2636 (Rfree = 0.000) for 1695 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 3.02 Search for helices and strands: 0 residues in 0 chains, 1726 seeds are put forward NCS extension: 0 residues added, 1726 seeds are put forward Round 1: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.350 Round 2: 119 peptides, 21 chains. Longest chain 13 peptides. Score 0.392 Round 3: 119 peptides, 20 chains. Longest chain 11 peptides. Score 0.417 Round 4: 121 peptides, 21 chains. Longest chain 12 peptides. Score 0.404 Round 5: 134 peptides, 23 chains. Longest chain 11 peptides. Score 0.429 Taking the results from Round 5 Chains 23, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 4026 restraints for refining 1702 atoms. 3605 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2962 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 12: After refmac, R = 0.2777 (Rfree = 0.000) for 1706 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 13: After refmac, R = 0.2729 (Rfree = 0.000) for 1706 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.2686 (Rfree = 0.000) for 1706 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2696 (Rfree = 0.000) for 1701 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 1725 seeds are put forward NCS extension: 0 residues added, 1725 seeds are put forward Round 1: 118 peptides, 21 chains. Longest chain 11 peptides. Score 0.386 Round 2: 130 peptides, 23 chains. Longest chain 10 peptides. Score 0.406 Round 3: 127 peptides, 19 chains. Longest chain 14 peptides. Score 0.484 Round 4: 132 peptides, 19 chains. Longest chain 15 peptides. Score 0.510 Round 5: 142 peptides, 21 chains. Longest chain 21 peptides. Score 0.516 Taking the results from Round 5 Chains 21, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3842 restraints for refining 1702 atoms. 3379 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3032 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 17: After refmac, R = 0.2788 (Rfree = 0.000) for 1707 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2711 (Rfree = 0.000) for 1704 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2668 (Rfree = 0.000) for 1696 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2618 (Rfree = 0.000) for 1694 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 1721 seeds are put forward NCS extension: 0 residues added, 1721 seeds are put forward Round 1: 107 peptides, 21 chains. Longest chain 10 peptides. Score 0.320 Round 2: 124 peptides, 24 chains. Longest chain 9 peptides. Score 0.347 Round 3: 122 peptides, 22 chains. Longest chain 12 peptides. Score 0.385 Round 4: 119 peptides, 20 chains. Longest chain 11 peptides. Score 0.417 Round 5: 127 peptides, 20 chains. Longest chain 13 peptides. Score 0.461 Taking the results from Round 5 Chains 20, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3909 restraints for refining 1700 atoms. 3501 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2881 (Rfree = 0.000) for 1700 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 22: After refmac, R = 0.2741 (Rfree = 0.000) for 1705 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.2635 (Rfree = 0.000) for 1705 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.2594 (Rfree = 0.000) for 1701 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.2548 (Rfree = 0.000) for 1695 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 1722 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1742 seeds are put forward Round 1: 99 peptides, 17 chains. Longest chain 10 peptides. Score 0.376 Round 2: 109 peptides, 14 chains. Longest chain 28 peptides. Score 0.507 Round 3: 116 peptides, 15 chains. Longest chain 29 peptides. Score 0.520 Round 4: 118 peptides, 17 chains. Longest chain 15 peptides. Score 0.483 Round 5: 118 peptides, 17 chains. Longest chain 16 peptides. Score 0.483 Taking the results from Round 3 Chains 15, Residues 101, Estimated correctness of the model 0.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3977 restraints for refining 1702 atoms. 3588 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2848 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 27: After refmac, R = 0.2735 (Rfree = 0.000) for 1708 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.2648 (Rfree = 0.000) for 1703 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2622 (Rfree = 0.000) for 1696 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2599 (Rfree = 0.000) for 1695 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 1714 seeds are put forward NCS extension: 63 residues added (0 deleted due to clashes), 1777 seeds are put forward Round 1: 116 peptides, 20 chains. Longest chain 10 peptides. Score 0.400 Round 2: 108 peptides, 15 chains. Longest chain 13 peptides. Score 0.478 Round 3: 115 peptides, 17 chains. Longest chain 13 peptides. Score 0.467 Round 4: 119 peptides, 18 chains. Longest chain 19 peptides. Score 0.465 Round 5: 123 peptides, 18 chains. Longest chain 15 peptides. Score 0.486 Taking the results from Round 5 Chains 18, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 4046 restraints for refining 1702 atoms. 3644 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2890 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 32: After refmac, R = 0.2756 (Rfree = 0.000) for 1708 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.2700 (Rfree = 0.000) for 1705 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2711 (Rfree = 0.000) for 1701 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2693 (Rfree = 0.000) for 1700 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 1724 seeds are put forward NCS extension: 0 residues added, 1724 seeds are put forward Round 1: 110 peptides, 20 chains. Longest chain 16 peptides. Score 0.364 Round 2: 122 peptides, 18 chains. Longest chain 13 peptides. Score 0.481 Round 3: 124 peptides, 18 chains. Longest chain 17 peptides. Score 0.492 Round 4: 115 peptides, 16 chains. Longest chain 13 peptides. Score 0.491 Round 5: 120 peptides, 17 chains. Longest chain 21 peptides. Score 0.494 Taking the results from Round 5 Chains 17, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3984 restraints for refining 1702 atoms. 3589 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2796 (Rfree = 0.000) for 1702 atoms. Found 9 (12 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.2632 (Rfree = 0.000) for 1704 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.2574 (Rfree = 0.000) for 1702 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2558 (Rfree = 0.000) for 1696 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.2510 (Rfree = 0.000) for 1693 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 1716 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 1753 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 7 peptides. Score 0.290 Round 2: 104 peptides, 18 chains. Longest chain 10 peptides. Score 0.380 Round 3: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.378 Round 4: 100 peptides, 16 chains. Longest chain 11 peptides. Score 0.408 Round 5: 110 peptides, 16 chains. Longest chain 19 peptides. Score 0.464 Taking the results from Round 5 Chains 16, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 4065 restraints for refining 1702 atoms. 3705 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2711 (Rfree = 0.000) for 1702 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 42: After refmac, R = 0.2617 (Rfree = 0.000) for 1702 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2671 (Rfree = 0.000) for 1701 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2614 (Rfree = 0.000) for 1700 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2718 (Rfree = 0.000) for 1697 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 1725 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1751 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 8 peptides. Score 0.291 Round 2: 112 peptides, 19 chains. Longest chain 12 peptides. Score 0.402 Round 3: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.366 Round 4: 106 peptides, 18 chains. Longest chain 8 peptides. Score 0.392 Round 5: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.398 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 93, 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. 3967 reflections ( 98.17 % complete ) and 4166 restraints for refining 1702 atoms. 3813 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2764 (Rfree = 0.000) for 1702 atoms. Found 0 (12 requested) and removed 0 (6 requested) atoms. Cycle 47: After refmac, R = 0.2601 (Rfree = 0.000) for 1702 atoms. Found 0 (12 requested) and removed 2 (6 requested) atoms. Cycle 48: After refmac, R = 0.2559 (Rfree = 0.000) for 1699 atoms. Found 0 (12 requested) and removed 1 (6 requested) atoms. Cycle 49: After refmac, R = 0.2755 (Rfree = 0.000) for 1698 atoms. Found 0 (12 requested) and removed 0 (6 requested) atoms. Writing output files ... TimeTaking 24.8