null Sun 23 Dec 22:23:07 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 2nyh-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2nyh-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-3.4-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/2nyh-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-3.4-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 ============================================================ Sun 23 Dec 22:23:16 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/2nyh-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2nyh-3.4-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 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-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: 20 Cell parameters: 70.985 88.344 88.592 90.000 90.000 90.000 Input sequence file: 2nyh-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 58.28 3967 reflections ( 98.17 % complete ) and 0 restraints for refining 2073 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3540 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2743 (Rfree = 0.000) for 2073 atoms. Found 5 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 2103 seeds are put forward NCS extension: 0 residues added, 2103 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 8 peptides. Score 0.308 Round 2: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.375 Round 3: 135 peptides, 22 chains. Longest chain 15 peptides. Score 0.457 Round 4: 128 peptides, 22 chains. Longest chain 14 peptides. Score 0.419 Round 5: 142 peptides, 23 chains. Longest chain 12 peptides. Score 0.472 Taking the results from Round 5 Chains 23, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3801 restraints for refining 1702 atoms. 3348 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2949 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 2: After refmac, R = 0.2903 (Rfree = 0.000) for 1699 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2785 (Rfree = 0.000) for 1693 atoms. Found 2 (12 requested) and removed 7 (6 requested) atoms. Cycle 4: After refmac, R = 0.2721 (Rfree = 0.000) for 1688 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 5: After refmac, R = 0.2686 (Rfree = 0.000) for 1684 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 1726 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 1738 seeds are put forward Round 1: 123 peptides, 22 chains. Longest chain 12 peptides. Score 0.391 Round 2: 133 peptides, 22 chains. Longest chain 12 peptides. Score 0.447 Round 3: 127 peptides, 20 chains. Longest chain 11 peptides. Score 0.461 Round 4: 135 peptides, 20 chains. Longest chain 15 peptides. Score 0.503 Round 5: 131 peptides, 21 chains. Longest chain 9 peptides. Score 0.459 Taking the results from Round 4 Chains 20, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3839 restraints for refining 1702 atoms. 3399 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2948 (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 1706 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 8: After refmac, R = 0.2712 (Rfree = 0.000) for 1699 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.2640 (Rfree = 0.000) for 1695 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 10: After refmac, R = 0.2613 (Rfree = 0.000) for 1688 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.01 Search for helices and strands: 0 residues in 0 chains, 1730 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1751 seeds are put forward Round 1: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.392 Round 2: 115 peptides, 19 chains. Longest chain 9 peptides. Score 0.419 Round 3: 120 peptides, 18 chains. Longest chain 14 peptides. Score 0.471 Round 4: 119 peptides, 23 chains. Longest chain 9 peptides. Score 0.342 Round 5: 132 peptides, 20 chains. Longest chain 12 peptides. Score 0.487 Taking the results from Round 5 Chains 20, Residues 112, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3740 restraints for refining 1702 atoms. 3264 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2917 (Rfree = 0.000) for 1702 atoms. Found 10 (12 requested) and removed 6 (6 requested) atoms. Cycle 12: After refmac, R = 0.2764 (Rfree = 0.000) for 1705 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.2668 (Rfree = 0.000) for 1705 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 14: After refmac, R = 0.2631 (Rfree = 0.000) for 1702 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.2612 (Rfree = 0.000) for 1698 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 1738 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1757 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 12 peptides. Score 0.354 Round 2: 130 peptides, 20 chains. Longest chain 13 peptides. Score 0.477 Round 3: 133 peptides, 22 chains. Longest chain 12 peptides. Score 0.447 Round 4: 131 peptides, 20 chains. Longest chain 11 peptides. Score 0.482 Round 5: 131 peptides, 19 chains. Longest chain 13 peptides. Score 0.505 Taking the results from Round 5 Chains 19, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3819 restraints for refining 1702 atoms. 3390 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2810 (Rfree = 0.000) for 1702 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 17: After refmac, R = 0.2627 (Rfree = 0.000) for 1699 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 18: After refmac, R = 0.2586 (Rfree = 0.000) for 1693 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.2554 (Rfree = 0.000) for 1690 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 20: After refmac, R = 0.2515 (Rfree = 0.000) for 1688 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 1725 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 1736 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 9 peptides. Score 0.334 Round 2: 118 peptides, 17 chains. Longest chain 11 peptides. Score 0.483 Round 3: 108 peptides, 17 chains. Longest chain 14 peptides. Score 0.429 Round 4: 115 peptides, 15 chains. Longest chain 15 peptides. Score 0.515 Round 5: 120 peptides, 19 chains. Longest chain 11 peptides. Score 0.447 Taking the results from Round 4 Chains 15, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3914 restraints for refining 1702 atoms. 3529 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2761 (Rfree = 0.000) for 1702 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 22: After refmac, R = 0.2647 (Rfree = 0.000) for 1707 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.2535 (Rfree = 0.000) for 1703 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.2495 (Rfree = 0.000) for 1701 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.2479 (Rfree = 0.000) for 1696 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 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: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.375 Round 2: 122 peptides, 20 chains. Longest chain 20 peptides. Score 0.434 Round 3: 121 peptides, 20 chains. Longest chain 11 peptides. Score 0.428 Round 4: 127 peptides, 22 chains. Longest chain 11 peptides. Score 0.413 Round 5: 135 peptides, 20 chains. Longest chain 13 peptides. Score 0.503 Taking the results from Round 5 Chains 20, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3811 restraints for refining 1702 atoms. 3371 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2677 (Rfree = 0.000) for 1702 atoms. Found 8 (12 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.2566 (Rfree = 0.000) for 1698 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.2635 (Rfree = 0.000) for 1697 atoms. Found 7 (12 requested) and removed 6 (6 requested) atoms. Cycle 29: After refmac, R = 0.2524 (Rfree = 0.000) for 1693 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.2481 (Rfree = 0.000) for 1691 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 1722 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1737 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 8 peptides. Score 0.265 Round 2: 115 peptides, 19 chains. Longest chain 12 peptides. Score 0.419 Round 3: 103 peptides, 17 chains. Longest chain 10 peptides. Score 0.400 Round 4: 113 peptides, 16 chains. Longest chain 13 peptides. Score 0.481 Round 5: 123 peptides, 21 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 4 Chains 16, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3875 restraints for refining 1702 atoms. 3503 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2644 (Rfree = 0.000) for 1702 atoms. Found 10 (12 requested) and removed 7 (6 requested) atoms. Cycle 32: After refmac, R = 0.2520 (Rfree = 0.000) for 1704 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 33: After refmac, R = 0.2489 (Rfree = 0.000) for 1696 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.2479 (Rfree = 0.000) for 1693 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.2474 (Rfree = 0.000) for 1688 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 1713 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1728 seeds are put forward Round 1: 97 peptides, 18 chains. Longest chain 10 peptides. Score 0.337 Round 2: 108 peptides, 17 chains. Longest chain 11 peptides. Score 0.429 Round 3: 106 peptides, 17 chains. Longest chain 11 peptides. Score 0.417 Round 4: 107 peptides, 16 chains. Longest chain 12 peptides. Score 0.448 Round 5: 115 peptides, 18 chains. Longest chain 14 peptides. Score 0.443 Taking the results from Round 4 Chains 16, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3956 restraints for refining 1702 atoms. 3608 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2708 (Rfree = 0.000) for 1702 atoms. Found 9 (12 requested) and removed 6 (6 requested) atoms. Cycle 37: After refmac, R = 0.2642 (Rfree = 0.000) for 1704 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 38: After refmac, R = 0.2601 (Rfree = 0.000) for 1699 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. Cycle 39: After refmac, R = 0.2752 (Rfree = 0.000) for 1696 atoms. Found 12 (12 requested) and removed 34 (6 requested) atoms. Cycle 40: After refmac, R = 0.2722 (Rfree = 0.000) for 1673 atoms. Found 5 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.10 Search for helices and strands: 0 residues in 0 chains, 1697 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1711 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.314 Round 2: 113 peptides, 18 chains. Longest chain 12 peptides. Score 0.432 Round 3: 106 peptides, 18 chains. Longest chain 10 peptides. Score 0.392 Round 4: 104 peptides, 17 chains. Longest chain 12 peptides. Score 0.406 Round 5: 113 peptides, 19 chains. Longest chain 11 peptides. Score 0.407 Taking the results from Round 2 Chains 18, Residues 95, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3967 reflections ( 98.17 % complete ) and 3859 restraints for refining 1702 atoms. 3468 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2879 (Rfree = 0.000) for 1702 atoms. Found 11 (12 requested) and removed 7 (6 requested) atoms. Cycle 42: After refmac, R = 0.2738 (Rfree = 0.000) for 1704 atoms. Found 6 (12 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2647 (Rfree = 0.000) for 1704 atoms. Found 3 (12 requested) and removed 6 (6 requested) atoms. Cycle 44: After refmac, R = 0.2588 (Rfree = 0.000) for 1700 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2618 (Rfree = 0.000) for 1695 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 1719 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 1736 seeds are put forward Round 1: 79 peptides, 16 chains. Longest chain 9 peptides. Score 0.276 Round 2: 92 peptides, 14 chains. Longest chain 12 peptides. Score 0.413 Round 3: 97 peptides, 15 chains. Longest chain 11 peptides. Score 0.416 Round 4: 91 peptides, 13 chains. Longest chain 12 peptides. Score 0.434 Round 5: 90 peptides, 14 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 78, 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 4030 restraints for refining 1702 atoms. 3731 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2731 (Rfree = 0.000) for 1702 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2603 (Rfree = 0.000) for 1696 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2839 (Rfree = 0.000) for 1688 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2635 (Rfree = 0.000) for 1680 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:06 GMT 2018 Job finished. TimeTaking 30.98 Used memory is bytes: 4418528