Mon 24 Dec 07:54:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2nyh-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2nyh-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2nyh-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-parrot-noncs ############### 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 07:54:09 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/noncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2nyh-3.6-parrot-noncs/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-noncs.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-noncs.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 3.600 Wilson plot Bfac: 64.85 3363 reflections ( 98.05 % complete ) and 0 restraints for refining 2081 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3553 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2672 (Rfree = 0.000) for 2081 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 2102 seeds are put forward NCS extension: 0 residues added, 2102 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 10 peptides. Score 0.314 Round 2: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.370 Round 3: 127 peptides, 21 chains. Longest chain 13 peptides. Score 0.437 Round 4: 135 peptides, 21 chains. Longest chain 15 peptides. Score 0.480 Round 5: 122 peptides, 20 chains. Longest chain 16 peptides. Score 0.434 Taking the results from Round 4 Chains 21, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3818 restraints for refining 1697 atoms. 3383 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2930 (Rfree = 0.000) for 1697 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 2: After refmac, R = 0.2741 (Rfree = 0.000) for 1693 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 3: After refmac, R = 0.2670 (Rfree = 0.000) for 1686 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 4: After refmac, R = 0.2620 (Rfree = 0.000) for 1681 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2594 (Rfree = 0.000) for 1676 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 1713 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 1741 seeds are put forward Round 1: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.346 Round 2: 141 peptides, 21 chains. Longest chain 15 peptides. Score 0.511 Round 3: 128 peptides, 17 chains. Longest chain 16 peptides. Score 0.534 Round 4: 125 peptides, 17 chains. Longest chain 13 peptides. Score 0.519 Round 5: 132 peptides, 19 chains. Longest chain 17 peptides. Score 0.510 Taking the results from Round 3 Chains 17, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3879 restraints for refining 1696 atoms. 3452 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2843 (Rfree = 0.000) for 1696 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 7: After refmac, R = 0.2745 (Rfree = 0.000) for 1699 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 8: After refmac, R = 0.2678 (Rfree = 0.000) for 1700 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.2629 (Rfree = 0.000) for 1698 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2576 (Rfree = 0.000) for 1695 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 1710 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 1725 seeds are put forward Round 1: 111 peptides, 22 chains. Longest chain 11 peptides. Score 0.319 Round 2: 130 peptides, 20 chains. Longest chain 21 peptides. Score 0.477 Round 3: 132 peptides, 19 chains. Longest chain 21 peptides. Score 0.510 Round 4: 129 peptides, 19 chains. Longest chain 19 peptides. Score 0.495 Round 5: 123 peptides, 19 chains. Longest chain 15 peptides. Score 0.463 Taking the results from Round 3 Chains 19, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3889 restraints for refining 1697 atoms. 3456 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2831 (Rfree = 0.000) for 1697 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 12: After refmac, R = 0.2667 (Rfree = 0.000) for 1701 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 13: After refmac, R = 0.2596 (Rfree = 0.000) for 1698 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 14: After refmac, R = 0.2547 (Rfree = 0.000) for 1692 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.2509 (Rfree = 0.000) for 1688 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 1717 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 1739 seeds are put forward Round 1: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.342 Round 2: 113 peptides, 17 chains. Longest chain 13 peptides. Score 0.457 Round 3: 115 peptides, 16 chains. Longest chain 14 peptides. Score 0.491 Round 4: 111 peptides, 18 chains. Longest chain 12 peptides. Score 0.421 Round 5: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.419 Taking the results from Round 3 Chains 17, Residues 99, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3865 restraints for refining 1697 atoms. 3453 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2611 (Rfree = 0.000) for 1697 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 17: After refmac, R = 0.2453 (Rfree = 0.000) for 1693 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 18: After refmac, R = 0.2445 (Rfree = 0.000) for 1684 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 19: After refmac, R = 0.2383 (Rfree = 0.000) for 1684 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2359 (Rfree = 0.000) for 1679 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1717 seeds are put forward NCS extension: 0 residues added, 1717 seeds are put forward Round 1: 105 peptides, 22 chains. Longest chain 9 peptides. Score 0.281 Round 2: 115 peptides, 20 chains. Longest chain 13 peptides. Score 0.394 Round 3: 104 peptides, 18 chains. Longest chain 12 peptides. Score 0.380 Round 4: 107 peptides, 20 chains. Longest chain 9 peptides. Score 0.346 Round 5: 107 peptides, 17 chains. Longest chain 12 peptides. Score 0.423 Taking the results from Round 5 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3987 restraints for refining 1697 atoms. 3644 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2676 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 22: After refmac, R = 0.2477 (Rfree = 0.000) for 1698 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 23: After refmac, R = 0.2404 (Rfree = 0.000) for 1696 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2384 (Rfree = 0.000) for 1693 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2346 (Rfree = 0.000) for 1689 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1730 seeds are put forward NCS extension: 0 residues added, 1730 seeds are put forward Round 1: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.394 Round 2: 119 peptides, 18 chains. Longest chain 11 peptides. Score 0.465 Round 3: 117 peptides, 15 chains. Longest chain 16 peptides. Score 0.525 Round 4: 117 peptides, 18 chains. Longest chain 12 peptides. Score 0.454 Round 5: 107 peptides, 13 chains. Longest chain 14 peptides. Score 0.521 Taking the results from Round 3 Chains 15, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3884 restraints for refining 1697 atoms. 3491 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2638 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 27: After refmac, R = 0.2527 (Rfree = 0.000) for 1699 atoms. Found 8 (10 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2460 (Rfree = 0.000) for 1702 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2467 (Rfree = 0.000) for 1701 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2466 (Rfree = 0.000) for 1696 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1742 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 1768 seeds are put forward Round 1: 102 peptides, 18 chains. Longest chain 9 peptides. Score 0.368 Round 2: 102 peptides, 16 chains. Longest chain 10 peptides. Score 0.420 Round 3: 117 peptides, 17 chains. Longest chain 14 peptides. Score 0.478 Round 4: 111 peptides, 16 chains. Longest chain 13 peptides. Score 0.470 Round 5: 113 peptides, 15 chains. Longest chain 21 peptides. Score 0.504 Taking the results from Round 5 Chains 15, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3966 restraints for refining 1697 atoms. 3589 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2456 (Rfree = 0.000) for 1697 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 32: After refmac, R = 0.2277 (Rfree = 0.000) for 1695 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.2201 (Rfree = 0.000) for 1688 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 34: After refmac, R = 0.2170 (Rfree = 0.000) for 1681 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2143 (Rfree = 0.000) for 1679 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 1704 seeds are put forward NCS extension: 0 residues added, 1704 seeds are put forward Round 1: 94 peptides, 18 chains. Longest chain 12 peptides. Score 0.318 Round 2: 104 peptides, 17 chains. Longest chain 13 peptides. Score 0.406 Round 3: 104 peptides, 16 chains. Longest chain 11 peptides. Score 0.431 Round 4: 102 peptides, 16 chains. Longest chain 10 peptides. Score 0.420 Round 5: 101 peptides, 16 chains. Longest chain 11 peptides. Score 0.414 Taking the results from Round 3 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 4123 restraints for refining 1697 atoms. 3787 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2429 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 37: After refmac, R = 0.2290 (Rfree = 0.000) for 1698 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2221 (Rfree = 0.000) for 1697 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.2195 (Rfree = 0.000) for 1693 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2137 (Rfree = 0.000) for 1689 atoms. Found 2 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 1716 seeds are put forward NCS extension: 0 residues added, 1716 seeds are put forward Round 1: 91 peptides, 15 chains. Longest chain 11 peptides. Score 0.381 Round 2: 103 peptides, 15 chains. Longest chain 13 peptides. Score 0.451 Round 3: 107 peptides, 17 chains. Longest chain 11 peptides. Score 0.423 Round 4: 98 peptides, 16 chains. Longest chain 13 peptides. Score 0.396 Round 5: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.394 Taking the results from Round 2 Chains 15, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3363 reflections ( 98.05 % complete ) and 3967 restraints for refining 1697 atoms. 3630 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2390 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 42: After refmac, R = 0.2291 (Rfree = 0.000) for 1700 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.2238 (Rfree = 0.000) for 1698 atoms. Found 5 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2207 (Rfree = 0.000) for 1697 atoms. Found 1 (10 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2172 (Rfree = 0.000) for 1693 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 1718 seeds are put forward NCS extension: 0 residues added, 1718 seeds are put forward Round 1: 88 peptides, 16 chains. Longest chain 11 peptides. Score 0.335 Round 2: 96 peptides, 19 chains. Longest chain 9 peptides. Score 0.304 Round 3: 96 peptides, 17 chains. Longest chain 9 peptides. Score 0.358 Round 4: 84 peptides, 15 chains. Longest chain 8 peptides. Score 0.337 Round 5: 85 peptides, 14 chains. Longest chain 10 peptides. Score 0.371 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 71, 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. 3363 reflections ( 98.05 % complete ) and 4069 restraints for refining 1697 atoms. 3799 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2419 (Rfree = 0.000) for 1697 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2334 (Rfree = 0.000) for 1692 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2287 (Rfree = 0.000) for 1683 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2261 (Rfree = 0.000) for 1678 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... TimeTaking 24.2