null Sun 23 Dec 22:22:59 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 2a6b-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a6b-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.6-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/2a6b-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.6-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 22:23:07 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/2a6b-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a6b-3.6-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 239 and 0 Target number of residues in the AU: 239 Target solvent content: 0.6066 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 234 Adjusted target solvent content: 0.61 Input MTZ file: 2a6b-3.6-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: 90 Cell parameters: 119.176 119.176 46.302 90.000 90.000 90.000 Input sequence file: 2a6b-3.6-parrot-hancs.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 Loops will be built when appropriate and at the last cycle Resolution range: 29.794 3.600 Wilson plot Bfac: 55.32 4150 reflections ( 99.09 % complete ) and 0 restraints for refining 2069 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3185 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3206 (Rfree = 0.000) for 2069 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.75 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 9 peptides. Score 0.252 Round 2: 140 peptides, 24 chains. Longest chain 16 peptides. Score 0.406 Round 3: 156 peptides, 20 chains. Longest chain 22 peptides. Score 0.554 Round 4: 153 peptides, 19 chains. Longest chain 18 peptides. Score 0.560 Round 5: 146 peptides, 18 chains. Longest chain 20 peptides. Score 0.551 Taking the results from Round 4 Chains 19, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3600 restraints for refining 1696 atoms. 3083 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2834 (Rfree = 0.000) for 1696 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 2: After refmac, R = 0.2676 (Rfree = 0.000) for 1668 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 3: After refmac, R = 0.2504 (Rfree = 0.000) for 1644 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.2477 (Rfree = 0.000) for 1634 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2397 (Rfree = 0.000) for 1629 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 2.80 Search for helices and strands: 0 residues in 0 chains, 1720 seeds are put forward Round 1: 143 peptides, 25 chains. Longest chain 13 peptides. Score 0.399 Round 2: 144 peptides, 21 chains. Longest chain 14 peptides. Score 0.485 Round 3: 160 peptides, 23 chains. Longest chain 18 peptides. Score 0.516 Round 4: 166 peptides, 23 chains. Longest chain 30 peptides. Score 0.540 Round 5: 144 peptides, 19 chains. Longest chain 18 peptides. Score 0.524 Taking the results from Round 4 Chains 25, Residues 143, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3469 restraints for refining 1697 atoms. 2829 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2557 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 7: After refmac, R = 0.2444 (Rfree = 0.000) for 1675 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. Cycle 8: After refmac, R = 0.2359 (Rfree = 0.000) for 1661 atoms. Found 6 (10 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2388 (Rfree = 0.000) for 1651 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.2310 (Rfree = 0.000) for 1648 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.83 Search for helices and strands: 0 residues in 0 chains, 1738 seeds are put forward Round 1: 133 peptides, 24 chains. Longest chain 11 peptides. Score 0.371 Round 2: 142 peptides, 21 chains. Longest chain 15 peptides. Score 0.476 Round 3: 133 peptides, 19 chains. Longest chain 13 peptides. Score 0.476 Round 4: 128 peptides, 17 chains. Longest chain 13 peptides. Score 0.494 Round 5: 144 peptides, 20 chains. Longest chain 21 peptides. Score 0.504 Taking the results from Round 5 Chains 22, Residues 124, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3718 restraints for refining 1697 atoms. 3212 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2737 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 12: After refmac, R = 0.2637 (Rfree = 0.000) for 1677 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 13: After refmac, R = 0.2758 (Rfree = 0.000) for 1677 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 14: After refmac, R = 0.2643 (Rfree = 0.000) for 1673 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 15: After refmac, R = 0.2423 (Rfree = 0.000) for 1670 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 2.81 Search for helices and strands: 0 residues in 0 chains, 1767 seeds are put forward Round 1: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.362 Round 2: 124 peptides, 17 chains. Longest chain 17 peptides. Score 0.476 Round 3: 136 peptides, 19 chains. Longest chain 15 peptides. Score 0.489 Round 4: 126 peptides, 17 chains. Longest chain 13 peptides. Score 0.485 Round 5: 129 peptides, 17 chains. Longest chain 19 peptides. Score 0.498 Taking the results from Round 5 Chains 17, Residues 112, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3771 restraints for refining 1697 atoms. 3340 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2940 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 17: After refmac, R = 0.2528 (Rfree = 0.000) for 1678 atoms. Found 7 (10 requested) and removed 10 (5 requested) atoms. Cycle 18: After refmac, R = 0.2638 (Rfree = 0.000) for 1671 atoms. Found 8 (10 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.2435 (Rfree = 0.000) for 1668 atoms. Found 3 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2399 (Rfree = 0.000) for 1659 atoms. Found 3 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 2.79 Search for helices and strands: 0 residues in 0 chains, 1757 seeds are put forward Round 1: 120 peptides, 24 chains. Longest chain 9 peptides. Score 0.304 Round 2: 141 peptides, 22 chains. Longest chain 11 peptides. Score 0.451 Round 3: 134 peptides, 22 chains. Longest chain 16 peptides. Score 0.418 Round 4: 139 peptides, 22 chains. Longest chain 17 peptides. Score 0.442 Round 5: 131 peptides, 18 chains. Longest chain 24 peptides. Score 0.487 Taking the results from Round 5 Chains 18, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3814 restraints for refining 1697 atoms. 3380 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2644 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 22: After refmac, R = 0.2408 (Rfree = 0.000) for 1693 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 23: After refmac, R = 0.2407 (Rfree = 0.000) for 1687 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2376 (Rfree = 0.000) for 1684 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 25: After refmac, R = 0.2133 (Rfree = 0.000) for 1682 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.77 Search for helices and strands: 0 residues in 0 chains, 1771 seeds are put forward Round 1: 108 peptides, 21 chains. Longest chain 10 peptides. Score 0.307 Round 2: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.407 Round 3: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.415 Round 4: 134 peptides, 19 chains. Longest chain 15 peptides. Score 0.480 Round 5: 127 peptides, 19 chains. Longest chain 11 peptides. Score 0.448 Taking the results from Round 4 Chains 19, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3766 restraints for refining 1697 atoms. 3325 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2582 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 27: After refmac, R = 0.2391 (Rfree = 0.000) for 1684 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.2342 (Rfree = 0.000) for 1683 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 29: After refmac, R = 0.2093 (Rfree = 0.000) for 1682 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 30: After refmac, R = 0.2016 (Rfree = 0.000) for 1676 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.78 Search for helices and strands: 0 residues in 0 chains, 1762 seeds are put forward Round 1: 112 peptides, 22 chains. Longest chain 11 peptides. Score 0.306 Round 2: 134 peptides, 23 chains. Longest chain 13 peptides. Score 0.397 Round 3: 127 peptides, 19 chains. Longest chain 14 peptides. Score 0.448 Round 4: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.415 Round 5: 129 peptides, 22 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 3 Chains 19, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3805 restraints for refining 1697 atoms. 3392 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2450 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 32: After refmac, R = 0.2266 (Rfree = 0.000) for 1686 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 33: After refmac, R = 0.2229 (Rfree = 0.000) for 1681 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 34: After refmac, R = 0.2119 (Rfree = 0.000) for 1676 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2184 (Rfree = 0.000) for 1676 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 2.75 Search for helices and strands: 0 residues in 0 chains, 1752 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 9 peptides. Score 0.264 Round 2: 115 peptides, 22 chains. Longest chain 8 peptides. Score 0.322 Round 3: 114 peptides, 19 chains. Longest chain 16 peptides. Score 0.385 Round 4: 128 peptides, 21 chains. Longest chain 16 peptides. Score 0.411 Round 5: 127 peptides, 22 chains. Longest chain 16 peptides. Score 0.384 Taking the results from Round 4 Chains 21, Residues 107, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3635 restraints for refining 1696 atoms. 3153 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2456 (Rfree = 0.000) for 1696 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 37: After refmac, R = 0.2306 (Rfree = 0.000) for 1680 atoms. Found 9 (10 requested) and removed 11 (5 requested) atoms. Cycle 38: After refmac, R = 0.2255 (Rfree = 0.000) for 1675 atoms. Found 6 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2288 (Rfree = 0.000) for 1671 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.2170 (Rfree = 0.000) for 1668 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 2.81 Search for helices and strands: 0 residues in 0 chains, 1758 seeds are put forward Round 1: 105 peptides, 21 chains. Longest chain 11 peptides. Score 0.291 Round 2: 120 peptides, 21 chains. Longest chain 12 peptides. Score 0.371 Round 3: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.343 Round 4: 129 peptides, 23 chains. Longest chain 13 peptides. Score 0.373 Round 5: 129 peptides, 21 chains. Longest chain 14 peptides. Score 0.415 Taking the results from Round 5 Chains 21, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4150 reflections ( 99.09 % complete ) and 3773 restraints for refining 1697 atoms. 3362 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2580 (Rfree = 0.000) for 1697 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.2395 (Rfree = 0.000) for 1684 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2359 (Rfree = 0.000) for 1680 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 44: After refmac, R = 0.2270 (Rfree = 0.000) for 1676 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 45: After refmac, R = 0.2207 (Rfree = 0.000) for 1679 atoms. Found 3 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.80 Search for helices and strands: 0 residues in 0 chains, 1760 seeds are put forward Round 1: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.299 Round 2: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.349 Round 3: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.349 Round 4: 128 peptides, 22 chains. Longest chain 9 peptides. Score 0.389 Round 5: 119 peptides, 19 chains. Longest chain 9 peptides. Score 0.409 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 100, 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 2a6b-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4150 reflections ( 99.09 % complete ) and 3849 restraints for refining 1697 atoms. 3468 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2505 (Rfree = 0.000) for 1697 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2463 (Rfree = 0.000) for 1683 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2409 (Rfree = 0.000) for 1674 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2365 (Rfree = 0.000) for 1666 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:50 GMT 2018 Job finished. TimeTaking 33.86 Used memory is bytes: 8445440