null Sun 23 Dec 22:23:05 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 2pg3-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.2-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/2pg3-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.2-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 22:23:15 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/2pg3-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.2-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 160 and 0 Target number of residues in the AU: 160 Target solvent content: 0.6354 Checking the provided sequence file Detected sequence length: 232 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 232 Adjusted target solvent content: 0.47 Input MTZ file: 2pg3-3.2-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: 92 Cell parameters: 78.154 78.154 77.755 90.000 90.000 90.000 Input sequence file: 2pg3-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1856 target number of atoms Had to go as low as 0.65 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: 27.561 3.200 Wilson plot Bfac: 69.43 4295 reflections ( 99.74 % complete ) and 0 restraints for refining 2047 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3763 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3634 (Rfree = 0.000) for 2047 atoms. Found 17 (18 requested) and removed 29 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.40 Search for helices and strands: 0 residues in 0 chains, 2082 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 7 peptides. Score 0.306 Round 2: 100 peptides, 20 chains. Longest chain 11 peptides. Score 0.319 Round 3: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.391 Round 4: 116 peptides, 21 chains. Longest chain 11 peptides. Score 0.401 Round 5: 117 peptides, 17 chains. Longest chain 20 peptides. Score 0.514 Taking the results from Round 5 Chains 21, Residues 100, Estimated correctness of the model 15.8 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3698 restraints for refining 1693 atoms. 3258 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3083 (Rfree = 0.000) for 1693 atoms. Found 6 (15 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.2781 (Rfree = 0.000) for 1654 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 3: After refmac, R = 0.2704 (Rfree = 0.000) for 1649 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.2678 (Rfree = 0.000) for 1642 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2657 (Rfree = 0.000) for 1636 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.38 Search for helices and strands: 0 residues in 0 chains, 1699 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 8 peptides. Score 0.303 Round 2: 108 peptides, 18 chains. Longest chain 10 peptides. Score 0.432 Round 3: 107 peptides, 16 chains. Longest chain 11 peptides. Score 0.481 Round 4: 115 peptides, 15 chains. Longest chain 12 peptides. Score 0.553 Round 5: 118 peptides, 15 chains. Longest chain 18 peptides. Score 0.570 Taking the results from Round 5 Chains 15, Residues 103, Estimated correctness of the model 32.7 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3710 restraints for refining 1694 atoms. 3237 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3040 (Rfree = 0.000) for 1694 atoms. Found 13 (15 requested) and removed 25 (7 requested) atoms. Cycle 7: After refmac, R = 0.2869 (Rfree = 0.000) for 1667 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 8: After refmac, R = 0.2699 (Rfree = 0.000) for 1662 atoms. Found 5 (14 requested) and removed 17 (7 requested) atoms. Cycle 9: After refmac, R = 0.2749 (Rfree = 0.000) for 1646 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. Cycle 10: After refmac, R = 0.2785 (Rfree = 0.000) for 1637 atoms. Found 3 (14 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 3.17 Search for helices and strands: 0 residues in 0 chains, 1704 seeds are put forward Round 1: 108 peptides, 18 chains. Longest chain 12 peptides. Score 0.432 Round 2: 116 peptides, 19 chains. Longest chain 13 peptides. Score 0.455 Round 3: 114 peptides, 16 chains. Longest chain 21 peptides. Score 0.522 Round 4: 123 peptides, 22 chains. Longest chain 8 peptides. Score 0.419 Round 5: 124 peptides, 19 chains. Longest chain 13 peptides. Score 0.504 Taking the results from Round 3 Chains 16, Residues 98, Estimated correctness of the model 18.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3916 restraints for refining 1694 atoms. 3540 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2844 (Rfree = 0.000) for 1694 atoms. Found 12 (15 requested) and removed 15 (7 requested) atoms. Cycle 12: After refmac, R = 0.2703 (Rfree = 0.000) for 1680 atoms. Found 5 (15 requested) and removed 14 (7 requested) atoms. Cycle 13: After refmac, R = 0.2621 (Rfree = 0.000) for 1667 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.2584 (Rfree = 0.000) for 1657 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 15: After refmac, R = 0.2560 (Rfree = 0.000) for 1650 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.28 Search for helices and strands: 0 residues in 0 chains, 1708 seeds are put forward Round 1: 84 peptides, 17 chains. Longest chain 10 peptides. Score 0.294 Round 2: 104 peptides, 17 chains. Longest chain 11 peptides. Score 0.434 Round 3: 111 peptides, 19 chains. Longest chain 11 peptides. Score 0.424 Round 4: 104 peptides, 15 chains. Longest chain 17 peptides. Score 0.489 Round 5: 108 peptides, 15 chains. Longest chain 19 peptides. Score 0.513 Taking the results from Round 5 Chains 15, Residues 93, Estimated correctness of the model 15.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3974 restraints for refining 1694 atoms. 3617 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2944 (Rfree = 0.000) for 1694 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.2798 (Rfree = 0.000) for 1689 atoms. Found 13 (15 requested) and removed 9 (7 requested) atoms. Cycle 18: After refmac, R = 0.2614 (Rfree = 0.000) for 1689 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 19: After refmac, R = 0.2466 (Rfree = 0.000) for 1685 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.2446 (Rfree = 0.000) for 1682 atoms. Found 2 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.32 Search for helices and strands: 0 residues in 0 chains, 1744 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.321 Round 2: 100 peptides, 16 chains. Longest chain 16 peptides. Score 0.436 Round 3: 102 peptides, 16 chains. Longest chain 11 peptides. Score 0.449 Round 4: 122 peptides, 17 chains. Longest chain 13 peptides. Score 0.543 Round 5: 119 peptides, 15 chains. Longest chain 19 peptides. Score 0.575 Taking the results from Round 5 Chains 17, Residues 104, Estimated correctness of the model 34.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3726 restraints for refining 1694 atoms. 3295 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2743 (Rfree = 0.000) for 1694 atoms. Found 11 (15 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2729 (Rfree = 0.000) for 1689 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 23: After refmac, R = 0.2608 (Rfree = 0.000) for 1685 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.2637 (Rfree = 0.000) for 1681 atoms. Found 5 (15 requested) and removed 9 (7 requested) atoms. Cycle 25: After refmac, R = 0.2631 (Rfree = 0.000) for 1675 atoms. Found 1 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.28 Search for helices and strands: 0 residues in 0 chains, 1742 seeds are put forward Round 1: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.364 Round 2: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.383 Round 3: 101 peptides, 17 chains. Longest chain 10 peptides. Score 0.415 Round 4: 109 peptides, 17 chains. Longest chain 12 peptides. Score 0.466 Round 5: 105 peptides, 17 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 4 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3875 restraints for refining 1694 atoms. 3524 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2719 (Rfree = 0.000) for 1694 atoms. Found 11 (15 requested) and removed 9 (7 requested) atoms. Cycle 27: After refmac, R = 0.2558 (Rfree = 0.000) for 1681 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 28: After refmac, R = 0.2627 (Rfree = 0.000) for 1675 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 29: After refmac, R = 0.2511 (Rfree = 0.000) for 1672 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.2499 (Rfree = 0.000) for 1666 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.31 Search for helices and strands: 0 residues in 0 chains, 1729 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 9 peptides. Score 0.276 Round 2: 91 peptides, 15 chains. Longest chain 11 peptides. Score 0.406 Round 3: 100 peptides, 16 chains. Longest chain 15 peptides. Score 0.436 Round 4: 100 peptides, 15 chains. Longest chain 15 peptides. Score 0.465 Round 5: 114 peptides, 15 chains. Longest chain 15 peptides. Score 0.548 Taking the results from Round 5 Chains 15, Residues 99, Estimated correctness of the model 26.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3798 restraints for refining 1694 atoms. 3417 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2587 (Rfree = 0.000) for 1694 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.2445 (Rfree = 0.000) for 1690 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.2394 (Rfree = 0.000) for 1681 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.2382 (Rfree = 0.000) for 1675 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.2375 (Rfree = 0.000) for 1672 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.32 Search for helices and strands: 0 residues in 0 chains, 1722 seeds are put forward Round 1: 87 peptides, 15 chains. Longest chain 13 peptides. Score 0.378 Round 2: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.410 Round 3: 94 peptides, 16 chains. Longest chain 10 peptides. Score 0.397 Round 4: 93 peptides, 15 chains. Longest chain 11 peptides. Score 0.419 Round 5: 88 peptides, 14 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 4 Chains 15, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3983 restraints for refining 1694 atoms. 3686 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2543 (Rfree = 0.000) for 1694 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.2469 (Rfree = 0.000) for 1691 atoms. Found 5 (15 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.2410 (Rfree = 0.000) for 1687 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.2411 (Rfree = 0.000) for 1681 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.2361 (Rfree = 0.000) for 1676 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.43 Search for helices and strands: 0 residues in 0 chains, 1708 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 9 peptides. Score 0.300 Round 2: 98 peptides, 16 chains. Longest chain 18 peptides. Score 0.423 Round 3: 96 peptides, 16 chains. Longest chain 15 peptides. Score 0.410 Round 4: 103 peptides, 16 chains. Longest chain 10 peptides. Score 0.456 Round 5: 107 peptides, 17 chains. Longest chain 10 peptides. Score 0.453 Taking the results from Round 4 Chains 16, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4295 reflections ( 99.74 % complete ) and 3837 restraints for refining 1694 atoms. 3505 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2526 (Rfree = 0.000) for 1694 atoms. Found 9 (15 requested) and removed 8 (7 requested) atoms. Cycle 42: After refmac, R = 0.2417 (Rfree = 0.000) for 1693 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.2392 (Rfree = 0.000) for 1684 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.2362 (Rfree = 0.000) for 1681 atoms. Found 2 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.2319 (Rfree = 0.000) for 1675 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.42 Search for helices and strands: 0 residues in 0 chains, 1710 seeds are put forward Round 1: 90 peptides, 19 chains. Longest chain 9 peptides. Score 0.277 Round 2: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.324 Round 3: 92 peptides, 16 chains. Longest chain 9 peptides. Score 0.383 Round 4: 102 peptides, 17 chains. Longest chain 10 peptides. Score 0.421 Round 5: 95 peptides, 17 chains. Longest chain 8 peptides. Score 0.374 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 85, 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 2pg3-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4295 reflections ( 99.74 % complete ) and 3951 restraints for refining 1690 atoms. 3628 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2538 (Rfree = 0.000) for 1690 atoms. Found 0 (15 requested) and removed 2 (7 requested) atoms. Cycle 47: After refmac, R = 0.2457 (Rfree = 0.000) for 1687 atoms. Found 0 (15 requested) and removed 3 (7 requested) atoms. Cycle 48: After refmac, R = 0.2378 (Rfree = 0.000) for 1681 atoms. Found 0 (15 requested) and removed 2 (7 requested) atoms. Cycle 49: After refmac, R = 0.2387 (Rfree = 0.000) for 1679 atoms. Found 0 (15 requested) and removed 3 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:07 GMT 2018 Job finished. TimeTaking 31.04 Used memory is bytes: 16609288