null Sun 23 Dec 22:22:44 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 2huj-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huj-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huj-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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/2huj-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 22:22:52 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/2huj-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huj-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 138 and 0 Target number of residues in the AU: 138 Target solvent content: 0.6122 Checking the provided sequence file Detected sequence length: 140 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 140 Adjusted target solvent content: 0.61 Input MTZ file: 2huj-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: 182 Cell parameters: 100.110 100.110 66.570 90.000 90.000 120.000 Input sequence file: 2huj-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1120 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: 86.698 3.201 Wilson plot Bfac: 57.66 3532 reflections ( 99.75 % complete ) and 0 restraints for refining 1240 atoms. Observations/parameters ratio is 0.71 ------------------------------------------------------ Starting model: R = 0.3373 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2699 (Rfree = 0.000) for 1240 atoms. Found 6 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.10 2.67 Search for helices and strands: 0 residues in 0 chains, 1273 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 8 peptides. Score 0.333 Round 2: 82 peptides, 14 chains. Longest chain 10 peptides. Score 0.408 Round 3: 89 peptides, 10 chains. Longest chain 15 peptides. Score 0.591 Round 4: 90 peptides, 9 chains. Longest chain 22 peptides. Score 0.626 Round 5: 90 peptides, 8 chains. Longest chain 35 peptides. Score 0.654 Taking the results from Round 5 Chains 10, Residues 82, Estimated correctness of the model 54.8 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 2014 restraints for refining 1022 atoms. 1613 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3191 (Rfree = 0.000) for 1022 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 2: After refmac, R = 0.3310 (Rfree = 0.000) for 997 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 3: After refmac, R = 0.3195 (Rfree = 0.000) for 977 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 4: After refmac, R = 0.3034 (Rfree = 0.000) for 966 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 5: After refmac, R = 0.2745 (Rfree = 0.000) for 962 atoms. Found 2 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.02 2.60 Search for helices and strands: 0 residues in 0 chains, 1010 seeds are put forward Round 1: 92 peptides, 12 chains. Longest chain 28 peptides. Score 0.550 Round 2: 101 peptides, 12 chains. Longest chain 35 peptides. Score 0.608 Round 3: 94 peptides, 11 chains. Longest chain 28 peptides. Score 0.593 Round 4: 94 peptides, 9 chains. Longest chain 31 peptides. Score 0.650 Round 5: 95 peptides, 10 chains. Longest chain 23 peptides. Score 0.628 Taking the results from Round 4 Chains 9, Residues 85, Estimated correctness of the model 53.8 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 1881 restraints for refining 1001 atoms. 1425 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3086 (Rfree = 0.000) for 1001 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. Cycle 7: After refmac, R = 0.2810 (Rfree = 0.000) for 994 atoms. Found 8 (9 requested) and removed 9 (4 requested) atoms. Cycle 8: After refmac, R = 0.2742 (Rfree = 0.000) for 984 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2680 (Rfree = 0.000) for 980 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2722 (Rfree = 0.000) for 970 atoms. Found 1 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.05 2.63 Search for helices and strands: 0 residues in 0 chains, 1009 seeds are put forward Round 1: 98 peptides, 10 chains. Longest chain 39 peptides. Score 0.646 Round 2: 106 peptides, 10 chains. Longest chain 42 peptides. Score 0.689 Round 3: 109 peptides, 10 chains. Longest chain 35 peptides. Score 0.704 Round 4: 106 peptides, 9 chains. Longest chain 29 peptides. Score 0.713 Round 5: 106 peptides, 9 chains. Longest chain 30 peptides. Score 0.713 Taking the results from Round 5 Chains 11, Residues 97, Estimated correctness of the model 67.9 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 1926 restraints for refining 1021 atoms. 1470 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3300 (Rfree = 0.000) for 1021 atoms. Found 6 (9 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.2901 (Rfree = 0.000) for 1005 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2765 (Rfree = 0.000) for 994 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2651 (Rfree = 0.000) for 993 atoms. Found 1 (8 requested) and removed 4 (4 requested) atoms. Cycle 15: After refmac, R = 0.2529 (Rfree = 0.000) for 985 atoms. Found 0 (7 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 2.64 Search for helices and strands: 0 residues in 0 chains, 1033 seeds are put forward Round 1: 90 peptides, 13 chains. Longest chain 15 peptides. Score 0.504 Round 2: 92 peptides, 10 chains. Longest chain 24 peptides. Score 0.610 Round 3: 92 peptides, 12 chains. Longest chain 18 peptides. Score 0.550 Round 4: 94 peptides, 11 chains. Longest chain 19 peptides. Score 0.593 Round 5: 90 peptides, 11 chains. Longest chain 19 peptides. Score 0.567 Taking the results from Round 2 Chains 10, Residues 82, Estimated correctness of the model 43.7 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 2031 restraints for refining 994 atoms. 1647 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2747 (Rfree = 0.000) for 994 atoms. Found 5 (7 requested) and removed 6 (4 requested) atoms. Cycle 17: After refmac, R = 0.2645 (Rfree = 0.000) for 988 atoms. Found 6 (7 requested) and removed 6 (4 requested) atoms. Cycle 18: After refmac, R = 0.2459 (Rfree = 0.000) for 983 atoms. Found 7 (7 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.2423 (Rfree = 0.000) for 977 atoms. Found 4 (7 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2309 (Rfree = 0.000) for 971 atoms. Found 6 (7 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 2.65 Search for helices and strands: 0 residues in 0 chains, 1015 seeds are put forward Round 1: 92 peptides, 13 chains. Longest chain 17 peptides. Score 0.519 Round 2: 104 peptides, 11 chains. Longest chain 19 peptides. Score 0.653 Round 3: 105 peptides, 13 chains. Longest chain 17 peptides. Score 0.605 Round 4: 102 peptides, 10 chains. Longest chain 23 peptides. Score 0.668 Round 5: 93 peptides, 9 chains. Longest chain 31 peptides. Score 0.644 Taking the results from Round 4 Chains 10, Residues 92, Estimated correctness of the model 58.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 1991 restraints for refining 1016 atoms. 1548 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2804 (Rfree = 0.000) for 1016 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. Cycle 22: After refmac, R = 0.2603 (Rfree = 0.000) for 1009 atoms. Found 3 (8 requested) and removed 5 (4 requested) atoms. Cycle 23: After refmac, R = 0.2519 (Rfree = 0.000) for 1007 atoms. Found 3 (8 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2468 (Rfree = 0.000) for 1005 atoms. Found 2 (8 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2573 (Rfree = 0.000) for 1003 atoms. Found 7 (7 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 2.66 Search for helices and strands: 0 residues in 0 chains, 1056 seeds are put forward Round 1: 96 peptides, 11 chains. Longest chain 34 peptides. Score 0.606 Round 2: 101 peptides, 10 chains. Longest chain 29 peptides. Score 0.662 Round 3: 100 peptides, 8 chains. Longest chain 34 peptides. Score 0.707 Round 4: 103 peptides, 11 chains. Longest chain 21 peptides. Score 0.647 Round 5: 104 peptides, 10 chains. Longest chain 21 peptides. Score 0.678 Taking the results from Round 3 Chains 9, Residues 92, Estimated correctness of the model 66.6 % 2 chains (39 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 106 A and 115 A 7 chains (94 residues) following loop building 1 chains (47 residues) in sequence following loop building ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 1677 restraints for refining 1023 atoms. 1096 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3066 (Rfree = 0.000) for 1023 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 27: After refmac, R = 0.2841 (Rfree = 0.000) for 1012 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2728 (Rfree = 0.000) for 1011 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2716 (Rfree = 0.000) for 1008 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.2509 (Rfree = 0.000) for 1007 atoms. Found 7 (7 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 2.77 Search for helices and strands: 0 residues in 0 chains, 1058 seeds are put forward Round 1: 87 peptides, 10 chains. Longest chain 19 peptides. Score 0.578 Round 2: 91 peptides, 9 chains. Longest chain 19 peptides. Score 0.632 Round 3: 97 peptides, 9 chains. Longest chain 22 peptides. Score 0.666 Round 4: 89 peptides, 9 chains. Longest chain 17 peptides. Score 0.620 Round 5: 100 peptides, 9 chains. Longest chain 19 peptides. Score 0.683 Taking the results from Round 5 Chains 10, Residues 91, Estimated correctness of the model 61.5 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 1858 restraints for refining 1022 atoms. 1383 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2920 (Rfree = 0.000) for 1022 atoms. Found 7 (7 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2654 (Rfree = 0.000) for 1020 atoms. Found 2 (7 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.2634 (Rfree = 0.000) for 1016 atoms. Found 4 (7 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2594 (Rfree = 0.000) for 1014 atoms. Found 5 (7 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2466 (Rfree = 0.000) for 1012 atoms. Found 2 (7 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 2.75 Search for helices and strands: 0 residues in 0 chains, 1054 seeds are put forward Round 1: 84 peptides, 11 chains. Longest chain 17 peptides. Score 0.526 Round 2: 91 peptides, 12 chains. Longest chain 11 peptides. Score 0.543 Round 3: 99 peptides, 8 chains. Longest chain 51 peptides. Score 0.702 Round 4: 102 peptides, 11 chains. Longest chain 17 peptides. Score 0.642 Round 5: 99 peptides, 9 chains. Longest chain 19 peptides. Score 0.677 Taking the results from Round 3 Chains 8, Residues 91, Estimated correctness of the model 65.6 % 1 chains (50 residues) have been docked in sequence ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 1679 restraints for refining 1023 atoms. 1097 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2731 (Rfree = 0.000) for 1023 atoms. Found 7 (7 requested) and removed 21 (4 requested) atoms. Cycle 37: After refmac, R = 0.2482 (Rfree = 0.000) for 997 atoms. Found 7 (7 requested) and removed 6 (4 requested) atoms. Cycle 38: After refmac, R = 0.2412 (Rfree = 0.000) for 996 atoms. Found 3 (6 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.2385 (Rfree = 0.000) for 992 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.2379 (Rfree = 0.000) for 988 atoms. Found 2 (6 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.72 Search for helices and strands: 0 residues in 0 chains, 1040 seeds are put forward Round 1: 81 peptides, 11 chains. Longest chain 12 peptides. Score 0.504 Round 2: 89 peptides, 8 chains. Longest chain 32 peptides. Score 0.649 Round 3: 92 peptides, 7 chains. Longest chain 34 peptides. Score 0.692 Round 4: 90 peptides, 7 chains. Longest chain 25 peptides. Score 0.681 Round 5: 80 peptides, 6 chains. Longest chain 30 peptides. Score 0.653 Taking the results from Round 3 Chains 7, Residues 85, Estimated correctness of the model 63.4 % 1 chains (33 residues) have been docked in sequence ------------------------------------------------------ 3532 reflections ( 99.75 % complete ) and 1898 restraints for refining 1018 atoms. 1433 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2676 (Rfree = 0.000) for 1018 atoms. Found 5 (6 requested) and removed 7 (4 requested) atoms. Cycle 42: After refmac, R = 0.2425 (Rfree = 0.000) for 1016 atoms. Found 3 (6 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.2399 (Rfree = 0.000) for 1013 atoms. Found 0 (6 requested) and removed 5 (4 requested) atoms. Cycle 44: After refmac, R = 0.2342 (Rfree = 0.000) for 1005 atoms. Found 3 (6 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2327 (Rfree = 0.000) for 1000 atoms. Found 1 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 1046 seeds are put forward Round 1: 88 peptides, 8 chains. Longest chain 31 peptides. Score 0.643 Round 2: 102 peptides, 10 chains. Longest chain 30 peptides. Score 0.668 Round 3: 102 peptides, 9 chains. Longest chain 28 peptides. Score 0.693 Round 4: 104 peptides, 11 chains. Longest chain 23 peptides. Score 0.653 Round 5: 92 peptides, 11 chains. Longest chain 28 peptides. Score 0.580 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 93, Estimated correctness of the model 63.6 % 1 chains (27 residues) have been docked in sequence Sequence coverage is 28 % Consider running further cycles of model building using 2huj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3532 reflections ( 99.75 % complete ) and 1954 restraints for refining 1023 atoms. 1486 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2636 (Rfree = 0.000) for 1023 atoms. Found 0 (6 requested) and removed 2 (4 requested) atoms. Cycle 47: After refmac, R = 0.2498 (Rfree = 0.000) for 1021 atoms. Found 0 (6 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2443 (Rfree = 0.000) for 1014 atoms. Found 0 (6 requested) and removed 1 (4 requested) atoms. Cycle 49: After refmac, R = 0.2406 (Rfree = 0.000) for 1013 atoms. Found 0 (6 requested) and removed 2 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:11 GMT 2018 Job finished. TimeTaking 30.45 Used memory is bytes: 6911552