null Sun 23 Dec 22:22:42 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 2hhz-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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/2hhz-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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 22:23:44 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/2hhz-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-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 99 and 0 Target number of residues in the AU: 99 Target solvent content: 0.6364 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 150 Adjusted target solvent content: 0.45 Input MTZ file: 2hhz-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: 96 Cell parameters: 71.030 71.030 58.410 90.000 90.000 90.000 Input sequence file: 2hhz-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1200 target number of atoms Had to go as low as 0.70 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: 50.226 3.201 Wilson plot Bfac: 69.03 2700 reflections ( 99.56 % complete ) and 0 restraints for refining 1329 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3385 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2753 (Rfree = 0.000) for 1329 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 1336 seeds are put forward Round 1: 55 peptides, 9 chains. Longest chain 12 peptides. Score 0.405 Round 2: 85 peptides, 10 chains. Longest chain 23 peptides. Score 0.639 Round 3: 93 peptides, 9 chains. Longest chain 35 peptides. Score 0.723 Round 4: 94 peptides, 12 chains. Longest chain 15 peptides. Score 0.639 Round 5: 100 peptides, 12 chains. Longest chain 16 peptides. Score 0.680 Taking the results from Round 3 Chains 10, Residues 84, Estimated correctness of the model 69.9 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 2366 restraints for refining 1096 atoms. 1999 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2880 (Rfree = 0.000) for 1096 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2847 (Rfree = 0.000) for 1068 atoms. Found 6 (9 requested) and removed 12 (4 requested) atoms. Cycle 3: After refmac, R = 0.2459 (Rfree = 0.000) for 1053 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. Cycle 4: After refmac, R = 0.2905 (Rfree = 0.000) for 1047 atoms. Found 5 (8 requested) and removed 14 (4 requested) atoms. Cycle 5: After refmac, R = 0.2297 (Rfree = 0.000) for 1034 atoms. Found 1 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 1067 seeds are put forward Round 1: 88 peptides, 12 chains. Longest chain 23 peptides. Score 0.593 Round 2: 93 peptides, 8 chains. Longest chain 37 peptides. Score 0.750 Round 3: 95 peptides, 10 chains. Longest chain 35 peptides. Score 0.707 Round 4: 88 peptides, 11 chains. Longest chain 19 peptides. Score 0.628 Round 5: 95 peptides, 12 chains. Longest chain 22 peptides. Score 0.646 Taking the results from Round 2 Chains 8, Residues 85, Estimated correctness of the model 75.0 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 1932 restraints for refining 1058 atoms. 1457 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2521 (Rfree = 0.000) for 1058 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.2742 (Rfree = 0.000) for 1049 atoms. Found 3 (8 requested) and removed 7 (4 requested) atoms. Cycle 8: After refmac, R = 0.2920 (Rfree = 0.000) for 1036 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 9: After refmac, R = 0.2497 (Rfree = 0.000) for 1024 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2287 (Rfree = 0.000) for 1014 atoms. Found 3 (7 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.47 Search for helices and strands: 0 residues in 0 chains, 1042 seeds are put forward Round 1: 92 peptides, 10 chains. Longest chain 37 peptides. Score 0.688 Round 2: 98 peptides, 12 chains. Longest chain 26 peptides. Score 0.667 Round 3: 94 peptides, 10 chains. Longest chain 25 peptides. Score 0.701 Round 4: 98 peptides, 9 chains. Longest chain 38 peptides. Score 0.751 Round 5: 101 peptides, 9 chains. Longest chain 33 peptides. Score 0.767 Taking the results from Round 5 Chains 9, Residues 92, Estimated correctness of the model 78.1 % 1 chains (32 residues) have been docked in sequence ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 1892 restraints for refining 1059 atoms. 1400 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2885 (Rfree = 0.000) for 1059 atoms. Found 4 (7 requested) and removed 26 (4 requested) atoms. Cycle 12: After refmac, R = 0.2752 (Rfree = 0.000) for 1031 atoms. Found 6 (7 requested) and removed 10 (4 requested) atoms. Cycle 13: After refmac, R = 0.2493 (Rfree = 0.000) for 1020 atoms. Found 4 (7 requested) and removed 8 (4 requested) atoms. Cycle 14: After refmac, R = 0.2589 (Rfree = 0.000) for 1011 atoms. Found 2 (7 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2471 (Rfree = 0.000) for 998 atoms. Found 2 (6 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 3.42 Search for helices and strands: 0 residues in 0 chains, 1044 seeds are put forward Round 1: 77 peptides, 10 chains. Longest chain 22 peptides. Score 0.576 Round 2: 87 peptides, 8 chains. Longest chain 26 peptides. Score 0.716 Round 3: 87 peptides, 7 chains. Longest chain 39 peptides. Score 0.744 Round 4: 91 peptides, 8 chains. Longest chain 26 peptides. Score 0.739 Round 5: 92 peptides, 12 chains. Longest chain 24 peptides. Score 0.624 Taking the results from Round 3 Chains 9, Residues 80, Estimated correctness of the model 73.9 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 1830 restraints for refining 1029 atoms. 1385 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2748 (Rfree = 0.000) for 1029 atoms. Found 5 (6 requested) and removed 14 (4 requested) atoms. Cycle 17: After refmac, R = 0.2945 (Rfree = 0.000) for 1013 atoms. Found 4 (6 requested) and removed 10 (4 requested) atoms. Cycle 18: After refmac, R = 0.2570 (Rfree = 0.000) for 997 atoms. Found 3 (6 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2563 (Rfree = 0.000) for 992 atoms. Found 2 (5 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.2455 (Rfree = 0.000) for 988 atoms. Found 5 (5 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 1016 seeds are put forward Round 1: 75 peptides, 8 chains. Longest chain 36 peptides. Score 0.633 Round 2: 81 peptides, 7 chains. Longest chain 26 peptides. Score 0.708 Round 3: 77 peptides, 9 chains. Longest chain 18 peptides. Score 0.613 Round 4: 81 peptides, 7 chains. Longest chain 26 peptides. Score 0.708 Round 5: 82 peptides, 9 chains. Longest chain 22 peptides. Score 0.651 Taking the results from Round 4 Chains 8, Residues 74, Estimated correctness of the model 66.8 % 2 chains (42 residues) have been docked in sequence Building loops using Loopy2018 8 chains (74 residues) following loop building 2 chains (42 residues) in sequence following loop building ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 1722 restraints for refining 1029 atoms. 1263 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2755 (Rfree = 0.000) for 1029 atoms. Found 5 (5 requested) and removed 8 (4 requested) atoms. Cycle 22: After refmac, R = 0.2378 (Rfree = 0.000) for 1023 atoms. Found 5 (5 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.2856 (Rfree = 0.000) for 1024 atoms. Found 5 (5 requested) and removed 8 (4 requested) atoms. Cycle 24: After refmac, R = 0.2230 (Rfree = 0.000) for 1018 atoms. Found 3 (5 requested) and removed 5 (4 requested) atoms. Cycle 25: After refmac, R = 0.2050 (Rfree = 0.000) for 1016 atoms. Found 2 (5 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 1047 seeds are put forward Round 1: 72 peptides, 7 chains. Longest chain 36 peptides. Score 0.646 Round 2: 87 peptides, 10 chains. Longest chain 15 peptides. Score 0.654 Round 3: 85 peptides, 8 chains. Longest chain 25 peptides. Score 0.703 Round 4: 86 peptides, 8 chains. Longest chain 36 peptides. Score 0.710 Round 5: 87 peptides, 9 chains. Longest chain 25 peptides. Score 0.686 Taking the results from Round 4 Chains 8, Residues 78, Estimated correctness of the model 67.2 % 1 chains (35 residues) have been docked in sequence ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 1869 restraints for refining 1058 atoms. 1426 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2342 (Rfree = 0.000) for 1058 atoms. Found 4 (4 requested) and removed 16 (4 requested) atoms. Cycle 27: After refmac, R = 0.2345 (Rfree = 0.000) for 1044 atoms. Found 4 (4 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2402 (Rfree = 0.000) for 1041 atoms. Found 3 (4 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.2456 (Rfree = 0.000) for 1037 atoms. Found 4 (4 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2146 (Rfree = 0.000) for 1034 atoms. Found 4 (4 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 1070 seeds are put forward Round 1: 85 peptides, 9 chains. Longest chain 24 peptides. Score 0.672 Round 2: 93 peptides, 10 chains. Longest chain 21 peptides. Score 0.694 Round 3: 86 peptides, 10 chains. Longest chain 25 peptides. Score 0.646 Round 4: 92 peptides, 10 chains. Longest chain 25 peptides. Score 0.688 Round 5: 85 peptides, 10 chains. Longest chain 13 peptides. Score 0.639 Taking the results from Round 2 Chains 10, Residues 83, Estimated correctness of the model 63.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 1982 restraints for refining 1057 atoms. 1611 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2205 (Rfree = 0.000) for 1057 atoms. Found 4 (4 requested) and removed 8 (4 requested) atoms. Cycle 32: After refmac, R = 0.2671 (Rfree = 0.000) for 1053 atoms. Found 4 (4 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2277 (Rfree = 0.000) for 1046 atoms. Found 4 (4 requested) and removed 5 (4 requested) atoms. Cycle 34: After refmac, R = 0.2701 (Rfree = 0.000) for 1041 atoms. Found 4 (4 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2100 (Rfree = 0.000) for 1036 atoms. Found 1 (4 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.42 Search for helices and strands: 0 residues in 0 chains, 1063 seeds are put forward Round 1: 72 peptides, 10 chains. Longest chain 15 peptides. Score 0.531 Round 2: 79 peptides, 9 chains. Longest chain 20 peptides. Score 0.628 Round 3: 85 peptides, 10 chains. Longest chain 15 peptides. Score 0.639 Round 4: 85 peptides, 9 chains. Longest chain 29 peptides. Score 0.672 Round 5: 84 peptides, 9 chains. Longest chain 23 peptides. Score 0.665 Taking the results from Round 4 Chains 10, Residues 76, Estimated correctness of the model 59.0 % 1 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 2026 restraints for refining 1064 atoms. 1633 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2277 (Rfree = 0.000) for 1064 atoms. Found 4 (4 requested) and removed 9 (4 requested) atoms. Cycle 37: After refmac, R = 0.2187 (Rfree = 0.000) for 1057 atoms. Found 4 (4 requested) and removed 5 (4 requested) atoms. Cycle 38: After refmac, R = 0.2161 (Rfree = 0.000) for 1056 atoms. Found 4 (4 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2319 (Rfree = 0.000) for 1053 atoms. Found 4 (4 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.2106 (Rfree = 0.000) for 1049 atoms. Found 4 (4 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 1076 seeds are put forward Round 1: 70 peptides, 10 chains. Longest chain 12 peptides. Score 0.513 Round 2: 89 peptides, 10 chains. Longest chain 36 peptides. Score 0.668 Round 3: 79 peptides, 10 chains. Longest chain 26 peptides. Score 0.592 Round 4: 79 peptides, 7 chains. Longest chain 36 peptides. Score 0.696 Round 5: 74 peptides, 9 chains. Longest chain 22 peptides. Score 0.588 Taking the results from Round 4 Chains 7, Residues 72, Estimated correctness of the model 64.3 % 1 chains (35 residues) have been docked in sequence ------------------------------------------------------ 2700 reflections ( 99.56 % complete ) and 1925 restraints for refining 1096 atoms. 1505 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2804 (Rfree = 0.000) for 1096 atoms. Found 4 (4 requested) and removed 27 (4 requested) atoms. Cycle 42: After refmac, R = 0.2364 (Rfree = 0.000) for 1065 atoms. Found 4 (4 requested) and removed 7 (4 requested) atoms. Cycle 43: After refmac, R = 0.2475 (Rfree = 0.000) for 1058 atoms. Found 4 (4 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.2330 (Rfree = 0.000) for 1051 atoms. Found 4 (4 requested) and removed 9 (4 requested) atoms. Cycle 45: After refmac, R = 0.2366 (Rfree = 0.000) for 1044 atoms. Found 3 (4 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.43 Search for helices and strands: 0 residues in 0 chains, 1074 seeds are put forward Round 1: 67 peptides, 8 chains. Longest chain 17 peptides. Score 0.568 Round 2: 79 peptides, 9 chains. Longest chain 17 peptides. Score 0.628 Round 3: 75 peptides, 8 chains. Longest chain 19 peptides. Score 0.633 Round 4: 79 peptides, 8 chains. Longest chain 19 peptides. Score 0.663 Round 5: 88 peptides, 8 chains. Longest chain 20 peptides. Score 0.722 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 80, Estimated correctness of the model 69.7 % 1 chains (19 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 2hhz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2700 reflections ( 99.56 % complete ) and 1808 restraints for refining 1041 atoms. 1417 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2623 (Rfree = 0.000) for 1041 atoms. Found 0 (4 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2089 (Rfree = 0.000) for 1033 atoms. Found 0 (4 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2035 (Rfree = 0.000) for 1028 atoms. Found 0 (4 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2274 (Rfree = 0.000) for 1024 atoms. Found 0 (4 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:23:53 GMT 2018 Job finished. TimeTaking 61.2 Used memory is bytes: 3866072