null Sun 23 Dec 22:23:10 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 2pim-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pim-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pim-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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/2pim-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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 22:23:19 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/2pim-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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 117 and 0 Target number of residues in the AU: 117 Target solvent content: 0.6217 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 141 Adjusted target solvent content: 0.54 Input MTZ file: 2pim-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: 177 Cell parameters: 111.771 111.771 46.411 90.000 90.000 120.000 Input sequence file: 2pim-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1128 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: 96.797 3.201 Wilson plot Bfac: 60.93 3081 reflections ( 99.45 % complete ) and 0 restraints for refining 1251 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3243 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3099 (Rfree = 0.000) for 1251 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 2.92 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward Round 1: 83 peptides, 8 chains. Longest chain 35 peptides. Score 0.652 Round 2: 98 peptides, 9 chains. Longest chain 44 peptides. Score 0.713 Round 3: 94 peptides, 9 chains. Longest chain 30 peptides. Score 0.690 Round 4: 103 peptides, 8 chains. Longest chain 56 peptides. Score 0.762 Round 5: 110 peptides, 6 chains. Longest chain 56 peptides. Score 0.831 Taking the results from Round 5 Chains 6, Residues 104, Estimated correctness of the model 87.8 % 1 chains (55 residues) have been docked in sequence ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1597 restraints for refining 1030 atoms. 997 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3210 (Rfree = 0.000) for 1030 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 2: After refmac, R = 0.3016 (Rfree = 0.000) for 1004 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 3: After refmac, R = 0.2957 (Rfree = 0.000) for 975 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 4: After refmac, R = 0.2873 (Rfree = 0.000) for 964 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 5: After refmac, R = 0.2539 (Rfree = 0.000) for 958 atoms. Found 7 (7 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 2.92 Search for helices and strands: 0 residues in 0 chains, 982 seeds are put forward Round 1: 101 peptides, 8 chains. Longest chain 56 peptides. Score 0.753 Round 2: 94 peptides, 6 chains. Longest chain 36 peptides. Score 0.767 Round 3: 102 peptides, 8 chains. Longest chain 36 peptides. Score 0.758 Round 4: 107 peptides, 9 chains. Longest chain 36 peptides. Score 0.758 Round 5: 104 peptides, 8 chains. Longest chain 36 peptides. Score 0.767 Taking the results from Round 5 Chains 9, Residues 96, Estimated correctness of the model 78.1 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1938 restraints for refining 1030 atoms. 1463 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3058 (Rfree = 0.000) for 1030 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 7: After refmac, R = 0.2780 (Rfree = 0.000) for 1010 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 8: After refmac, R = 0.2627 (Rfree = 0.000) for 995 atoms. Found 6 (7 requested) and removed 6 (4 requested) atoms. Cycle 9: After refmac, R = 0.2457 (Rfree = 0.000) for 992 atoms. Found 4 (7 requested) and removed 8 (4 requested) atoms. Cycle 10: After refmac, R = 0.2539 (Rfree = 0.000) for 985 atoms. Found 4 (7 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 1011 seeds are put forward Round 1: 95 peptides, 12 chains. Longest chain 22 peptides. Score 0.608 Round 2: 107 peptides, 7 chains. Longest chain 38 peptides. Score 0.801 Round 3: 99 peptides, 9 chains. Longest chain 30 peptides. Score 0.718 Round 4: 106 peptides, 6 chains. Longest chain 38 peptides. Score 0.817 Round 5: 112 peptides, 7 chains. Longest chain 68 peptides. Score 0.820 Taking the results from Round 5 Chains 7, Residues 105, Estimated correctness of the model 86.3 % 1 chains (67 residues) have been docked in sequence ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1488 restraints for refining 1030 atoms. 850 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3229 (Rfree = 0.000) for 1030 atoms. Found 7 (7 requested) and removed 28 (4 requested) atoms. Cycle 12: After refmac, R = 0.2816 (Rfree = 0.000) for 988 atoms. Found 7 (7 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2573 (Rfree = 0.000) for 978 atoms. Found 6 (6 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.2431 (Rfree = 0.000) for 967 atoms. Found 6 (6 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2575 (Rfree = 0.000) for 963 atoms. Found 6 (6 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.05 2.89 Search for helices and strands: 0 residues in 0 chains, 996 seeds are put forward Round 1: 96 peptides, 10 chains. Longest chain 36 peptides. Score 0.674 Round 2: 104 peptides, 8 chains. Longest chain 56 peptides. Score 0.767 Round 3: 102 peptides, 6 chains. Longest chain 39 peptides. Score 0.802 Round 4: 97 peptides, 7 chains. Longest chain 44 peptides. Score 0.758 Round 5: 103 peptides, 7 chains. Longest chain 51 peptides. Score 0.785 Taking the results from Round 3 Chains 8, Residues 96, Estimated correctness of the model 83.7 % 2 chains (36 residues) have been docked in sequence Building loops using Loopy2018 8 chains (96 residues) following loop building 2 chains (36 residues) in sequence following loop building ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1696 restraints for refining 1030 atoms. 1187 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2698 (Rfree = 0.000) for 1030 atoms. Found 6 (6 requested) and removed 23 (4 requested) atoms. Cycle 17: After refmac, R = 0.2840 (Rfree = 0.000) for 1007 atoms. Found 6 (6 requested) and removed 17 (4 requested) atoms. Cycle 18: After refmac, R = 0.2578 (Rfree = 0.000) for 991 atoms. Found 5 (5 requested) and removed 15 (4 requested) atoms. Cycle 19: After refmac, R = 0.2698 (Rfree = 0.000) for 978 atoms. Found 5 (5 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.2393 (Rfree = 0.000) for 966 atoms. Found 5 (5 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 992 seeds are put forward Round 1: 92 peptides, 11 chains. Longest chain 29 peptides. Score 0.619 Round 2: 89 peptides, 10 chains. Longest chain 30 peptides. Score 0.630 Round 3: 96 peptides, 8 chains. Longest chain 27 peptides. Score 0.728 Round 4: 100 peptides, 10 chains. Longest chain 30 peptides. Score 0.698 Round 5: 105 peptides, 9 chains. Longest chain 34 peptides. Score 0.749 Taking the results from Round 5 Chains 11, Residues 96, Estimated correctness of the model 74.9 % 2 chains (41 residues) have been docked in sequence Building loops using Loopy2018 11 chains (96 residues) following loop building 2 chains (41 residues) in sequence following loop building ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1646 restraints for refining 1003 atoms. 1123 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2671 (Rfree = 0.000) for 1003 atoms. Found 5 (5 requested) and removed 21 (4 requested) atoms. Cycle 22: After refmac, R = 0.2392 (Rfree = 0.000) for 986 atoms. Found 4 (5 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2338 (Rfree = 0.000) for 983 atoms. Found 1 (4 requested) and removed 5 (4 requested) atoms. Cycle 24: After refmac, R = 0.2548 (Rfree = 0.000) for 977 atoms. Found 4 (4 requested) and removed 6 (4 requested) atoms. Cycle 25: After refmac, R = 0.2180 (Rfree = 0.000) for 972 atoms. Found 4 (4 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 2.94 Search for helices and strands: 0 residues in 0 chains, 998 seeds are put forward Round 1: 99 peptides, 8 chains. Longest chain 28 peptides. Score 0.743 Round 2: 97 peptides, 6 chains. Longest chain 44 peptides. Score 0.781 Round 3: 101 peptides, 7 chains. Longest chain 30 peptides. Score 0.776 Round 4: 103 peptides, 7 chains. Longest chain 44 peptides. Score 0.785 Round 5: 106 peptides, 7 chains. Longest chain 43 peptides. Score 0.797 Taking the results from Round 5 Chains 7, Residues 99, Estimated correctness of the model 82.9 % 2 chains (45 residues) have been docked in sequence Building loops using Loopy2018 7 chains (99 residues) following loop building 2 chains (45 residues) in sequence following loop building ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1616 restraints for refining 1022 atoms. 1067 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2590 (Rfree = 0.000) for 1022 atoms. Found 4 (4 requested) and removed 20 (4 requested) atoms. Cycle 27: After refmac, R = 0.2488 (Rfree = 0.000) for 998 atoms. Found 4 (4 requested) and removed 14 (4 requested) atoms. Cycle 28: After refmac, R = 0.2318 (Rfree = 0.000) for 983 atoms. Found 4 (4 requested) and removed 11 (4 requested) atoms. Cycle 29: After refmac, R = 0.1905 (Rfree = 0.000) for 975 atoms. Found 4 (4 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2133 (Rfree = 0.000) for 970 atoms. Found 4 (4 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 2.90 Search for helices and strands: 0 residues in 0 chains, 1013 seeds are put forward Round 1: 88 peptides, 8 chains. Longest chain 42 peptides. Score 0.683 Round 2: 94 peptides, 7 chains. Longest chain 43 peptides. Score 0.743 Round 3: 98 peptides, 8 chains. Longest chain 44 peptides. Score 0.738 Round 4: 101 peptides, 9 chains. Longest chain 43 peptides. Score 0.729 Round 5: 103 peptides, 8 chains. Longest chain 33 peptides. Score 0.762 Taking the results from Round 5 Chains 8, Residues 95, Estimated correctness of the model 77.2 % 1 chains (32 residues) have been docked in sequence ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1768 restraints for refining 1021 atoms. 1271 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2354 (Rfree = 0.000) for 1021 atoms. Found 4 (4 requested) and removed 16 (4 requested) atoms. Cycle 32: After refmac, R = 0.2224 (Rfree = 0.000) for 1007 atoms. Found 4 (4 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.2128 (Rfree = 0.000) for 1005 atoms. Found 3 (4 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.2042 (Rfree = 0.000) for 1001 atoms. Found 1 (4 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2066 (Rfree = 0.000) for 995 atoms. Found 1 (4 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 2.91 Search for helices and strands: 0 residues in 0 chains, 1019 seeds are put forward Round 1: 93 peptides, 11 chains. Longest chain 20 peptides. Score 0.626 Round 2: 103 peptides, 9 chains. Longest chain 41 peptides. Score 0.739 Round 3: 106 peptides, 8 chains. Longest chain 42 peptides. Score 0.776 Round 4: 105 peptides, 8 chains. Longest chain 25 peptides. Score 0.771 Round 5: 106 peptides, 9 chains. Longest chain 28 peptides. Score 0.753 Taking the results from Round 3 Chains 8, Residues 98, Estimated correctness of the model 79.6 % 2 chains (53 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 122 A and 125 A 7 chains (99 residues) following loop building 1 chains (55 residues) in sequence following loop building ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1471 restraints for refining 996 atoms. 934 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2593 (Rfree = 0.000) for 996 atoms. Found 4 (4 requested) and removed 14 (4 requested) atoms. Cycle 37: After refmac, R = 0.2366 (Rfree = 0.000) for 980 atoms. Found 4 (4 requested) and removed 17 (4 requested) atoms. Cycle 38: After refmac, R = 0.2260 (Rfree = 0.000) for 964 atoms. Found 4 (4 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.2073 (Rfree = 0.000) for 956 atoms. Found 4 (4 requested) and removed 8 (4 requested) atoms. Cycle 40: After refmac, R = 0.1976 (Rfree = 0.000) for 950 atoms. Found 2 (4 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 2.93 Search for helices and strands: 0 residues in 0 chains, 995 seeds are put forward Round 1: 93 peptides, 10 chains. Longest chain 35 peptides. Score 0.656 Round 2: 94 peptides, 8 chains. Longest chain 39 peptides. Score 0.717 Round 3: 101 peptides, 9 chains. Longest chain 40 peptides. Score 0.729 Round 4: 95 peptides, 9 chains. Longest chain 32 peptides. Score 0.696 Round 5: 99 peptides, 8 chains. Longest chain 42 peptides. Score 0.743 Taking the results from Round 5 Chains 8, Residues 91, Estimated correctness of the model 73.7 % 1 chains (41 residues) have been docked in sequence ------------------------------------------------------ 3081 reflections ( 99.45 % complete ) and 1761 restraints for refining 1030 atoms. 1251 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2456 (Rfree = 0.000) for 1030 atoms. Found 4 (4 requested) and removed 17 (4 requested) atoms. Cycle 42: After refmac, R = 0.2419 (Rfree = 0.000) for 1014 atoms. Found 4 (4 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.2163 (Rfree = 0.000) for 1003 atoms. Found 4 (4 requested) and removed 7 (4 requested) atoms. Cycle 44: After refmac, R = 0.2382 (Rfree = 0.000) for 999 atoms. Found 4 (4 requested) and removed 14 (4 requested) atoms. Cycle 45: After refmac, R = 0.1967 (Rfree = 0.000) for 988 atoms. Found 4 (4 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.93 Search for helices and strands: 0 residues in 0 chains, 1017 seeds are put forward Round 1: 80 peptides, 8 chains. Longest chain 18 peptides. Score 0.632 Round 2: 88 peptides, 6 chains. Longest chain 40 peptides. Score 0.738 Round 3: 97 peptides, 10 chains. Longest chain 33 peptides. Score 0.680 Round 4: 95 peptides, 8 chains. Longest chain 41 peptides. Score 0.723 Round 5: 104 peptides, 9 chains. Longest chain 33 peptides. Score 0.744 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 95, Estimated correctness of the model 73.9 % 3 chains (53 residues) have been docked in sequence Sequence coverage is 55 % Consider running further cycles of model building using 2pim-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 77 A and 82 A 8 chains (98 residues) following loop building 2 chains (57 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3081 reflections ( 99.45 % complete ) and 1579 restraints for refining 1030 atoms. 1005 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2575 (Rfree = 0.000) for 1030 atoms. Found 0 (4 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2585 (Rfree = 0.000) for 1021 atoms. Found 0 (4 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2343 (Rfree = 0.000) for 1014 atoms. Found 0 (4 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2577 (Rfree = 0.000) for 1010 atoms. Found 0 (4 requested) and removed 2 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:56:22 GMT 2018 Job finished. TimeTaking 33.2 Used memory is bytes: 7735544