null Sun 23 Dec 22:22:43 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 2fg9-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fg9-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-2.2-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/2fg9-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-2.2-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 22:22:53 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/2fg9-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fg9-2.2-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 161 and 0 Target number of residues in the AU: 161 Target solvent content: 0.5654 Checking the provided sequence file Detected sequence length: 178 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 178 Adjusted target solvent content: 0.52 Input MTZ file: 2fg9-2.2-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: 211 Cell parameters: 134.000 134.000 134.000 90.000 90.000 90.000 Input sequence file: 2fg9-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1424 target number of atoms Had to go as low as 0.55 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 1 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: 94.752 2.201 Wilson plot Bfac: 39.92 10741 reflections ( 99.89 % complete ) and 0 restraints for refining 1571 atoms. Observations/parameters ratio is 1.71 ------------------------------------------------------ Starting model: R = 0.3347 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2906 (Rfree = 0.000) for 1571 atoms. Found 13 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.56 2.49 Round 1: 126 peptides, 15 chains. Longest chain 24 peptides. Score 0.661 Round 2: 142 peptides, 11 chains. Longest chain 23 peptides. Score 0.804 Round 3: 147 peptides, 10 chains. Longest chain 34 peptides. Score 0.833 Round 4: 156 peptides, 7 chains. Longest chain 50 peptides. Score 0.890 Round 5: 158 peptides, 7 chains. Longest chain 57 peptides. Score 0.894 Taking the results from Round 5 Chains 7, Residues 151, Estimated correctness of the model 98.4 % 4 chains (122 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 106 A 6 chains (157 residues) following loop building 3 chains (128 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1875 restraints for refining 1518 atoms. 704 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3346 (Rfree = 0.000) for 1518 atoms. Found 36 (39 requested) and removed 23 (19 requested) atoms. Cycle 2: After refmac, R = 0.3025 (Rfree = 0.000) for 1512 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. Cycle 3: After refmac, R = 0.2878 (Rfree = 0.000) for 1485 atoms. Found 17 (37 requested) and removed 19 (19 requested) atoms. Cycle 4: After refmac, R = 0.2773 (Rfree = 0.000) for 1476 atoms. Found 13 (36 requested) and removed 19 (19 requested) atoms. Cycle 5: After refmac, R = 0.2735 (Rfree = 0.000) for 1459 atoms. Found 16 (35 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.52 2.45 Round 1: 157 peptides, 10 chains. Longest chain 43 peptides. Score 0.858 Round 2: 162 peptides, 6 chains. Longest chain 55 peptides. Score 0.910 Round 3: 159 peptides, 7 chains. Longest chain 50 peptides. Score 0.895 Round 4: 161 peptides, 7 chains. Longest chain 83 peptides. Score 0.899 Round 5: 153 peptides, 7 chains. Longest chain 44 peptides. Score 0.885 Taking the results from Round 2 Chains 6, Residues 156, Estimated correctness of the model 98.8 % 4 chains (146 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 107 A Built loop between residues 123 A and 126 A 4 chains (165 residues) following loop building 2 chains (155 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1662 restraints for refining 1511 atoms. 337 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3107 (Rfree = 0.000) for 1511 atoms. Found 23 (35 requested) and removed 28 (19 requested) atoms. Cycle 7: After refmac, R = 0.2788 (Rfree = 0.000) for 1500 atoms. Found 10 (34 requested) and removed 20 (19 requested) atoms. Cycle 8: After refmac, R = 0.2676 (Rfree = 0.000) for 1485 atoms. Found 12 (33 requested) and removed 20 (19 requested) atoms. Cycle 9: After refmac, R = 0.2574 (Rfree = 0.000) for 1475 atoms. Found 6 (32 requested) and removed 19 (19 requested) atoms. Cycle 10: After refmac, R = 0.2538 (Rfree = 0.000) for 1462 atoms. Found 11 (31 requested) and removed 16 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.44 2.38 Round 1: 158 peptides, 5 chains. Longest chain 55 peptides. Score 0.914 Round 2: 161 peptides, 5 chains. Longest chain 43 peptides. Score 0.918 Round 3: 155 peptides, 8 chains. Longest chain 50 peptides. Score 0.877 Round 4: 153 peptides, 6 chains. Longest chain 73 peptides. Score 0.896 Round 5: 160 peptides, 3 chains. Longest chain 71 peptides. Score 0.934 Taking the results from Round 5 Chains 6, Residues 157, Estimated correctness of the model 99.3 % 4 chains (151 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 A and 65 A Built loop between residues 98 A and 105 A Built loop between residues 134 A and 139 A 1 chains (166 residues) following loop building 1 chains (166 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1586 restraints for refining 1506 atoms. 215 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3127 (Rfree = 0.000) for 1506 atoms. Found 23 (31 requested) and removed 26 (19 requested) atoms. Cycle 12: After refmac, R = 0.2804 (Rfree = 0.000) for 1500 atoms. Found 13 (30 requested) and removed 19 (19 requested) atoms. Cycle 13: After refmac, R = 0.2667 (Rfree = 0.000) for 1492 atoms. Found 18 (29 requested) and removed 19 (19 requested) atoms. Cycle 14: After refmac, R = 0.2589 (Rfree = 0.000) for 1490 atoms. Found 11 (28 requested) and removed 19 (19 requested) atoms. Cycle 15: After refmac, R = 0.2520 (Rfree = 0.000) for 1479 atoms. Found 16 (27 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.44 2.38 Round 1: 161 peptides, 5 chains. Longest chain 56 peptides. Score 0.918 Round 2: 163 peptides, 5 chains. Longest chain 72 peptides. Score 0.921 Round 3: 165 peptides, 3 chains. Longest chain 73 peptides. Score 0.940 Round 4: 161 peptides, 5 chains. Longest chain 43 peptides. Score 0.918 Round 5: 161 peptides, 4 chains. Longest chain 71 peptides. Score 0.927 Taking the results from Round 3 Chains 3, Residues 162, Estimated correctness of the model 99.4 % 3 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 76 A Built loop between residues 101 A and 105 A 1 chains (169 residues) following loop building 1 chains (169 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1528 restraints for refining 1504 atoms. 126 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3020 (Rfree = 0.000) for 1504 atoms. Found 21 (27 requested) and removed 22 (19 requested) atoms. Cycle 17: After refmac, R = 0.2768 (Rfree = 0.000) for 1499 atoms. Found 18 (27 requested) and removed 19 (19 requested) atoms. Cycle 18: After refmac, R = 0.2633 (Rfree = 0.000) for 1496 atoms. Found 17 (26 requested) and removed 19 (19 requested) atoms. Cycle 19: After refmac, R = 0.2539 (Rfree = 0.000) for 1494 atoms. Found 19 (24 requested) and removed 19 (19 requested) atoms. Cycle 20: After refmac, R = 0.2509 (Rfree = 0.000) for 1492 atoms. Found 17 (24 requested) and removed 17 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.49 2.42 Round 1: 157 peptides, 6 chains. Longest chain 43 peptides. Score 0.902 Round 2: 163 peptides, 4 chains. Longest chain 68 peptides. Score 0.929 Round 3: 164 peptides, 5 chains. Longest chain 44 peptides. Score 0.922 Round 4: 160 peptides, 5 chains. Longest chain 44 peptides. Score 0.917 Round 5: 159 peptides, 7 chains. Longest chain 44 peptides. Score 0.895 Taking the results from Round 2 Chains 4, Residues 159, Estimated correctness of the model 99.2 % 4 chains (159 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 A and 34 A Built loop between residues 100 A and 105 A Built loop between residues 117 A and 121 A 1 chains (168 residues) following loop building 1 chains (168 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1538 restraints for refining 1518 atoms. 147 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2933 (Rfree = 0.000) for 1518 atoms. Found 19 (23 requested) and removed 20 (19 requested) atoms. Cycle 22: After refmac, R = 0.2622 (Rfree = 0.000) for 1511 atoms. Found 17 (23 requested) and removed 19 (19 requested) atoms. Cycle 23: After refmac, R = 0.2526 (Rfree = 0.000) for 1506 atoms. Found 15 (22 requested) and removed 19 (19 requested) atoms. Cycle 24: After refmac, R = 0.2426 (Rfree = 0.000) for 1500 atoms. Found 21 (21 requested) and removed 17 (19 requested) atoms. Cycle 25: After refmac, R = 0.2417 (Rfree = 0.000) for 1503 atoms. Found 13 (20 requested) and removed 17 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.51 2.44 Round 1: 164 peptides, 5 chains. Longest chain 68 peptides. Score 0.922 Round 2: 162 peptides, 5 chains. Longest chain 58 peptides. Score 0.919 Round 3: 161 peptides, 4 chains. Longest chain 68 peptides. Score 0.927 Round 4: 163 peptides, 4 chains. Longest chain 72 peptides. Score 0.929 Round 5: 166 peptides, 4 chains. Longest chain 69 peptides. Score 0.933 Taking the results from Round 5 Chains 6, Residues 162, Estimated correctness of the model 99.3 % 4 chains (155 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 A and 38 A Built loop between residues 101 A and 105 A Built loop between residues 123 A and 129 A 1 chains (169 residues) following loop building 1 chains (169 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1538 restraints for refining 1520 atoms. 136 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2898 (Rfree = 0.000) for 1520 atoms. Found 19 (19 requested) and removed 23 (19 requested) atoms. Cycle 27: After refmac, R = 0.2643 (Rfree = 0.000) for 1513 atoms. Found 18 (19 requested) and removed 19 (19 requested) atoms. Cycle 28: After refmac, R = 0.2526 (Rfree = 0.000) for 1511 atoms. Found 15 (19 requested) and removed 19 (19 requested) atoms. Cycle 29: After refmac, R = 0.2491 (Rfree = 0.000) for 1507 atoms. Found 16 (19 requested) and removed 19 (19 requested) atoms. Cycle 30: After refmac, R = 0.2436 (Rfree = 0.000) for 1503 atoms. Found 19 (19 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.50 2.43 Round 1: 162 peptides, 6 chains. Longest chain 51 peptides. Score 0.910 Round 2: 163 peptides, 5 chains. Longest chain 64 peptides. Score 0.921 Round 3: 163 peptides, 6 chains. Longest chain 43 peptides. Score 0.912 Round 4: 165 peptides, 3 chains. Longest chain 71 peptides. Score 0.940 Round 5: 163 peptides, 4 chains. Longest chain 72 peptides. Score 0.929 Taking the results from Round 4 Chains 3, Residues 162, Estimated correctness of the model 99.4 % 3 chains (162 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 66 A Built loop between residues 101 A and 106 A 1 chains (168 residues) following loop building 1 chains (168 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1542 restraints for refining 1513 atoms. 149 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2894 (Rfree = 0.000) for 1513 atoms. Found 15 (19 requested) and removed 23 (19 requested) atoms. Cycle 32: After refmac, R = 0.2671 (Rfree = 0.000) for 1504 atoms. Found 18 (19 requested) and removed 19 (19 requested) atoms. Cycle 33: After refmac, R = 0.2550 (Rfree = 0.000) for 1503 atoms. Found 14 (19 requested) and removed 19 (19 requested) atoms. Cycle 34: After refmac, R = 0.2484 (Rfree = 0.000) for 1495 atoms. Found 16 (19 requested) and removed 21 (19 requested) atoms. Cycle 35: After refmac, R = 0.2473 (Rfree = 0.000) for 1488 atoms. Found 19 (19 requested) and removed 17 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.49 2.42 Round 1: 163 peptides, 5 chains. Longest chain 72 peptides. Score 0.921 Round 2: 162 peptides, 6 chains. Longest chain 56 peptides. Score 0.910 Round 3: 164 peptides, 4 chains. Longest chain 60 peptides. Score 0.931 Round 4: 154 peptides, 7 chains. Longest chain 58 peptides. Score 0.886 Round 5: 162 peptides, 7 chains. Longest chain 38 peptides. Score 0.900 Taking the results from Round 3 Chains 5, Residues 160, Estimated correctness of the model 99.3 % 4 chains (156 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 66 A Built loop between residues 99 A and 107 A Built loop between residues 161 A and 164 A 1 chains (168 residues) following loop building 1 chains (168 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1540 restraints for refining 1520 atoms. 149 conditional restraints added. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2939 (Rfree = 0.000) for 1520 atoms. Found 19 (19 requested) and removed 28 (19 requested) atoms. Cycle 37: After refmac, R = 0.2682 (Rfree = 0.000) for 1509 atoms. Found 19 (19 requested) and removed 19 (19 requested) atoms. Cycle 38: After refmac, R = 0.2547 (Rfree = 0.000) for 1507 atoms. Found 19 (19 requested) and removed 19 (19 requested) atoms. Cycle 39: After refmac, R = 0.2471 (Rfree = 0.000) for 1507 atoms. Found 18 (19 requested) and removed 19 (19 requested) atoms. Cycle 40: After refmac, R = 0.2463 (Rfree = 0.000) for 1503 atoms. Found 15 (19 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.50 2.43 Round 1: 153 peptides, 8 chains. Longest chain 42 peptides. Score 0.873 Round 2: 160 peptides, 4 chains. Longest chain 73 peptides. Score 0.926 Round 3: 162 peptides, 3 chains. Longest chain 73 peptides. Score 0.937 Round 4: 159 peptides, 7 chains. Longest chain 48 peptides. Score 0.895 Round 5: 156 peptides, 8 chains. Longest chain 30 peptides. Score 0.879 Taking the results from Round 3 Chains 4, Residues 159, Estimated correctness of the model 99.4 % 3 chains (158 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 65 A Built loop between residues 101 A and 105 A 1 chains (168 residues) following loop building 1 chains (168 residues) in sequence following loop building ------------------------------------------------------ 10741 reflections ( 99.89 % complete ) and 1541 restraints for refining 1538 atoms. 150 conditional restraints added. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2880 (Rfree = 0.000) for 1538 atoms. Found 20 (20 requested) and removed 27 (20 requested) atoms. Cycle 42: After refmac, R = 0.2661 (Rfree = 0.000) for 1526 atoms. Found 17 (19 requested) and removed 19 (19 requested) atoms. Cycle 43: After refmac, R = 0.2567 (Rfree = 0.000) for 1518 atoms. Found 15 (19 requested) and removed 19 (19 requested) atoms. Cycle 44: After refmac, R = 0.2493 (Rfree = 0.000) for 1514 atoms. Found 14 (19 requested) and removed 19 (19 requested) atoms. Cycle 45: After refmac, R = 0.2458 (Rfree = 0.000) for 1509 atoms. Found 13 (19 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.48 2.41 Round 1: 161 peptides, 5 chains. Longest chain 43 peptides. Score 0.918 Round 2: 162 peptides, 5 chains. Longest chain 58 peptides. Score 0.919 Round 3: 159 peptides, 6 chains. Longest chain 58 peptides. Score 0.905 Round 4: 159 peptides, 7 chains. Longest chain 44 peptides. Score 0.895 Round 5: 161 peptides, 6 chains. Longest chain 46 peptides. Score 0.909 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 157, Estimated correctness of the model 99.0 % 5 chains (156 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 27 A and 31 A Built loop between residues 75 A and 79 A Built loop between residues 101 A and 105 A Built loop between residues 116 A and 119 A 1 chains (167 residues) following loop building 1 chains (167 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 10741 reflections ( 99.89 % complete ) and 1382 restraints for refining 1352 atoms. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3340 (Rfree = 0.000) for 1352 atoms. Found 7 (17 requested) and removed 0 (17 requested) atoms. Cycle 47: After refmac, R = 0.3144 (Rfree = 0.000) for 1352 atoms. Found 6 (17 requested) and removed 0 (17 requested) atoms. Cycle 48: After refmac, R = 0.3018 (Rfree = 0.000) for 1352 atoms. Found 2 (17 requested) and removed 0 (17 requested) atoms. Cycle 49: After refmac, R = 0.2893 (Rfree = 0.000) for 1352 atoms. Found 1 (17 requested) and removed 0 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:25:34 GMT 2018 Job finished. TimeTaking 62.84 Used memory is bytes: 15430672