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 1vrb-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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/1vrb-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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 22:22:56 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/1vrb-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-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 972 and 0 Target number of residues in the AU: 972 Target solvent content: 0.6290 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-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: 19 Cell parameters: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 10944 target number of atoms Had to go as low as 0.60 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 48.979 3.200 Wilson plot Bfac: 66.01 23615 reflections ( 96.55 % complete ) and 0 restraints for refining 12142 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3344 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2649 (Rfree = 0.000) for 12142 atoms. Found 66 (108 requested) and removed 219 (54 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.19 Search for helices and strands: 0 residues in 0 chains, 12226 seeds are put forward NCS extension: 0 residues added, 12226 seeds are put forward Round 1: 518 peptides, 102 chains. Longest chain 16 peptides. Score 0.312 Round 2: 633 peptides, 109 chains. Longest chain 15 peptides. Score 0.412 Round 3: 671 peptides, 98 chains. Longest chain 25 peptides. Score 0.502 Round 4: 662 peptides, 102 chains. Longest chain 22 peptides. Score 0.475 Round 5: 695 peptides, 108 chains. Longest chain 21 peptides. Score 0.482 Taking the results from Round 3 Chains 101, Residues 573, Estimated correctness of the model 12.0 % 8 chains (45 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22762 restraints for refining 9983 atoms. 20425 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2638 (Rfree = 0.000) for 9983 atoms. Found 57 (89 requested) and removed 70 (44 requested) atoms. Cycle 2: After refmac, R = 0.2533 (Rfree = 0.000) for 9832 atoms. Found 46 (89 requested) and removed 56 (44 requested) atoms. Cycle 3: After refmac, R = 0.2469 (Rfree = 0.000) for 9749 atoms. Found 40 (88 requested) and removed 54 (44 requested) atoms. Cycle 4: After refmac, R = 0.2436 (Rfree = 0.000) for 9681 atoms. Found 33 (87 requested) and removed 49 (43 requested) atoms. Cycle 5: After refmac, R = 0.2373 (Rfree = 0.000) for 9618 atoms. Found 32 (86 requested) and removed 57 (43 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 3.19 Search for helices and strands: 0 residues in 0 chains, 9922 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 9953 seeds are put forward Round 1: 586 peptides, 105 chains. Longest chain 15 peptides. Score 0.378 Round 2: 683 peptides, 107 chains. Longest chain 23 peptides. Score 0.475 Round 3: 687 peptides, 99 chains. Longest chain 24 peptides. Score 0.514 Round 4: 665 peptides, 91 chains. Longest chain 28 peptides. Score 0.527 Round 5: 703 peptides, 99 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 5 Chains 102, Residues 604, Estimated correctness of the model 20.5 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 21509 restraints for refining 9724 atoms. 18962 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2545 (Rfree = 0.000) for 9724 atoms. Found 77 (87 requested) and removed 85 (43 requested) atoms. Cycle 7: After refmac, R = 0.2381 (Rfree = 0.000) for 9663 atoms. Found 29 (87 requested) and removed 59 (43 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2306 (Rfree = 0.000) for 9619 atoms. Found 23 (86 requested) and removed 52 (43 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2246 (Rfree = 0.000) for 9570 atoms. Found 17 (86 requested) and removed 47 (43 requested) atoms. Cycle 10: After refmac, R = 0.2203 (Rfree = 0.000) for 9520 atoms. Found 16 (85 requested) and removed 43 (42 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 9762 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 9774 seeds are put forward Round 1: 573 peptides, 103 chains. Longest chain 14 peptides. Score 0.373 Round 2: 666 peptides, 98 chains. Longest chain 18 peptides. Score 0.497 Round 3: 650 peptides, 87 chains. Longest chain 29 peptides. Score 0.530 Round 4: 675 peptides, 93 chains. Longest chain 27 peptides. Score 0.528 Round 5: 684 peptides, 91 chains. Longest chain 27 peptides. Score 0.545 Taking the results from Round 5 Chains 91, Residues 593, Estimated correctness of the model 25.4 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22262 restraints for refining 9725 atoms. 19901 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2427 (Rfree = 0.000) for 9725 atoms. Found 55 (87 requested) and removed 71 (43 requested) atoms. Cycle 12: After refmac, R = 0.2272 (Rfree = 0.000) for 9685 atoms. Found 31 (87 requested) and removed 51 (43 requested) atoms. Cycle 13: After refmac, R = 0.2176 (Rfree = 0.000) for 9649 atoms. Found 26 (86 requested) and removed 44 (43 requested) atoms. Cycle 14: After refmac, R = 0.2116 (Rfree = 0.000) for 9625 atoms. Found 11 (86 requested) and removed 43 (43 requested) atoms. Cycle 15: After refmac, R = 0.2072 (Rfree = 0.000) for 9587 atoms. Found 9 (86 requested) and removed 43 (43 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 9867 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 9892 seeds are put forward Round 1: 622 peptides, 105 chains. Longest chain 21 peptides. Score 0.419 Round 2: 689 peptides, 101 chains. Longest chain 25 peptides. Score 0.507 Round 3: 688 peptides, 97 chains. Longest chain 18 peptides. Score 0.523 Round 4: 725 peptides, 106 chains. Longest chain 18 peptides. Score 0.521 Round 5: 678 peptides, 98 chains. Longest chain 20 peptides. Score 0.509 Taking the results from Round 3 Chains 97, Residues 591, Estimated correctness of the model 18.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22707 restraints for refining 9781 atoms. 20440 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2330 (Rfree = 0.000) for 9781 atoms. Found 70 (87 requested) and removed 51 (43 requested) atoms. Cycle 17: After refmac, R = 0.2174 (Rfree = 0.000) for 9783 atoms. Found 23 (87 requested) and removed 45 (43 requested) atoms. Cycle 18: After refmac, R = 0.2121 (Rfree = 0.000) for 9739 atoms. Found 22 (87 requested) and removed 45 (43 requested) atoms. Cycle 19: After refmac, R = 0.2055 (Rfree = 0.000) for 9701 atoms. Found 22 (87 requested) and removed 43 (43 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2026 (Rfree = 0.000) for 9671 atoms. Found 10 (86 requested) and removed 44 (43 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 9922 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 9939 seeds are put forward Round 1: 602 peptides, 104 chains. Longest chain 18 peptides. Score 0.401 Round 2: 670 peptides, 97 chains. Longest chain 27 peptides. Score 0.506 Round 3: 680 peptides, 97 chains. Longest chain 18 peptides. Score 0.515 Round 4: 706 peptides, 99 chains. Longest chain 31 peptides. Score 0.532 Round 5: 716 peptides, 100 chains. Longest chain 20 peptides. Score 0.537 Taking the results from Round 5 Chains 100, Residues 616, Estimated correctness of the model 23.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22751 restraints for refining 9919 atoms. 20387 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2496 (Rfree = 0.000) for 9919 atoms. Found 74 (89 requested) and removed 53 (44 requested) atoms. Cycle 22: After refmac, R = 0.2236 (Rfree = 0.000) for 9932 atoms. Found 22 (89 requested) and removed 48 (44 requested) atoms. Cycle 23: After refmac, R = 0.2161 (Rfree = 0.000) for 9893 atoms. Found 16 (88 requested) and removed 44 (44 requested) atoms. Cycle 24: After refmac, R = 0.2111 (Rfree = 0.000) for 9854 atoms. Found 13 (88 requested) and removed 45 (44 requested) atoms. Cycle 25: After refmac, R = 0.2078 (Rfree = 0.000) for 9812 atoms. Found 11 (88 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 10064 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10078 seeds are put forward Round 1: 598 peptides, 104 chains. Longest chain 15 peptides. Score 0.397 Round 2: 673 peptides, 99 chains. Longest chain 17 peptides. Score 0.500 Round 3: 702 peptides, 101 chains. Longest chain 20 peptides. Score 0.520 Round 4: 698 peptides, 96 chains. Longest chain 23 peptides. Score 0.537 Round 5: 705 peptides, 93 chains. Longest chain 29 peptides. Score 0.556 Taking the results from Round 5 Chains 98, Residues 612, Estimated correctness of the model 28.7 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22247 restraints for refining 9991 atoms. 19673 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2341 (Rfree = 0.000) for 9991 atoms. Found 73 (89 requested) and removed 55 (44 requested) atoms. Cycle 27: After refmac, R = 0.2171 (Rfree = 0.000) for 9987 atoms. Found 29 (89 requested) and removed 50 (44 requested) atoms. Cycle 28: After refmac, R = 0.2106 (Rfree = 0.000) for 9944 atoms. Found 24 (89 requested) and removed 46 (44 requested) atoms. Cycle 29: After refmac, R = 0.2158 (Rfree = 0.000) for 9909 atoms. Found 14 (89 requested) and removed 45 (44 requested) atoms. Cycle 30: After refmac, R = 0.2029 (Rfree = 0.000) for 9859 atoms. Found 19 (88 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 10061 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 10084 seeds are put forward Round 1: 556 peptides, 94 chains. Longest chain 14 peptides. Score 0.398 Round 2: 643 peptides, 89 chains. Longest chain 17 peptides. Score 0.514 Round 3: 649 peptides, 95 chains. Longest chain 18 peptides. Score 0.494 Round 4: 648 peptides, 86 chains. Longest chain 27 peptides. Score 0.532 Round 5: 643 peptides, 89 chains. Longest chain 22 peptides. Score 0.514 Taking the results from Round 4 Chains 91, Residues 562, Estimated correctness of the model 21.4 % 7 chains (74 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 22246 restraints for refining 9988 atoms. 19807 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2315 (Rfree = 0.000) for 9988 atoms. Found 59 (89 requested) and removed 51 (44 requested) atoms. Cycle 32: After refmac, R = 0.2207 (Rfree = 0.000) for 9972 atoms. Found 24 (89 requested) and removed 50 (44 requested) atoms. Cycle 33: After refmac, R = 0.2175 (Rfree = 0.000) for 9936 atoms. Found 24 (89 requested) and removed 49 (44 requested) atoms. Cycle 34: After refmac, R = 0.2108 (Rfree = 0.000) for 9892 atoms. Found 23 (88 requested) and removed 46 (44 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2077 (Rfree = 0.000) for 9860 atoms. Found 10 (88 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.28 Search for helices and strands: 0 residues in 0 chains, 10087 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 10107 seeds are put forward Round 1: 538 peptides, 95 chains. Longest chain 15 peptides. Score 0.372 Round 2: 603 peptides, 88 chains. Longest chain 25 peptides. Score 0.478 Round 3: 618 peptides, 91 chains. Longest chain 19 peptides. Score 0.480 Round 4: 640 peptides, 92 chains. Longest chain 20 peptides. Score 0.498 Round 5: 615 peptides, 89 chains. Longest chain 22 peptides. Score 0.486 Taking the results from Round 4 Chains 92, Residues 548, Estimated correctness of the model 10.7 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 23067 restraints for refining 9989 atoms. 20923 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2284 (Rfree = 0.000) for 9989 atoms. Found 60 (89 requested) and removed 53 (44 requested) atoms. Cycle 37: After refmac, R = 0.2194 (Rfree = 0.000) for 9983 atoms. Found 31 (89 requested) and removed 45 (44 requested) atoms. Cycle 38: After refmac, R = 0.2103 (Rfree = 0.000) for 9957 atoms. Found 19 (89 requested) and removed 44 (44 requested) atoms. Cycle 39: After refmac, R = 0.2089 (Rfree = 0.000) for 9927 atoms. Found 18 (89 requested) and removed 44 (44 requested) atoms. Cycle 40: After refmac, R = 0.2035 (Rfree = 0.000) for 9892 atoms. Found 23 (88 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 10151 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 10171 seeds are put forward Round 1: 493 peptides, 95 chains. Longest chain 13 peptides. Score 0.318 Round 2: 545 peptides, 84 chains. Longest chain 16 peptides. Score 0.435 Round 3: 574 peptides, 89 chains. Longest chain 20 peptides. Score 0.443 Round 4: 583 peptides, 89 chains. Longest chain 16 peptides. Score 0.452 Round 5: 574 peptides, 84 chains. Longest chain 16 peptides. Score 0.466 Taking the results from Round 5 Chains 86, Residues 490, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 23615 reflections ( 96.55 % complete ) and 23160 restraints for refining 9990 atoms. 21165 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2263 (Rfree = 0.000) for 9990 atoms. Found 69 (89 requested) and removed 54 (44 requested) atoms. Cycle 42: After refmac, R = 0.2161 (Rfree = 0.000) for 9987 atoms. Found 38 (89 requested) and removed 46 (44 requested) atoms. Cycle 43: After refmac, R = 0.2123 (Rfree = 0.000) for 9974 atoms. Found 23 (89 requested) and removed 45 (44 requested) atoms. Cycle 44: After refmac, R = 0.2097 (Rfree = 0.000) for 9946 atoms. Found 25 (89 requested) and removed 48 (44 requested) atoms. Cycle 45: After refmac, R = 0.2099 (Rfree = 0.000) for 9912 atoms. Found 29 (89 requested) and removed 44 (44 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 10107 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 10123 seeds are put forward Round 1: 452 peptides, 88 chains. Longest chain 14 peptides. Score 0.304 Round 2: 511 peptides, 86 chains. Longest chain 15 peptides. Score 0.386 Round 3: 518 peptides, 85 chains. Longest chain 14 peptides. Score 0.400 Round 4: 548 peptides, 92 chains. Longest chain 14 peptides. Score 0.399 Round 5: 558 peptides, 89 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 90, Residues 469, Estimated correctness of the model 0.0 % 10 chains (43 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 90 chains (469 residues) following loop building 10 chains (43 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23615 reflections ( 96.55 % complete ) and 23132 restraints for refining 9990 atoms. 21234 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2248 (Rfree = 0.000) for 9990 atoms. Found 0 (89 requested) and removed 44 (44 requested) atoms. Cycle 47: After refmac, R = 0.2265 (Rfree = 0.000) for 9932 atoms. Found 0 (89 requested) and removed 28 (44 requested) atoms. Cycle 48: After refmac, R = 0.2274 (Rfree = 0.000) for 9889 atoms. Found 0 (88 requested) and removed 24 (44 requested) atoms. Cycle 49: After refmac, R = 0.2270 (Rfree = 0.000) for 9856 atoms. TimeTaking 224.03