null Mon 24 Dec 07:59:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr5-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:59:46 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/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-parrot-noncs/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 1020 and 0 Target number of residues in the AU: 1020 Target solvent content: 0.6477 Checking the provided sequence file Detected sequence length: 547 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1094 Adjusted target solvent content: 0.62 Input MTZ file: 1vr5-3.6-parrot-noncs.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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 8752 target number of atoms Had to go as low as 0.90 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: 115.780 3.600 Wilson plot Bfac: 76.58 18746 reflections ( 99.62 % complete ) and 0 restraints for refining 9668 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3225 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2817 (Rfree = 0.000) for 9668 atoms. Found 62 (62 requested) and removed 38 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 2.95 Search for helices and strands: 0 residues in 0 chains, 9869 seeds are put forward NCS extension: 0 residues added, 9869 seeds are put forward Round 1: 694 peptides, 103 chains. Longest chain 22 peptides. Score 0.480 Round 2: 770 peptides, 90 chains. Longest chain 26 peptides. Score 0.595 Round 3: 776 peptides, 86 chains. Longest chain 27 peptides. Score 0.614 Round 4: 793 peptides, 81 chains. Longest chain 33 peptides. Score 0.644 Round 5: 782 peptides, 70 chains. Longest chain 28 peptides. Score 0.672 Taking the results from Round 5 Chains 75, Residues 712, Estimated correctness of the model 40.6 % 6 chains (91 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16022 restraints for refining 8052 atoms. 12843 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2589 (Rfree = 0.000) for 8052 atoms. Found 51 (51 requested) and removed 42 (25 requested) atoms. Cycle 2: After refmac, R = 0.2443 (Rfree = 0.000) for 7880 atoms. Found 44 (51 requested) and removed 35 (25 requested) atoms. Cycle 3: After refmac, R = 0.2320 (Rfree = 0.000) for 7795 atoms. Found 50 (50 requested) and removed 31 (25 requested) atoms. Cycle 4: After refmac, R = 0.2263 (Rfree = 0.000) for 7757 atoms. Found 45 (50 requested) and removed 29 (25 requested) atoms. Cycle 5: After refmac, R = 0.2231 (Rfree = 0.000) for 7723 atoms. Found 45 (49 requested) and removed 34 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 2.92 Search for helices and strands: 0 residues in 0 chains, 7974 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 8011 seeds are put forward Round 1: 757 peptides, 93 chains. Longest chain 25 peptides. Score 0.574 Round 2: 791 peptides, 81 chains. Longest chain 32 peptides. Score 0.642 Round 3: 820 peptides, 80 chains. Longest chain 28 peptides. Score 0.665 Round 4: 816 peptides, 76 chains. Longest chain 31 peptides. Score 0.675 Round 5: 836 peptides, 81 chains. Longest chain 30 peptides. Score 0.673 Taking the results from Round 4 Chains 86, Residues 740, Estimated correctness of the model 41.6 % 10 chains (117 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15342 restraints for refining 7933 atoms. 11974 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2372 (Rfree = 0.000) for 7933 atoms. Found 48 (50 requested) and removed 48 (25 requested) atoms. Cycle 7: After refmac, R = 0.2225 (Rfree = 0.000) for 7845 atoms. Found 32 (50 requested) and removed 33 (25 requested) atoms. Cycle 8: After refmac, R = 0.2108 (Rfree = 0.000) for 7814 atoms. Found 24 (50 requested) and removed 38 (25 requested) atoms. Cycle 9: After refmac, R = 0.2041 (Rfree = 0.000) for 7781 atoms. Found 20 (50 requested) and removed 39 (25 requested) atoms. Cycle 10: After refmac, R = 0.1985 (Rfree = 0.000) for 7757 atoms. Found 17 (49 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.94 Search for helices and strands: 0 residues in 0 chains, 7962 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7977 seeds are put forward Round 1: 764 peptides, 89 chains. Longest chain 29 peptides. Score 0.594 Round 2: 807 peptides, 91 chains. Longest chain 30 peptides. Score 0.620 Round 3: 809 peptides, 84 chains. Longest chain 29 peptides. Score 0.645 Round 4: 797 peptides, 79 chains. Longest chain 36 peptides. Score 0.653 Round 5: 821 peptides, 81 chains. Longest chain 36 peptides. Score 0.663 Taking the results from Round 5 Chains 87, Residues 740, Estimated correctness of the model 37.6 % 9 chains (129 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15394 restraints for refining 7934 atoms. 11969 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2408 (Rfree = 0.000) for 7934 atoms. Found 50 (50 requested) and removed 51 (25 requested) atoms. Cycle 12: After refmac, R = 0.2231 (Rfree = 0.000) for 7864 atoms. Found 43 (50 requested) and removed 32 (25 requested) atoms. Cycle 13: After refmac, R = 0.2159 (Rfree = 0.000) for 7847 atoms. Found 22 (50 requested) and removed 32 (25 requested) atoms. Cycle 14: After refmac, R = 0.2093 (Rfree = 0.000) for 7813 atoms. Found 18 (50 requested) and removed 28 (25 requested) atoms. Cycle 15: After refmac, R = 0.2069 (Rfree = 0.000) for 7787 atoms. Found 16 (50 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 2.95 Search for helices and strands: 0 residues in 0 chains, 8013 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 8041 seeds are put forward Round 1: 719 peptides, 93 chains. Longest chain 33 peptides. Score 0.543 Round 2: 767 peptides, 75 chains. Longest chain 36 peptides. Score 0.645 Round 3: 802 peptides, 81 chains. Longest chain 30 peptides. Score 0.650 Round 4: 802 peptides, 75 chains. Longest chain 35 peptides. Score 0.669 Round 5: 791 peptides, 76 chains. Longest chain 31 peptides. Score 0.659 Taking the results from Round 4 Chains 79, Residues 727, Estimated correctness of the model 39.6 % 7 chains (87 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15934 restraints for refining 7931 atoms. 12735 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2345 (Rfree = 0.000) for 7931 atoms. Found 50 (50 requested) and removed 43 (25 requested) atoms. Cycle 17: After refmac, R = 0.2194 (Rfree = 0.000) for 7890 atoms. Found 37 (50 requested) and removed 35 (25 requested) atoms. Cycle 18: After refmac, R = 0.2070 (Rfree = 0.000) for 7865 atoms. Found 32 (50 requested) and removed 36 (25 requested) atoms. Cycle 19: After refmac, R = 0.2009 (Rfree = 0.000) for 7843 atoms. Found 22 (50 requested) and removed 31 (25 requested) atoms. Cycle 20: After refmac, R = 0.1944 (Rfree = 0.000) for 7821 atoms. Found 16 (50 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 8063 seeds are put forward NCS extension: 34 residues added (8 deleted due to clashes), 8097 seeds are put forward Round 1: 724 peptides, 92 chains. Longest chain 31 peptides. Score 0.551 Round 2: 769 peptides, 75 chains. Longest chain 30 peptides. Score 0.647 Round 3: 786 peptides, 74 chains. Longest chain 53 peptides. Score 0.662 Round 4: 793 peptides, 78 chains. Longest chain 40 peptides. Score 0.653 Round 5: 777 peptides, 79 chains. Longest chain 36 peptides. Score 0.639 Taking the results from Round 3 Chains 83, Residues 712, Estimated correctness of the model 37.3 % 9 chains (151 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15334 restraints for refining 7933 atoms. 11886 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2391 (Rfree = 0.000) for 7933 atoms. Found 50 (50 requested) and removed 42 (25 requested) atoms. Cycle 22: After refmac, R = 0.2292 (Rfree = 0.000) for 7887 atoms. Found 33 (50 requested) and removed 35 (25 requested) atoms. Cycle 23: After refmac, R = 0.2165 (Rfree = 0.000) for 7851 atoms. Found 14 (50 requested) and removed 30 (25 requested) atoms. Cycle 24: After refmac, R = 0.2122 (Rfree = 0.000) for 7817 atoms. Found 15 (50 requested) and removed 31 (25 requested) atoms. Cycle 25: After refmac, R = 0.2049 (Rfree = 0.000) for 7789 atoms. Found 12 (50 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 2.98 Search for helices and strands: 0 residues in 0 chains, 7987 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 8006 seeds are put forward Round 1: 690 peptides, 89 chains. Longest chain 31 peptides. Score 0.533 Round 2: 765 peptides, 78 chains. Longest chain 65 peptides. Score 0.634 Round 3: 762 peptides, 72 chains. Longest chain 33 peptides. Score 0.652 Round 4: 768 peptides, 78 chains. Longest chain 48 peptides. Score 0.636 Round 5: 786 peptides, 82 chains. Longest chain 32 peptides. Score 0.635 Taking the results from Round 3 Chains 72, Residues 690, Estimated correctness of the model 33.9 % 4 chains (70 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16258 restraints for refining 7933 atoms. 13263 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2262 (Rfree = 0.000) for 7933 atoms. Found 50 (50 requested) and removed 38 (25 requested) atoms. Cycle 27: After refmac, R = 0.2139 (Rfree = 0.000) for 7905 atoms. Found 33 (50 requested) and removed 31 (25 requested) atoms. Cycle 28: After refmac, R = 0.2101 (Rfree = 0.000) for 7896 atoms. Found 28 (50 requested) and removed 31 (25 requested) atoms. Cycle 29: After refmac, R = 0.2088 (Rfree = 0.000) for 7884 atoms. Found 39 (50 requested) and removed 31 (25 requested) atoms. Cycle 30: After refmac, R = 0.1985 (Rfree = 0.000) for 7886 atoms. Found 33 (50 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 8108 seeds are put forward NCS extension: 12 residues added (17 deleted due to clashes), 8120 seeds are put forward Round 1: 623 peptides, 89 chains. Longest chain 21 peptides. Score 0.472 Round 2: 686 peptides, 77 chains. Longest chain 24 peptides. Score 0.576 Round 3: 705 peptides, 73 chains. Longest chain 26 peptides. Score 0.606 Round 4: 704 peptides, 80 chains. Longest chain 26 peptides. Score 0.580 Round 5: 713 peptides, 76 chains. Longest chain 29 peptides. Score 0.602 Taking the results from Round 3 Chains 78, Residues 632, Estimated correctness of the model 17.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 17075 restraints for refining 7934 atoms. 14492 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2122 (Rfree = 0.000) for 7934 atoms. Found 46 (50 requested) and removed 28 (25 requested) atoms. Cycle 32: After refmac, R = 0.2035 (Rfree = 0.000) for 7922 atoms. Found 45 (51 requested) and removed 30 (25 requested) atoms. Cycle 33: After refmac, R = 0.2027 (Rfree = 0.000) for 7918 atoms. Found 45 (50 requested) and removed 30 (25 requested) atoms. Cycle 34: After refmac, R = 0.1980 (Rfree = 0.000) for 7915 atoms. Found 43 (50 requested) and removed 27 (25 requested) atoms. Cycle 35: After refmac, R = 0.1957 (Rfree = 0.000) for 7923 atoms. Found 34 (50 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 8185 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 8214 seeds are put forward Round 1: 635 peptides, 99 chains. Longest chain 17 peptides. Score 0.441 Round 2: 684 peptides, 84 chains. Longest chain 24 peptides. Score 0.548 Round 3: 695 peptides, 83 chains. Longest chain 20 peptides. Score 0.561 Round 4: 718 peptides, 83 chains. Longest chain 23 peptides. Score 0.580 Round 5: 722 peptides, 82 chains. Longest chain 24 peptides. Score 0.587 Taking the results from Round 5 Chains 87, Residues 640, Estimated correctness of the model 9.5 % 5 chains (58 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16747 restraints for refining 7932 atoms. 14043 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2278 (Rfree = 0.000) for 7932 atoms. Found 50 (50 requested) and removed 31 (25 requested) atoms. Cycle 37: After refmac, R = 0.2142 (Rfree = 0.000) for 7925 atoms. Found 35 (51 requested) and removed 30 (25 requested) atoms. Cycle 38: After refmac, R = 0.2047 (Rfree = 0.000) for 7913 atoms. Found 21 (50 requested) and removed 29 (25 requested) atoms. Cycle 39: After refmac, R = 0.2013 (Rfree = 0.000) for 7892 atoms. Found 23 (50 requested) and removed 25 (25 requested) atoms. Cycle 40: After refmac, R = 0.1933 (Rfree = 0.000) for 7878 atoms. Found 17 (50 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 2.99 Search for helices and strands: 0 residues in 0 chains, 8073 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 8102 seeds are put forward Round 1: 627 peptides, 102 chains. Longest chain 15 peptides. Score 0.419 Round 2: 702 peptides, 90 chains. Longest chain 26 peptides. Score 0.540 Round 3: 702 peptides, 80 chains. Longest chain 24 peptides. Score 0.578 Round 4: 670 peptides, 76 chains. Longest chain 24 peptides. Score 0.567 Round 5: 696 peptides, 79 chains. Longest chain 28 peptides. Score 0.577 Taking the results from Round 3 Chains 83, Residues 622, Estimated correctness of the model 5.9 % 6 chains (65 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16930 restraints for refining 7933 atoms. 14226 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2252 (Rfree = 0.000) for 7933 atoms. Found 45 (50 requested) and removed 34 (25 requested) atoms. Cycle 42: After refmac, R = 0.2093 (Rfree = 0.000) for 7913 atoms. Found 23 (50 requested) and removed 33 (25 requested) atoms. Cycle 43: After refmac, R = 0.2060 (Rfree = 0.000) for 7890 atoms. Found 13 (50 requested) and removed 25 (25 requested) atoms. Cycle 44: After refmac, R = 0.2041 (Rfree = 0.000) for 7875 atoms. Found 12 (50 requested) and removed 25 (25 requested) atoms. Cycle 45: After refmac, R = 0.1985 (Rfree = 0.000) for 7855 atoms. Found 21 (50 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 2.98 Search for helices and strands: 0 residues in 0 chains, 8065 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8083 seeds are put forward Round 1: 604 peptides, 91 chains. Longest chain 20 peptides. Score 0.445 Round 2: 651 peptides, 81 chains. Longest chain 33 peptides. Score 0.531 Round 3: 659 peptides, 76 chains. Longest chain 29 peptides. Score 0.558 Round 4: 651 peptides, 80 chains. Longest chain 24 peptides. Score 0.535 Round 5: 670 peptides, 75 chains. Longest chain 36 peptides. Score 0.571 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 79, Residues 595, Estimated correctness of the model 3.0 % 6 chains (122 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 79 chains (595 residues) following loop building 6 chains (122 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18746 reflections ( 99.62 % complete ) and 16326 restraints for refining 7933 atoms. 13468 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2311 (Rfree = 0.000) for 7933 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 47: After refmac, R = 0.2146 (Rfree = 0.000) for 7869 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2140 (Rfree = 0.000) for 7834 atoms. Found 0 (50 requested) and removed 22 (25 requested) atoms. Cycle 49: After refmac, R = 0.2096 (Rfree = 0.000) for 7803 atoms. Found 0 (50 requested) and removed 11 (25 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:34:57 GMT 2018 Job finished. TimeTaking 95.26 Used memory is bytes: 16101856