Tue 25 Dec 19:27:57 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 1vr5-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-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/1vr5-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-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 ============================================================ Tue 25 Dec 19:28:07 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/1vr5-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-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 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-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-3.6-parrot-hancs.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 9712 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3167 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2858 (Rfree = 0.000) for 9712 atoms. Found 62 (62 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 2.97 Search for helices and strands: 0 residues in 0 chains, 9886 seeds are put forward NCS extension: 0 residues added, 9886 seeds are put forward Round 1: 677 peptides, 104 chains. Longest chain 19 peptides. Score 0.460 Round 2: 773 peptides, 92 chains. Longest chain 23 peptides. Score 0.591 Round 3: 818 peptides, 80 chains. Longest chain 30 peptides. Score 0.664 Round 4: 820 peptides, 78 chains. Longest chain 29 peptides. Score 0.672 Round 5: 819 peptides, 77 chains. Longest chain 31 peptides. Score 0.674 Taking the results from Round 5 Chains 87, Residues 742, Estimated correctness of the model 41.3 % 10 chains (143 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 18746 reflections ( 99.62 % complete ) and 15467 restraints for refining 8084 atoms. 11972 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2461 (Rfree = 0.000) for 8084 atoms. Found 51 (51 requested) and removed 55 (25 requested) atoms. Cycle 2: After refmac, R = 0.2260 (Rfree = 0.000) for 7927 atoms. Found 34 (51 requested) and removed 46 (25 requested) atoms. Cycle 3: After refmac, R = 0.2130 (Rfree = 0.000) for 7853 atoms. Found 31 (50 requested) and removed 32 (25 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 7819 atoms. Found 28 (50 requested) and removed 37 (25 requested) atoms. Cycle 5: After refmac, R = 0.2070 (Rfree = 0.000) for 7776 atoms. Found 26 (50 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 2.95 Search for helices and strands: 0 residues in 0 chains, 8014 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 8036 seeds are put forward Round 1: 781 peptides, 81 chains. Longest chain 35 peptides. Score 0.635 Round 2: 789 peptides, 75 chains. Longest chain 42 peptides. Score 0.660 Round 3: 793 peptides, 76 chains. Longest chain 30 peptides. Score 0.660 Round 4: 809 peptides, 78 chains. Longest chain 33 peptides. Score 0.664 Round 5: 816 peptides, 74 chains. Longest chain 36 peptides. Score 0.682 Taking the results from Round 5 Chains 93, Residues 742, Estimated correctness of the model 43.9 % 13 chains (187 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 14800 restraints for refining 7932 atoms. 11110 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2367 (Rfree = 0.000) for 7932 atoms. Found 50 (50 requested) and removed 55 (25 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2225 (Rfree = 0.000) for 7849 atoms. Found 48 (50 requested) and removed 36 (25 requested) atoms. Cycle 8: After refmac, R = 0.2103 (Rfree = 0.000) for 7844 atoms. Found 28 (50 requested) and removed 34 (25 requested) atoms. Cycle 9: After refmac, R = 0.2051 (Rfree = 0.000) for 7809 atoms. Found 23 (50 requested) and removed 36 (25 requested) atoms. Cycle 10: After refmac, R = 0.1971 (Rfree = 0.000) for 7777 atoms. Found 18 (50 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 8024 seeds are put forward NCS extension: 36 residues added (4 deleted due to clashes), 8060 seeds are put forward Round 1: 736 peptides, 97 chains. Longest chain 29 peptides. Score 0.542 Round 2: 785 peptides, 81 chains. Longest chain 39 peptides. Score 0.638 Round 3: 780 peptides, 80 chains. Longest chain 35 peptides. Score 0.638 Round 4: 795 peptides, 85 chains. Longest chain 32 peptides. Score 0.632 Round 5: 797 peptides, 75 chains. Longest chain 35 peptides. Score 0.666 Taking the results from Round 5 Chains 83, Residues 722, Estimated correctness of the model 38.6 % 8 chains (124 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15474 restraints for refining 7933 atoms. 12096 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2307 (Rfree = 0.000) for 7933 atoms. Found 50 (50 requested) and removed 55 (25 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2079 (Rfree = 0.000) for 7886 atoms. Found 26 (50 requested) and removed 38 (25 requested) atoms. Cycle 13: After refmac, R = 0.1990 (Rfree = 0.000) for 7850 atoms. Found 29 (50 requested) and removed 36 (25 requested) atoms. Cycle 14: After refmac, R = 0.1914 (Rfree = 0.000) for 7830 atoms. Found 21 (50 requested) and removed 32 (25 requested) atoms. Cycle 15: After refmac, R = 0.1853 (Rfree = 0.000) for 7803 atoms. Found 21 (50 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.92 Search for helices and strands: 0 residues in 0 chains, 8026 seeds are put forward NCS extension: 40 residues added (0 deleted due to clashes), 8066 seeds are put forward Round 1: 699 peptides, 97 chains. Longest chain 20 peptides. Score 0.509 Round 2: 736 peptides, 80 chains. Longest chain 31 peptides. Score 0.605 Round 3: 773 peptides, 88 chains. Longest chain 29 peptides. Score 0.605 Round 4: 756 peptides, 79 chains. Longest chain 39 peptides. Score 0.624 Round 5: 763 peptides, 83 chains. Longest chain 36 peptides. Score 0.615 Taking the results from Round 4 Chains 88, Residues 677, Estimated correctness of the model 23.8 % 10 chains (135 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15632 restraints for refining 7932 atoms. 12378 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2308 (Rfree = 0.000) for 7932 atoms. Found 50 (50 requested) and removed 44 (25 requested) atoms. Cycle 17: After refmac, R = 0.2154 (Rfree = 0.000) for 7895 atoms. Found 23 (50 requested) and removed 34 (25 requested) atoms. Cycle 18: After refmac, R = 0.2113 (Rfree = 0.000) for 7856 atoms. Found 32 (50 requested) and removed 35 (25 requested) atoms. Cycle 19: After refmac, R = 0.2053 (Rfree = 0.000) for 7838 atoms. Found 18 (50 requested) and removed 26 (25 requested) atoms. Cycle 20: After refmac, R = 0.2040 (Rfree = 0.000) for 7816 atoms. Found 28 (50 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 2.93 Search for helices and strands: 0 residues in 0 chains, 8040 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 8059 seeds are put forward Round 1: 665 peptides, 96 chains. Longest chain 24 peptides. Score 0.482 Round 2: 713 peptides, 83 chains. Longest chain 27 peptides. Score 0.576 Round 3: 725 peptides, 85 chains. Longest chain 24 peptides. Score 0.578 Round 4: 738 peptides, 86 chains. Longest chain 30 peptides. Score 0.585 Round 5: 739 peptides, 87 chains. Longest chain 25 peptides. Score 0.582 Taking the results from Round 4 Chains 92, Residues 652, Estimated correctness of the model 8.7 % 7 chains (106 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16130 restraints for refining 7933 atoms. 13180 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2238 (Rfree = 0.000) for 7933 atoms. Found 50 (50 requested) and removed 44 (25 requested) atoms. Cycle 22: After refmac, R = 0.2015 (Rfree = 0.000) for 7885 atoms. Found 29 (50 requested) and removed 38 (25 requested) atoms. Cycle 23: After refmac, R = 0.1977 (Rfree = 0.000) for 7852 atoms. Found 21 (50 requested) and removed 29 (25 requested) atoms. Cycle 24: After refmac, R = 0.1899 (Rfree = 0.000) for 7837 atoms. Found 20 (50 requested) and removed 34 (25 requested) atoms. Cycle 25: After refmac, R = 0.1841 (Rfree = 0.000) for 7813 atoms. Found 18 (50 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 2.95 Search for helices and strands: 0 residues in 0 chains, 8042 seeds are put forward NCS extension: 22 residues added (11 deleted due to clashes), 8064 seeds are put forward Round 1: 683 peptides, 96 chains. Longest chain 28 peptides. Score 0.499 Round 2: 729 peptides, 95 chains. Longest chain 31 peptides. Score 0.543 Round 3: 720 peptides, 91 chains. Longest chain 23 peptides. Score 0.551 Round 4: 738 peptides, 90 chains. Longest chain 25 peptides. Score 0.570 Round 5: 737 peptides, 90 chains. Longest chain 22 peptides. Score 0.569 Taking the results from Round 4 Chains 98, Residues 648, Estimated correctness of the model 2.6 % 9 chains (107 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 18746 reflections ( 99.62 % complete ) and 16135 restraints for refining 7933 atoms. 13141 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2208 (Rfree = 0.000) for 7933 atoms. Found 50 (50 requested) and removed 38 (25 requested) atoms. Cycle 27: After refmac, R = 0.2060 (Rfree = 0.000) for 7888 atoms. Found 33 (50 requested) and removed 34 (25 requested) atoms. Cycle 28: After refmac, R = 0.2012 (Rfree = 0.000) for 7859 atoms. Found 33 (50 requested) and removed 30 (25 requested) atoms. Cycle 29: After refmac, R = 0.1947 (Rfree = 0.000) for 7828 atoms. Found 32 (50 requested) and removed 28 (25 requested) atoms. Cycle 30: After refmac, R = 0.1895 (Rfree = 0.000) for 7818 atoms. Found 20 (50 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 2.95 Search for helices and strands: 0 residues in 0 chains, 8040 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 8067 seeds are put forward Round 1: 647 peptides, 103 chains. Longest chain 21 peptides. Score 0.435 Round 2: 711 peptides, 98 chains. Longest chain 28 peptides. Score 0.516 Round 3: 717 peptides, 91 chains. Longest chain 25 peptides. Score 0.549 Round 4: 709 peptides, 92 chains. Longest chain 32 peptides. Score 0.538 Round 5: 731 peptides, 89 chains. Longest chain 22 peptides. Score 0.568 Taking the results from Round 5 Chains 95, Residues 642, Estimated correctness of the model 1.7 % 5 chains (53 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16785 restraints for refining 7933 atoms. 14114 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2092 (Rfree = 0.000) for 7933 atoms. Found 50 (50 requested) and removed 31 (25 requested) atoms. Cycle 32: After refmac, R = 0.1913 (Rfree = 0.000) for 7908 atoms. Found 32 (51 requested) and removed 37 (25 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1855 (Rfree = 0.000) for 7875 atoms. Found 20 (50 requested) and removed 28 (25 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1772 (Rfree = 0.000) for 7859 atoms. Found 16 (50 requested) and removed 30 (25 requested) atoms. Cycle 35: After refmac, R = 0.1731 (Rfree = 0.000) for 7836 atoms. Found 10 (50 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 2.94 Search for helices and strands: 0 residues in 0 chains, 8102 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 8117 seeds are put forward Round 1: 639 peptides, 104 chains. Longest chain 16 peptides. Score 0.423 Round 2: 700 peptides, 87 chains. Longest chain 21 peptides. Score 0.550 Round 3: 702 peptides, 85 chains. Longest chain 22 peptides. Score 0.559 Round 4: 695 peptides, 80 chains. Longest chain 28 peptides. Score 0.572 Round 5: 718 peptides, 84 chains. Longest chain 26 peptides. Score 0.576 Taking the results from Round 5 Chains 94, Residues 634, Estimated correctness of the model 5.1 % 8 chains (93 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16514 restraints for refining 7934 atoms. 13710 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2167 (Rfree = 0.000) for 7934 atoms. Found 50 (50 requested) and removed 44 (25 requested) atoms. Cycle 37: After refmac, R = 0.1902 (Rfree = 0.000) for 7915 atoms. Found 12 (50 requested) and removed 31 (25 requested) atoms. Cycle 38: After refmac, R = 0.1834 (Rfree = 0.000) for 7874 atoms. Found 19 (50 requested) and removed 28 (25 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1798 (Rfree = 0.000) for 7860 atoms. Found 11 (50 requested) and removed 28 (25 requested) atoms. Cycle 40: After refmac, R = 0.1805 (Rfree = 0.000) for 7837 atoms. Found 12 (50 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 8022 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 8036 seeds are put forward Round 1: 605 peptides, 89 chains. Longest chain 24 peptides. Score 0.455 Round 2: 683 peptides, 77 chains. Longest chain 44 peptides. Score 0.574 Round 3: 696 peptides, 83 chains. Longest chain 39 peptides. Score 0.562 Round 4: 695 peptides, 77 chains. Longest chain 25 peptides. Score 0.584 Round 5: 703 peptides, 81 chains. Longest chain 38 peptides. Score 0.575 Taking the results from Round 4 Chains 85, Residues 618, Estimated correctness of the model 8.3 % 8 chains (101 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 18746 reflections ( 99.62 % complete ) and 16296 restraints for refining 7934 atoms. 13464 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2135 (Rfree = 0.000) for 7934 atoms. Found 50 (50 requested) and removed 49 (25 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1957 (Rfree = 0.000) for 7897 atoms. Found 18 (50 requested) and removed 32 (25 requested) atoms. Cycle 43: After refmac, R = 0.1900 (Rfree = 0.000) for 7860 atoms. Found 19 (50 requested) and removed 28 (25 requested) atoms. Cycle 44: After refmac, R = 0.1848 (Rfree = 0.000) for 7835 atoms. Found 13 (50 requested) and removed 30 (25 requested) atoms. Cycle 45: After refmac, R = 0.1842 (Rfree = 0.000) for 7807 atoms. Found 12 (50 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 2.93 Search for helices and strands: 0 residues in 0 chains, 8018 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 8046 seeds are put forward Round 1: 584 peptides, 98 chains. Longest chain 17 peptides. Score 0.393 Round 2: 659 peptides, 81 chains. Longest chain 27 peptides. Score 0.538 Round 3: 649 peptides, 84 chains. Longest chain 25 peptides. Score 0.517 Round 4: 687 peptides, 83 chains. Longest chain 36 peptides. Score 0.554 Round 5: 693 peptides, 75 chains. Longest chain 40 peptides. Score 0.590 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 82, Residues 618, Estimated correctness of the model 10.7 % 8 chains (129 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 82 chains (618 residues) following loop building 8 chains (129 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 18746 reflections ( 99.62 % complete ) and 15931 restraints for refining 7933 atoms. 12928 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2220 (Rfree = 0.000) for 7933 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 47: After refmac, R = 0.2168 (Rfree = 0.000) for 7878 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2085 (Rfree = 0.000) for 7838 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.2063 (Rfree = 0.000) for 7795 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Writing output files ... TimeTaking 123.21