null Mon 24 Dec 07:33:25 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 1vkn-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkn-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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/1vkn-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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 07:33:29 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/1vkn-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkn-3.2-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 1034 and 0 Target number of residues in the AU: 1034 Target solvent content: 0.6187 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-3.2-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 11232 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 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: 93.562 3.200 Wilson plot Bfac: 60.76 23822 reflections ( 98.91 % complete ) and 0 restraints for refining 12533 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3007 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2340 (Rfree = 0.000) for 12533 atoms. Found 112 (112 requested) and removed 91 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.24 Search for helices and strands: 0 residues in 0 chains, 12779 seeds are put forward NCS extension: 0 residues added, 12779 seeds are put forward Round 1: 722 peptides, 121 chains. Longest chain 15 peptides. Score 0.445 Round 2: 857 peptides, 104 chains. Longest chain 22 peptides. Score 0.632 Round 3: 913 peptides, 107 chains. Longest chain 23 peptides. Score 0.663 Round 4: 941 peptides, 98 chains. Longest chain 30 peptides. Score 0.708 Round 5: 959 peptides, 94 chains. Longest chain 38 peptides. Score 0.730 Taking the results from Round 5 Chains 102, Residues 865, Estimated correctness of the model 71.3 % 14 chains (206 residues) have been docked in sequence Building loops using Loopy2018 102 chains (865 residues) following loop building 14 chains (206 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 19802 restraints for refining 10248 atoms. 15681 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2394 (Rfree = 0.000) for 10248 atoms. Found 89 (92 requested) and removed 95 (46 requested) atoms. Cycle 2: After refmac, R = 0.2151 (Rfree = 0.000) for 10058 atoms. Found 50 (89 requested) and removed 63 (45 requested) atoms. Cycle 3: After refmac, R = 0.2052 (Rfree = 0.000) for 9989 atoms. Found 28 (86 requested) and removed 52 (45 requested) atoms. Cycle 4: After refmac, R = 0.2052 (Rfree = 0.000) for 9931 atoms. Found 38 (84 requested) and removed 50 (44 requested) atoms. Cycle 5: After refmac, R = 0.1995 (Rfree = 0.000) for 9893 atoms. Found 26 (82 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10164 seeds are put forward NCS extension: 32 residues added (21 deleted due to clashes), 10196 seeds are put forward Round 1: 878 peptides, 103 chains. Longest chain 36 peptides. Score 0.651 Round 2: 941 peptides, 89 chains. Longest chain 36 peptides. Score 0.733 Round 3: 991 peptides, 91 chains. Longest chain 51 peptides. Score 0.756 Round 4: 987 peptides, 92 chains. Longest chain 47 peptides. Score 0.751 Round 5: 983 peptides, 94 chains. Longest chain 33 peptides. Score 0.744 Taking the results from Round 3 Chains 99, Residues 900, Estimated correctness of the model 76.1 % 13 chains (285 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 227 B and 235 B 98 chains (896 residues) following loop building 12 chains (292 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 19198 restraints for refining 10251 atoms. 14739 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2407 (Rfree = 0.000) for 10251 atoms. Found 83 (83 requested) and removed 136 (46 requested) atoms. Cycle 7: After refmac, R = 0.2191 (Rfree = 0.000) for 10125 atoms. Found 57 (80 requested) and removed 65 (45 requested) atoms. Cycle 8: After refmac, R = 0.2137 (Rfree = 0.000) for 10081 atoms. Found 27 (77 requested) and removed 59 (45 requested) atoms. Cycle 9: After refmac, R = 0.2093 (Rfree = 0.000) for 10016 atoms. Found 40 (76 requested) and removed 53 (45 requested) atoms. Cycle 10: After refmac, R = 0.2040 (Rfree = 0.000) for 9974 atoms. Found 37 (73 requested) and removed 45 (44 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10286 seeds are put forward NCS extension: 36 residues added (13 deleted due to clashes), 10322 seeds are put forward Round 1: 889 peptides, 112 chains. Longest chain 27 peptides. Score 0.629 Round 2: 937 peptides, 92 chains. Longest chain 37 peptides. Score 0.723 Round 3: 919 peptides, 93 chains. Longest chain 37 peptides. Score 0.709 Round 4: 907 peptides, 95 chains. Longest chain 37 peptides. Score 0.696 Round 5: 915 peptides, 98 chains. Longest chain 26 peptides. Score 0.692 Taking the results from Round 2 Chains 105, Residues 845, Estimated correctness of the model 69.9 % 15 chains (220 residues) have been docked in sequence Building loops using Loopy2018 105 chains (845 residues) following loop building 15 chains (220 residues) in sequence following loop building ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 20386 restraints for refining 10252 atoms. 16237 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2207 (Rfree = 0.000) for 10252 atoms. Found 64 (74 requested) and removed 92 (46 requested) atoms. Cycle 12: After refmac, R = 0.2058 (Rfree = 0.000) for 10184 atoms. Found 24 (71 requested) and removed 59 (45 requested) atoms. Cycle 13: After refmac, R = 0.2009 (Rfree = 0.000) for 10137 atoms. Found 33 (69 requested) and removed 48 (45 requested) atoms. Cycle 14: After refmac, R = 0.1916 (Rfree = 0.000) for 10109 atoms. Found 17 (67 requested) and removed 57 (45 requested) atoms. Cycle 15: After refmac, R = 0.2065 (Rfree = 0.000) for 10061 atoms. Found 62 (65 requested) and removed 56 (45 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.13 3.21 Search for helices and strands: 0 residues in 0 chains, 10333 seeds are put forward NCS extension: 11 residues added (9 deleted due to clashes), 10344 seeds are put forward Round 1: 842 peptides, 104 chains. Longest chain 30 peptides. Score 0.620 Round 2: 884 peptides, 93 chains. Longest chain 41 peptides. Score 0.687 Round 3: 906 peptides, 99 chains. Longest chain 30 peptides. Score 0.683 Round 4: 906 peptides, 95 chains. Longest chain 43 peptides. Score 0.695 Round 5: 924 peptides, 98 chains. Longest chain 38 peptides. Score 0.698 Taking the results from Round 5 Chains 106, Residues 826, Estimated correctness of the model 64.8 % 10 chains (115 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 21626 restraints for refining 10252 atoms. 18013 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2245 (Rfree = 0.000) for 10252 atoms. Found 64 (64 requested) and removed 73 (46 requested) atoms. Cycle 17: After refmac, R = 0.2077 (Rfree = 0.000) for 10223 atoms. Found 37 (64 requested) and removed 50 (45 requested) atoms. Cycle 18: After refmac, R = 0.1976 (Rfree = 0.000) for 10193 atoms. Found 37 (64 requested) and removed 46 (45 requested) atoms. Cycle 19: After refmac, R = 0.1889 (Rfree = 0.000) for 10174 atoms. Found 25 (64 requested) and removed 46 (45 requested) atoms. Cycle 20: After refmac, R = 0.1863 (Rfree = 0.000) for 10141 atoms. Found 25 (64 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10397 seeds are put forward NCS extension: 17 residues added (12 deleted due to clashes), 10414 seeds are put forward Round 1: 779 peptides, 106 chains. Longest chain 29 peptides. Score 0.561 Round 2: 884 peptides, 96 chains. Longest chain 48 peptides. Score 0.677 Round 3: 883 peptides, 101 chains. Longest chain 34 peptides. Score 0.661 Round 4: 878 peptides, 102 chains. Longest chain 37 peptides. Score 0.654 Round 5: 892 peptides, 103 chains. Longest chain 43 peptides. Score 0.661 Taking the results from Round 2 Chains 101, Residues 788, Estimated correctness of the model 60.1 % 10 chains (187 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 20966 restraints for refining 10253 atoms. 17187 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2051 (Rfree = 0.000) for 10253 atoms. Found 64 (64 requested) and removed 92 (46 requested) atoms. Cycle 22: After refmac, R = 0.1950 (Rfree = 0.000) for 10204 atoms. Found 25 (64 requested) and removed 51 (45 requested) atoms. Cycle 23: After refmac, R = 0.1918 (Rfree = 0.000) for 10163 atoms. Found 26 (64 requested) and removed 50 (45 requested) atoms. Cycle 24: After refmac, R = 0.1883 (Rfree = 0.000) for 10127 atoms. Found 23 (63 requested) and removed 50 (45 requested) atoms. Cycle 25: After refmac, R = 0.1851 (Rfree = 0.000) for 10088 atoms. Found 19 (63 requested) and removed 47 (45 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10313 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 10330 seeds are put forward Round 1: 816 peptides, 109 chains. Longest chain 25 peptides. Score 0.581 Round 2: 878 peptides, 100 chains. Longest chain 41 peptides. Score 0.660 Round 3: 883 peptides, 102 chains. Longest chain 29 peptides. Score 0.658 Round 4: 873 peptides, 100 chains. Longest chain 32 peptides. Score 0.657 Round 5: 837 peptides, 99 chains. Longest chain 50 peptides. Score 0.634 Taking the results from Round 2 Chains 103, Residues 778, Estimated correctness of the model 56.2 % 9 chains (123 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 21573 restraints for refining 10253 atoms. 18071 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2038 (Rfree = 0.000) for 10253 atoms. Found 64 (64 requested) and removed 66 (46 requested) atoms. Cycle 27: After refmac, R = 0.1879 (Rfree = 0.000) for 10234 atoms. Found 29 (64 requested) and removed 47 (45 requested) atoms. Cycle 28: After refmac, R = 0.1837 (Rfree = 0.000) for 10204 atoms. Found 22 (64 requested) and removed 45 (45 requested) atoms. Cycle 29: After refmac, R = 0.1824 (Rfree = 0.000) for 10175 atoms. Found 18 (64 requested) and removed 45 (45 requested) atoms. Cycle 30: After refmac, R = 0.1748 (Rfree = 0.000) for 10140 atoms. Found 21 (64 requested) and removed 46 (45 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 10397 seeds are put forward NCS extension: 21 residues added (8 deleted due to clashes), 10418 seeds are put forward Round 1: 790 peptides, 110 chains. Longest chain 27 peptides. Score 0.555 Round 2: 896 peptides, 100 chains. Longest chain 30 peptides. Score 0.673 Round 3: 872 peptides, 101 chains. Longest chain 28 peptides. Score 0.653 Round 4: 861 peptides, 98 chains. Longest chain 39 peptides. Score 0.655 Round 5: 847 peptides, 95 chains. Longest chain 29 peptides. Score 0.655 Taking the results from Round 2 Chains 108, Residues 796, Estimated correctness of the model 59.2 % 14 chains (205 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 20554 restraints for refining 10254 atoms. 16663 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2029 (Rfree = 0.000) for 10254 atoms. Found 64 (64 requested) and removed 71 (46 requested) atoms. Cycle 32: After refmac, R = 0.1922 (Rfree = 0.000) for 10229 atoms. Found 18 (64 requested) and removed 45 (45 requested) atoms. Cycle 33: After refmac, R = 0.1867 (Rfree = 0.000) for 10195 atoms. Found 20 (64 requested) and removed 45 (45 requested) atoms. Cycle 34: After refmac, R = 0.1819 (Rfree = 0.000) for 10165 atoms. Found 22 (64 requested) and removed 45 (45 requested) atoms. Cycle 35: After refmac, R = 0.1801 (Rfree = 0.000) for 10135 atoms. Found 19 (64 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 10371 seeds are put forward NCS extension: 13 residues added (10 deleted due to clashes), 10384 seeds are put forward Round 1: 751 peptides, 104 chains. Longest chain 27 peptides. Score 0.544 Round 2: 822 peptides, 98 chains. Longest chain 29 peptides. Score 0.626 Round 3: 819 peptides, 99 chains. Longest chain 25 peptides. Score 0.620 Round 4: 808 peptides, 96 chains. Longest chain 31 peptides. Score 0.622 Round 5: 781 peptides, 95 chains. Longest chain 30 peptides. Score 0.604 Taking the results from Round 2 Chains 100, Residues 724, Estimated correctness of the model 47.9 % 7 chains (108 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 22136 restraints for refining 10254 atoms. 18910 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1968 (Rfree = 0.000) for 10254 atoms. Found 61 (64 requested) and removed 68 (46 requested) atoms. Cycle 37: After refmac, R = 0.1883 (Rfree = 0.000) for 10231 atoms. Found 31 (64 requested) and removed 46 (45 requested) atoms. Cycle 38: After refmac, R = 0.1841 (Rfree = 0.000) for 10208 atoms. Found 25 (64 requested) and removed 45 (45 requested) atoms. Cycle 39: After refmac, R = 0.1821 (Rfree = 0.000) for 10179 atoms. Found 19 (64 requested) and removed 45 (45 requested) atoms. Cycle 40: After refmac, R = 0.1782 (Rfree = 0.000) for 10147 atoms. Found 23 (64 requested) and removed 47 (45 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 10406 seeds are put forward NCS extension: 13 residues added (9 deleted due to clashes), 10419 seeds are put forward Round 1: 739 peptides, 107 chains. Longest chain 27 peptides. Score 0.521 Round 2: 795 peptides, 104 chains. Longest chain 27 peptides. Score 0.582 Round 3: 795 peptides, 106 chains. Longest chain 28 peptides. Score 0.575 Round 4: 806 peptides, 99 chains. Longest chain 31 peptides. Score 0.610 Round 5: 797 peptides, 96 chains. Longest chain 29 peptides. Score 0.614 Taking the results from Round 5 Chains 99, Residues 701, Estimated correctness of the model 44.8 % 5 chains (64 residues) have been docked in sequence ------------------------------------------------------ 23822 reflections ( 98.91 % complete ) and 22509 restraints for refining 10254 atoms. 19528 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2066 (Rfree = 0.000) for 10254 atoms. Found 64 (64 requested) and removed 56 (46 requested) atoms. Cycle 42: After refmac, R = 0.1906 (Rfree = 0.000) for 10251 atoms. Found 27 (64 requested) and removed 46 (46 requested) atoms. Cycle 43: After refmac, R = 0.1870 (Rfree = 0.000) for 10227 atoms. Found 19 (64 requested) and removed 47 (45 requested) atoms. Cycle 44: After refmac, R = 0.1816 (Rfree = 0.000) for 10192 atoms. Found 11 (64 requested) and removed 45 (45 requested) atoms. Cycle 45: After refmac, R = 0.1791 (Rfree = 0.000) for 10151 atoms. Found 19 (64 requested) and removed 45 (45 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 10383 seeds are put forward NCS extension: 12 residues added (9 deleted due to clashes), 10395 seeds are put forward Round 1: 709 peptides, 110 chains. Longest chain 18 peptides. Score 0.480 Round 2: 774 peptides, 101 chains. Longest chain 24 peptides. Score 0.576 Round 3: 767 peptides, 94 chains. Longest chain 28 peptides. Score 0.597 Round 4: 751 peptides, 95 chains. Longest chain 20 peptides. Score 0.579 Round 5: 765 peptides, 94 chains. Longest chain 26 peptides. Score 0.595 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 98, Residues 673, Estimated correctness of the model 40.2 % 9 chains (104 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 1vkn-3_warpNtrace.pdb as input Building loops using Loopy2018 98 chains (673 residues) following loop building 9 chains (104 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23822 reflections ( 98.91 % complete ) and 22495 restraints for refining 10254 atoms. 19527 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1998 (Rfree = 0.000) for 10254 atoms. Found 0 (64 requested) and removed 43 (46 requested) atoms. Cycle 47: After refmac, R = 0.1972 (Rfree = 0.000) for 10194 atoms. Found 0 (64 requested) and removed 23 (45 requested) atoms. Cycle 48: After refmac, R = 0.1941 (Rfree = 0.000) for 10163 atoms. Found 0 (64 requested) and removed 15 (45 requested) atoms. Cycle 49: After refmac, R = 0.1901 (Rfree = 0.000) for 10141 atoms. Found 0 (64 requested) and removed 12 (45 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:21:13 GMT 2018 Job finished. TimeTaking 107.82 Used memory is bytes: 13689816