null Sun 23 Dec 22:23:13 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 1vl6-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-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/1vl6-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-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 22:23:22 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/1vl6-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-3.2-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 1343 and 0 Target number of residues in the AU: 1343 Target solvent content: 0.6282 Checking the provided sequence file Detected sequence length: 388 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1552 Adjusted target solvent content: 0.57 Input MTZ file: 1vl6-3.2-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.85 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: 124.815 3.200 Wilson plot Bfac: 65.59 31643 reflections ( 99.89 % complete ) and 0 restraints for refining 13677 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3081 (Rfree = 0.000) for 13677 atoms. Found 122 (122 requested) and removed 125 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 13954 seeds are put forward NCS extension: 0 residues added, 13954 seeds are put forward Round 1: 745 peptides, 120 chains. Longest chain 15 peptides. Score 0.415 Round 2: 900 peptides, 120 chains. Longest chain 26 peptides. Score 0.532 Round 3: 961 peptides, 123 chains. Longest chain 36 peptides. Score 0.564 Round 4: 979 peptides, 121 chains. Longest chain 29 peptides. Score 0.582 Round 5: 1033 peptides, 120 chains. Longest chain 27 peptides. Score 0.618 Taking the results from Round 5 Chains 129, Residues 913, Estimated correctness of the model 45.8 % 19 chains (233 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22384 restraints for refining 11328 atoms. 17984 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2695 (Rfree = 0.000) for 11328 atoms. Found 101 (101 requested) and removed 91 (50 requested) atoms. Cycle 2: After refmac, R = 0.2478 (Rfree = 0.000) for 11084 atoms. Found 70 (101 requested) and removed 70 (50 requested) atoms. Cycle 3: After refmac, R = 0.2363 (Rfree = 0.000) for 10959 atoms. Found 51 (99 requested) and removed 56 (49 requested) atoms. Cycle 4: After refmac, R = 0.2288 (Rfree = 0.000) for 10880 atoms. Found 75 (98 requested) and removed 122 (49 requested) atoms. Cycle 5: After refmac, R = 0.2200 (Rfree = 0.000) for 10781 atoms. Found 37 (97 requested) and removed 79 (48 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 11109 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 11124 seeds are put forward Round 1: 971 peptides, 123 chains. Longest chain 27 peptides. Score 0.571 Round 2: 1033 peptides, 116 chains. Longest chain 35 peptides. Score 0.629 Round 3: 1023 peptides, 106 chains. Longest chain 31 peptides. Score 0.649 Round 4: 1031 peptides, 107 chains. Longest chain 36 peptides. Score 0.651 Round 5: 1040 peptides, 110 chains. Longest chain 33 peptides. Score 0.648 Taking the results from Round 4 Chains 120, Residues 924, Estimated correctness of the model 54.1 % 18 chains (320 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 21469 restraints for refining 11334 atoms. 16655 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2622 (Rfree = 0.000) for 11334 atoms. Found 96 (101 requested) and removed 186 (50 requested) atoms. Cycle 7: After refmac, R = 0.2421 (Rfree = 0.000) for 11134 atoms. Found 56 (100 requested) and removed 114 (50 requested) atoms. Cycle 8: After refmac, R = 0.2249 (Rfree = 0.000) for 11016 atoms. Found 83 (99 requested) and removed 66 (49 requested) atoms. Cycle 9: After refmac, R = 0.2131 (Rfree = 0.000) for 10977 atoms. Found 43 (99 requested) and removed 72 (49 requested) atoms. Cycle 10: After refmac, R = 0.2080 (Rfree = 0.000) for 10929 atoms. Found 43 (98 requested) and removed 64 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 11313 seeds are put forward NCS extension: 31 residues added (31 deleted due to clashes), 11344 seeds are put forward Round 1: 959 peptides, 119 chains. Longest chain 31 peptides. Score 0.575 Round 2: 1009 peptides, 115 chains. Longest chain 30 peptides. Score 0.617 Round 3: 1057 peptides, 110 chains. Longest chain 45 peptides. Score 0.658 Round 4: 1027 peptides, 119 chains. Longest chain 29 peptides. Score 0.617 Round 5: 1017 peptides, 104 chains. Longest chain 31 peptides. Score 0.651 Taking the results from Round 3 Chains 125, Residues 947, Estimated correctness of the model 55.7 % 21 chains (299 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 21659 restraints for refining 11335 atoms. 16890 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2554 (Rfree = 0.000) for 11335 atoms. Found 101 (101 requested) and removed 106 (50 requested) atoms. Cycle 12: After refmac, R = 0.2467 (Rfree = 0.000) for 11237 atoms. Found 92 (101 requested) and removed 90 (50 requested) atoms. Cycle 13: After refmac, R = 0.2181 (Rfree = 0.000) for 11176 atoms. Found 51 (100 requested) and removed 57 (50 requested) atoms. Cycle 14: After refmac, R = 0.2162 (Rfree = 0.000) for 11141 atoms. Found 30 (100 requested) and removed 67 (50 requested) atoms. Cycle 15: After refmac, R = 0.2078 (Rfree = 0.000) for 11087 atoms. Found 18 (99 requested) and removed 59 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 11436 seeds are put forward NCS extension: 9 residues added (9 deleted due to clashes), 11445 seeds are put forward Round 1: 931 peptides, 117 chains. Longest chain 26 peptides. Score 0.562 Round 2: 998 peptides, 114 chains. Longest chain 35 peptides. Score 0.613 Round 3: 982 peptides, 116 chains. Longest chain 27 peptides. Score 0.598 Round 4: 1045 peptides, 117 chains. Longest chain 29 peptides. Score 0.633 Round 5: 1065 peptides, 119 chains. Longest chain 28 peptides. Score 0.639 Taking the results from Round 5 Chains 128, Residues 946, Estimated correctness of the model 51.1 % 20 chains (288 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 21621 restraints for refining 11333 atoms. 16839 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2606 (Rfree = 0.000) for 11333 atoms. Found 101 (101 requested) and removed 89 (50 requested) atoms. Cycle 17: After refmac, R = 0.2284 (Rfree = 0.000) for 11283 atoms. Found 45 (101 requested) and removed 60 (50 requested) atoms. Cycle 18: After refmac, R = 0.2238 (Rfree = 0.000) for 11234 atoms. Found 33 (101 requested) and removed 63 (50 requested) atoms. Cycle 19: After refmac, R = 0.2148 (Rfree = 0.000) for 11173 atoms. Found 35 (100 requested) and removed 58 (50 requested) atoms. Cycle 20: After refmac, R = 0.2063 (Rfree = 0.000) for 11135 atoms. Found 24 (100 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 11497 seeds are put forward NCS extension: 20 residues added (9 deleted due to clashes), 11517 seeds are put forward Round 1: 936 peptides, 129 chains. Longest chain 24 peptides. Score 0.529 Round 2: 1027 peptides, 117 chains. Longest chain 30 peptides. Score 0.622 Round 3: 1010 peptides, 120 chains. Longest chain 36 peptides. Score 0.604 Round 4: 986 peptides, 113 chains. Longest chain 29 peptides. Score 0.609 Round 5: 1011 peptides, 122 chains. Longest chain 33 peptides. Score 0.599 Taking the results from Round 2 Chains 121, Residues 910, Estimated correctness of the model 46.9 % 23 chains (270 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22106 restraints for refining 11333 atoms. 17578 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2348 (Rfree = 0.000) for 11333 atoms. Found 69 (101 requested) and removed 66 (50 requested) atoms. Cycle 22: After refmac, R = 0.2263 (Rfree = 0.000) for 11281 atoms. Found 36 (101 requested) and removed 53 (50 requested) atoms. Cycle 23: After refmac, R = 0.2207 (Rfree = 0.000) for 11242 atoms. Found 26 (101 requested) and removed 54 (50 requested) atoms. Cycle 24: After refmac, R = 0.2108 (Rfree = 0.000) for 11190 atoms. Found 17 (100 requested) and removed 50 (50 requested) atoms. Cycle 25: After refmac, R = 0.2144 (Rfree = 0.000) for 11141 atoms. Found 25 (100 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.92 Search for helices and strands: 0 residues in 0 chains, 11519 seeds are put forward NCS extension: 1 residues added (13 deleted due to clashes), 11520 seeds are put forward Round 1: 932 peptides, 121 chains. Longest chain 32 peptides. Score 0.551 Round 2: 973 peptides, 115 chains. Longest chain 29 peptides. Score 0.595 Round 3: 983 peptides, 122 chains. Longest chain 32 peptides. Score 0.582 Round 4: 991 peptides, 113 chains. Longest chain 32 peptides. Score 0.612 Round 5: 970 peptides, 114 chains. Longest chain 47 peptides. Score 0.596 Taking the results from Round 4 Chains 122, Residues 878, Estimated correctness of the model 44.3 % 18 chains (221 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22763 restraints for refining 11334 atoms. 18537 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2542 (Rfree = 0.000) for 11334 atoms. Found 85 (101 requested) and removed 78 (50 requested) atoms. Cycle 27: After refmac, R = 0.2286 (Rfree = 0.000) for 11295 atoms. Found 43 (101 requested) and removed 56 (50 requested) atoms. Cycle 28: After refmac, R = 0.2195 (Rfree = 0.000) for 11245 atoms. Found 39 (101 requested) and removed 51 (50 requested) atoms. Cycle 29: After refmac, R = 0.2137 (Rfree = 0.000) for 11210 atoms. Found 20 (100 requested) and removed 51 (50 requested) atoms. Cycle 30: After refmac, R = 0.2118 (Rfree = 0.000) for 11173 atoms. Found 17 (100 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 2.93 Search for helices and strands: 0 residues in 0 chains, 11531 seeds are put forward NCS extension: 18 residues added (7 deleted due to clashes), 11549 seeds are put forward Round 1: 857 peptides, 116 chains. Longest chain 27 peptides. Score 0.515 Round 2: 921 peptides, 112 chains. Longest chain 31 peptides. Score 0.571 Round 3: 954 peptides, 113 chains. Longest chain 31 peptides. Score 0.589 Round 4: 955 peptides, 109 chains. Longest chain 34 peptides. Score 0.601 Round 5: 937 peptides, 108 chains. Longest chain 25 peptides. Score 0.593 Taking the results from Round 4 Chains 115, Residues 846, Estimated correctness of the model 41.3 % 13 chains (191 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 23434 restraints for refining 11335 atoms. 19427 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2427 (Rfree = 0.000) for 11335 atoms. Found 79 (101 requested) and removed 70 (50 requested) atoms. Cycle 32: After refmac, R = 0.2258 (Rfree = 0.000) for 11302 atoms. Found 32 (101 requested) and removed 62 (50 requested) atoms. Cycle 33: After refmac, R = 0.2193 (Rfree = 0.000) for 11250 atoms. Found 23 (101 requested) and removed 57 (50 requested) atoms. Cycle 34: After refmac, R = 0.2170 (Rfree = 0.000) for 11202 atoms. Found 24 (100 requested) and removed 52 (50 requested) atoms. Cycle 35: After refmac, R = 0.2404 (Rfree = 0.000) for 11159 atoms. Found 100 (100 requested) and removed 55 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 2.90 Search for helices and strands: 0 residues in 0 chains, 11626 seeds are put forward NCS extension: 10 residues added (20 deleted due to clashes), 11636 seeds are put forward Round 1: 851 peptides, 118 chains. Longest chain 25 peptides. Score 0.504 Round 2: 925 peptides, 110 chains. Longest chain 49 peptides. Score 0.579 Round 3: 930 peptides, 109 chains. Longest chain 27 peptides. Score 0.586 Round 4: 968 peptides, 110 chains. Longest chain 47 peptides. Score 0.606 Round 5: 917 peptides, 104 chains. Longest chain 30 peptides. Score 0.592 Taking the results from Round 4 Chains 115, Residues 858, Estimated correctness of the model 42.7 % 16 chains (249 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22479 restraints for refining 11335 atoms. 18161 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2486 (Rfree = 0.000) for 11335 atoms. Found 82 (101 requested) and removed 69 (50 requested) atoms. Cycle 37: After refmac, R = 0.2310 (Rfree = 0.000) for 11316 atoms. Found 35 (101 requested) and removed 56 (50 requested) atoms. Cycle 38: After refmac, R = 0.2273 (Rfree = 0.000) for 11255 atoms. Found 28 (101 requested) and removed 56 (50 requested) atoms. Cycle 39: After refmac, R = 0.2192 (Rfree = 0.000) for 11203 atoms. Found 21 (100 requested) and removed 51 (50 requested) atoms. Cycle 40: After refmac, R = 0.2168 (Rfree = 0.000) for 11140 atoms. Found 31 (100 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.92 Search for helices and strands: 0 residues in 0 chains, 11471 seeds are put forward NCS extension: 61 residues added (18 deleted due to clashes), 11532 seeds are put forward Round 1: 806 peptides, 107 chains. Longest chain 42 peptides. Score 0.507 Round 2: 881 peptides, 97 chains. Longest chain 43 peptides. Score 0.590 Round 3: 864 peptides, 104 chains. Longest chain 35 peptides. Score 0.557 Round 4: 860 peptides, 97 chains. Longest chain 33 peptides. Score 0.576 Round 5: 866 peptides, 98 chains. Longest chain 27 peptides. Score 0.577 Taking the results from Round 2 Chains 100, Residues 784, Estimated correctness of the model 38.3 % 17 chains (277 residues) have been docked in sequence ------------------------------------------------------ 31643 reflections ( 99.89 % complete ) and 22744 restraints for refining 11332 atoms. 18648 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2392 (Rfree = 0.000) for 11332 atoms. Found 76 (101 requested) and removed 76 (50 requested) atoms. Cycle 42: After refmac, R = 0.2212 (Rfree = 0.000) for 11300 atoms. Found 31 (101 requested) and removed 55 (50 requested) atoms. Cycle 43: After refmac, R = 0.2205 (Rfree = 0.000) for 11248 atoms. Found 43 (101 requested) and removed 55 (50 requested) atoms. Cycle 44: After refmac, R = 0.2188 (Rfree = 0.000) for 11222 atoms. Found 37 (100 requested) and removed 51 (50 requested) atoms. Cycle 45: After refmac, R = 0.2167 (Rfree = 0.000) for 11191 atoms. Found 38 (100 requested) and removed 51 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 11556 seeds are put forward NCS extension: 33 residues added (40 deleted due to clashes), 11589 seeds are put forward Round 1: 800 peptides, 117 chains. Longest chain 24 peptides. Score 0.469 Round 2: 882 peptides, 116 chains. Longest chain 30 peptides. Score 0.532 Round 3: 878 peptides, 119 chains. Longest chain 25 peptides. Score 0.520 Round 4: 874 peptides, 109 chains. Longest chain 25 peptides. Score 0.549 Round 5: 863 peptides, 111 chains. Longest chain 23 peptides. Score 0.535 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 116, Residues 765, Estimated correctness of the model 26.6 % 16 chains (183 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 1vl6-3_warpNtrace.pdb as input Building loops using Loopy2018 116 chains (765 residues) following loop building 16 chains (183 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 31643 reflections ( 99.89 % complete ) and 23919 restraints for refining 11333 atoms. 20295 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2419 (Rfree = 0.000) for 11333 atoms. Found 0 (101 requested) and removed 50 (50 requested) atoms. Cycle 47: After refmac, R = 0.2393 (Rfree = 0.000) for 11252 atoms. Found 0 (101 requested) and removed 46 (50 requested) atoms. Cycle 48: After refmac, R = 0.2357 (Rfree = 0.000) for 11181 atoms. Found 0 (100 requested) and removed 46 (50 requested) atoms. Cycle 49: After refmac, R = 0.2763 (Rfree = 0.000) for 11119 atoms. Found 0 (99 requested) and removed 49 (49 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:51:42 GMT 2018 Job finished. TimeTaking 148.47 Used memory is bytes: 9578728