null Mon 24 Dec 01:01:33 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkm-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.8-parrot-mrncs ############### 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 01:01:38 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-3.8-parrot-mrncs/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 1136 and 0 Target number of residues in the AU: 1136 Target solvent content: 0.6344 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-3.8-parrot-mrncs.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: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 14256 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: 75.160 3.800 Wilson plot Bfac: 68.83 17186 reflections ( 99.97 % complete ) and 0 restraints for refining 15702 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3163 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3126 (Rfree = 0.000) for 15702 atoms. Found 86 (86 requested) and removed 136 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.88 Search for helices and strands: 0 residues in 0 chains, 15993 seeds are put forward NCS extension: 0 residues added, 15993 seeds are put forward Round 1: 617 peptides, 131 chains. Longest chain 10 peptides. Score 0.271 Round 2: 791 peptides, 141 chains. Longest chain 16 peptides. Score 0.403 Round 3: 874 peptides, 134 chains. Longest chain 17 peptides. Score 0.503 Round 4: 922 peptides, 143 chains. Longest chain 17 peptides. Score 0.510 Round 5: 945 peptides, 135 chains. Longest chain 20 peptides. Score 0.555 Taking the results from Round 5 Chains 137, Residues 810, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30207 restraints for refining 12886 atoms. 27015 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2767 (Rfree = 0.000) for 12886 atoms. Found 53 (70 requested) and removed 117 (35 requested) atoms. Cycle 2: After refmac, R = 0.2524 (Rfree = 0.000) for 12596 atoms. Found 45 (70 requested) and removed 112 (35 requested) atoms. Cycle 3: After refmac, R = 0.2039 (Rfree = 0.000) for 12386 atoms. Found 23 (68 requested) and removed 82 (34 requested) atoms. Cycle 4: After refmac, R = 0.1871 (Rfree = 0.000) for 12253 atoms. Found 14 (67 requested) and removed 60 (33 requested) atoms. Cycle 5: After refmac, R = 0.1848 (Rfree = 0.000) for 12147 atoms. Found 18 (67 requested) and removed 49 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.76 Search for helices and strands: 0 residues in 0 chains, 12557 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 12573 seeds are put forward Round 1: 741 peptides, 145 chains. Longest chain 13 peptides. Score 0.338 Round 2: 915 peptides, 147 chains. Longest chain 17 peptides. Score 0.490 Round 3: 915 peptides, 151 chains. Longest chain 18 peptides. Score 0.475 Round 4: 940 peptides, 140 chains. Longest chain 17 peptides. Score 0.535 Round 5: 920 peptides, 140 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 4 Chains 141, Residues 800, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 27341 restraints for refining 12066 atoms. 24211 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2361 (Rfree = 0.000) for 12066 atoms. Found 66 (66 requested) and removed 107 (33 requested) atoms. Cycle 7: After refmac, R = 0.2192 (Rfree = 0.000) for 11920 atoms. Found 54 (66 requested) and removed 85 (33 requested) atoms. Cycle 8: After refmac, R = 0.2160 (Rfree = 0.000) for 11814 atoms. Found 59 (65 requested) and removed 70 (32 requested) atoms. Cycle 9: After refmac, R = 0.2075 (Rfree = 0.000) for 11761 atoms. Found 64 (64 requested) and removed 54 (32 requested) atoms. Cycle 10: After refmac, R = 0.2051 (Rfree = 0.000) for 11727 atoms. Found 63 (64 requested) and removed 59 (32 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 12206 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 12218 seeds are put forward Round 1: 758 peptides, 145 chains. Longest chain 13 peptides. Score 0.355 Round 2: 894 peptides, 144 chains. Longest chain 17 peptides. Score 0.483 Round 3: 905 peptides, 140 chains. Longest chain 18 peptides. Score 0.507 Round 4: 898 peptides, 134 chains. Longest chain 17 peptides. Score 0.522 Round 5: 880 peptides, 132 chains. Longest chain 19 peptides. Score 0.515 Taking the results from Round 4 Chains 135, Residues 764, Estimated correctness of the model 0.0 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 27749 restraints for refining 12332 atoms. 24660 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2341 (Rfree = 0.000) for 12332 atoms. Found 67 (67 requested) and removed 141 (33 requested) atoms. Cycle 12: After refmac, R = 0.2148 (Rfree = 0.000) for 12161 atoms. Found 64 (67 requested) and removed 72 (33 requested) atoms. Cycle 13: After refmac, R = 0.2044 (Rfree = 0.000) for 12089 atoms. Found 61 (66 requested) and removed 62 (33 requested) atoms. Cycle 14: After refmac, R = 0.1966 (Rfree = 0.000) for 12049 atoms. Found 66 (66 requested) and removed 68 (33 requested) atoms. Cycle 15: After refmac, R = 0.1911 (Rfree = 0.000) for 12010 atoms. Found 55 (66 requested) and removed 52 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 12427 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 12441 seeds are put forward Round 1: 741 peptides, 146 chains. Longest chain 14 peptides. Score 0.334 Round 2: 830 peptides, 140 chains. Longest chain 17 peptides. Score 0.442 Round 3: 837 peptides, 131 chains. Longest chain 18 peptides. Score 0.482 Round 4: 844 peptides, 135 chains. Longest chain 18 peptides. Score 0.474 Round 5: 825 peptides, 127 chains. Longest chain 22 peptides. Score 0.487 Taking the results from Round 5 Chains 127, Residues 698, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 29444 restraints for refining 12572 atoms. 26739 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2210 (Rfree = 0.000) for 12572 atoms. Found 69 (69 requested) and removed 115 (34 requested) atoms. Cycle 17: After refmac, R = 0.2062 (Rfree = 0.000) for 12432 atoms. Found 68 (68 requested) and removed 78 (34 requested) atoms. Cycle 18: After refmac, R = 0.1985 (Rfree = 0.000) for 12375 atoms. Found 60 (68 requested) and removed 61 (34 requested) atoms. Cycle 19: After refmac, R = 0.1970 (Rfree = 0.000) for 12337 atoms. Found 68 (68 requested) and removed 62 (34 requested) atoms. Cycle 20: After refmac, R = 0.1990 (Rfree = 0.000) for 12306 atoms. Found 67 (67 requested) and removed 55 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 12751 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 12785 seeds are put forward Round 1: 641 peptides, 134 chains. Longest chain 13 peptides. Score 0.283 Round 2: 747 peptides, 136 chains. Longest chain 15 peptides. Score 0.381 Round 3: 774 peptides, 131 chains. Longest chain 21 peptides. Score 0.427 Round 4: 780 peptides, 123 chains. Longest chain 24 peptides. Score 0.463 Round 5: 813 peptides, 128 chains. Longest chain 21 peptides. Score 0.473 Taking the results from Round 5 Chains 129, Residues 685, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 28829 restraints for refining 12560 atoms. 26190 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2104 (Rfree = 0.000) for 12560 atoms. Found 69 (69 requested) and removed 120 (34 requested) atoms. Cycle 22: After refmac, R = 0.1896 (Rfree = 0.000) for 12429 atoms. Found 68 (68 requested) and removed 78 (34 requested) atoms. Cycle 23: After refmac, R = 0.1807 (Rfree = 0.000) for 12386 atoms. Found 67 (68 requested) and removed 69 (34 requested) atoms. Cycle 24: After refmac, R = 0.1379 (Rfree = 0.000) for 12362 atoms. Found 17 (68 requested) and removed 44 (34 requested) atoms. Cycle 25: After refmac, R = 0.1303 (Rfree = 0.000) for 12321 atoms. Found 15 (67 requested) and removed 41 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 12728 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 12755 seeds are put forward Round 1: 639 peptides, 133 chains. Longest chain 12 peptides. Score 0.285 Round 2: 735 peptides, 126 chains. Longest chain 20 peptides. Score 0.410 Round 3: 719 peptides, 124 chains. Longest chain 20 peptides. Score 0.404 Round 4: 758 peptides, 122 chains. Longest chain 23 peptides. Score 0.448 Round 5: 772 peptides, 126 chains. Longest chain 17 peptides. Score 0.444 Taking the results from Round 4 Chains 122, Residues 636, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 29569 restraints for refining 12761 atoms. 27137 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2065 (Rfree = 0.000) for 12761 atoms. Found 70 (70 requested) and removed 101 (35 requested) atoms. Cycle 27: After refmac, R = 0.1945 (Rfree = 0.000) for 12661 atoms. Found 70 (70 requested) and removed 83 (35 requested) atoms. Cycle 28: After refmac, R = 0.1443 (Rfree = 0.000) for 12616 atoms. Found 25 (69 requested) and removed 55 (34 requested) atoms. Cycle 29: After refmac, R = 0.1324 (Rfree = 0.000) for 12571 atoms. Found 6 (69 requested) and removed 43 (34 requested) atoms. Cycle 30: After refmac, R = 0.1312 (Rfree = 0.000) for 12525 atoms. Found 10 (68 requested) and removed 42 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 12892 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 12907 seeds are put forward Round 1: 601 peptides, 123 chains. Longest chain 10 peptides. Score 0.289 Round 2: 649 peptides, 109 chains. Longest chain 15 peptides. Score 0.399 Round 3: 663 peptides, 112 chains. Longest chain 17 peptides. Score 0.400 Round 4: 663 peptides, 107 chains. Longest chain 15 peptides. Score 0.420 Round 5: 682 peptides, 109 chains. Longest chain 20 peptides. Score 0.430 Taking the results from Round 5 Chains 109, Residues 573, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30664 restraints for refining 12895 atoms. 28472 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1929 (Rfree = 0.000) for 12895 atoms. Found 70 (70 requested) and removed 94 (35 requested) atoms. Cycle 32: After refmac, R = 0.1925 (Rfree = 0.000) for 12822 atoms. Found 70 (70 requested) and removed 70 (35 requested) atoms. Cycle 33: After refmac, R = 0.1861 (Rfree = 0.000) for 12790 atoms. Found 70 (70 requested) and removed 71 (35 requested) atoms. Cycle 34: After refmac, R = 0.1848 (Rfree = 0.000) for 12766 atoms. Found 70 (70 requested) and removed 59 (35 requested) atoms. Cycle 35: After refmac, R = 0.1387 (Rfree = 0.000) for 12757 atoms. Found 16 (70 requested) and removed 44 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.78 Search for helices and strands: 0 residues in 0 chains, 13168 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 13191 seeds are put forward Round 1: 500 peptides, 109 chains. Longest chain 11 peptides. Score 0.242 Round 2: 589 peptides, 113 chains. Longest chain 16 peptides. Score 0.321 Round 3: 580 peptides, 106 chains. Longest chain 16 peptides. Score 0.343 Round 4: 575 peptides, 101 chains. Longest chain 16 peptides. Score 0.360 Round 5: 595 peptides, 103 chains. Longest chain 19 peptides. Score 0.371 Taking the results from Round 5 Chains 104, Residues 492, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 30377 restraints for refining 12847 atoms. 28466 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1814 (Rfree = 0.000) for 12847 atoms. Found 57 (70 requested) and removed 92 (35 requested) atoms. Cycle 37: After refmac, R = 0.1880 (Rfree = 0.000) for 12770 atoms. Found 70 (70 requested) and removed 73 (35 requested) atoms. Cycle 38: After refmac, R = 0.1382 (Rfree = 0.000) for 12728 atoms. Found 20 (70 requested) and removed 51 (35 requested) atoms. Cycle 39: After refmac, R = 0.1275 (Rfree = 0.000) for 12680 atoms. Found 17 (69 requested) and removed 42 (34 requested) atoms. Cycle 40: After refmac, R = 0.1242 (Rfree = 0.000) for 12642 atoms. Found 11 (69 requested) and removed 43 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.80 Search for helices and strands: 0 residues in 0 chains, 12936 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 12954 seeds are put forward Round 1: 505 peptides, 106 chains. Longest chain 10 peptides. Score 0.262 Round 2: 567 peptides, 109 chains. Longest chain 12 peptides. Score 0.316 Round 3: 628 peptides, 114 chains. Longest chain 19 peptides. Score 0.357 Round 4: 590 peptides, 100 chains. Longest chain 16 peptides. Score 0.379 Round 5: 604 peptides, 110 chains. Longest chain 15 peptides. Score 0.350 Taking the results from Round 4 Chains 100, Residues 490, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 17186 reflections ( 99.97 % complete ) and 29847 restraints for refining 12651 atoms. 27958 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1798 (Rfree = 0.000) for 12651 atoms. Found 59 (69 requested) and removed 94 (34 requested) atoms. Cycle 42: After refmac, R = 0.1900 (Rfree = 0.000) for 12585 atoms. Found 69 (69 requested) and removed 62 (34 requested) atoms. Cycle 43: After refmac, R = 0.1813 (Rfree = 0.000) for 12571 atoms. Found 69 (69 requested) and removed 63 (34 requested) atoms. Cycle 44: After refmac, R = 0.1421 (Rfree = 0.000) for 12561 atoms. Found 17 (69 requested) and removed 48 (34 requested) atoms. Cycle 45: After refmac, R = 0.1363 (Rfree = 0.000) for 12523 atoms. Found 7 (68 requested) and removed 44 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 12799 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 12827 seeds are put forward Round 1: 451 peptides, 98 chains. Longest chain 10 peptides. Score 0.239 Round 2: 542 peptides, 102 chains. Longest chain 17 peptides. Score 0.321 Round 3: 550 peptides, 97 chains. Longest chain 25 peptides. Score 0.352 Round 4: 530 peptides, 94 chains. Longest chain 12 peptides. Score 0.345 Round 5: 542 peptides, 98 chains. Longest chain 13 peptides. Score 0.339 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 97, Residues 453, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vkm-3_warpNtrace.pdb as input Building loops using Loopy2018 97 chains (453 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17186 reflections ( 99.97 % complete ) and 30033 restraints for refining 12721 atoms. 28274 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1943 (Rfree = 0.000) for 12721 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.1854 (Rfree = 0.000) for 12657 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.1562 (Rfree = 0.000) for 12601 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 49: After refmac, R = 0.1496 (Rfree = 0.000) for 12557 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:00:54 GMT 2018 Job finished. TimeTaking 119.35 Used memory is bytes: 12849472