Sun 23 Dec 23:44:45 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 1vl6-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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/1vl6-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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 ============================================================ Sun 23 Dec 23:44:49 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/1vl6-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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 1174 and 0 Target number of residues in the AU: 1174 Target solvent content: 0.6750 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: 1vl6-4.0-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12416 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: 124.815 4.000 Wilson plot Bfac: 96.72 16252 reflections ( 99.83 % complete ) and 0 restraints for refining 13736 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3492 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3406 (Rfree = 0.000) for 13736 atoms. Found 65 (65 requested) and removed 118 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.92 3.57 Search for helices and strands: 0 residues in 0 chains, 13884 seeds are put forward NCS extension: 0 residues added, 13884 seeds are put forward Round 1: 515 peptides, 100 chains. Longest chain 12 peptides. Score 0.288 Round 2: 683 peptides, 103 chains. Longest chain 21 peptides. Score 0.426 Round 3: 734 peptides, 105 chains. Longest chain 23 peptides. Score 0.459 Round 4: 791 peptides, 108 chains. Longest chain 21 peptides. Score 0.493 Round 5: 791 peptides, 99 chains. Longest chain 23 peptides. Score 0.523 Taking the results from Round 5 Chains 102, Residues 692, Estimated correctness of the model 0.0 % 9 chains (93 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25833 restraints for refining 11194 atoms. 22846 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2722 (Rfree = 0.000) for 11194 atoms. Found 53 (53 requested) and removed 100 (26 requested) atoms. Cycle 2: After refmac, R = 0.2442 (Rfree = 0.000) for 10876 atoms. Found 52 (52 requested) and removed 79 (26 requested) atoms. Cycle 3: After refmac, R = 0.2317 (Rfree = 0.000) for 10690 atoms. Found 51 (51 requested) and removed 67 (25 requested) atoms. Cycle 4: After refmac, R = 0.2225 (Rfree = 0.000) for 10588 atoms. Found 45 (50 requested) and removed 59 (25 requested) atoms. Cycle 5: After refmac, R = 0.2164 (Rfree = 0.000) for 10500 atoms. Found 41 (50 requested) and removed 71 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.43 Search for helices and strands: 0 residues in 0 chains, 10845 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 10869 seeds are put forward Round 1: 689 peptides, 120 chains. Longest chain 18 peptides. Score 0.368 Round 2: 805 peptides, 110 chains. Longest chain 19 peptides. Score 0.496 Round 3: 816 peptides, 111 chains. Longest chain 20 peptides. Score 0.501 Round 4: 808 peptides, 104 chains. Longest chain 23 peptides. Score 0.518 Round 5: 814 peptides, 109 chains. Longest chain 27 peptides. Score 0.506 Taking the results from Round 4 Chains 106, Residues 704, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25520 restraints for refining 11136 atoms. 22726 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2199 (Rfree = 0.000) for 11136 atoms. Found 37 (52 requested) and removed 101 (26 requested) atoms. Cycle 7: After refmac, R = 0.2071 (Rfree = 0.000) for 10952 atoms. Found 25 (52 requested) and removed 62 (26 requested) atoms. Cycle 8: After refmac, R = 0.2075 (Rfree = 0.000) for 10857 atoms. Found 51 (51 requested) and removed 60 (25 requested) atoms. Cycle 9: After refmac, R = 0.1977 (Rfree = 0.000) for 10801 atoms. Found 42 (51 requested) and removed 76 (25 requested) atoms. Cycle 10: After refmac, R = 0.1974 (Rfree = 0.000) for 10744 atoms. Found 50 (51 requested) and removed 53 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 11091 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 11124 seeds are put forward Round 1: 692 peptides, 115 chains. Longest chain 20 peptides. Score 0.389 Round 2: 759 peptides, 99 chains. Longest chain 25 peptides. Score 0.499 Round 3: 790 peptides, 105 chains. Longest chain 20 peptides. Score 0.502 Round 4: 791 peptides, 106 chains. Longest chain 19 peptides. Score 0.499 Round 5: 789 peptides, 103 chains. Longest chain 28 peptides. Score 0.508 Taking the results from Round 5 Chains 108, Residues 686, Estimated correctness of the model 0.0 % 9 chains (76 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25688 restraints for refining 11211 atoms. 22808 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2214 (Rfree = 0.000) for 11211 atoms. Found 45 (53 requested) and removed 63 (26 requested) atoms. Cycle 12: After refmac, R = 0.2084 (Rfree = 0.000) for 11111 atoms. Found 46 (53 requested) and removed 67 (26 requested) atoms. Cycle 13: After refmac, R = 0.1942 (Rfree = 0.000) for 11052 atoms. Found 30 (52 requested) and removed 59 (26 requested) atoms. Cycle 14: After refmac, R = 0.1905 (Rfree = 0.000) for 10971 atoms. Found 40 (52 requested) and removed 80 (26 requested) atoms. Cycle 15: After refmac, R = 0.1795 (Rfree = 0.000) for 10904 atoms. Found 33 (51 requested) and removed 45 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 11252 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 11277 seeds are put forward Round 1: 697 peptides, 123 chains. Longest chain 15 peptides. Score 0.364 Round 2: 772 peptides, 118 chains. Longest chain 18 peptides. Score 0.444 Round 3: 796 peptides, 118 chains. Longest chain 20 peptides. Score 0.463 Round 4: 799 peptides, 116 chains. Longest chain 20 peptides. Score 0.472 Round 5: 822 peptides, 115 chains. Longest chain 21 peptides. Score 0.492 Taking the results from Round 5 Chains 120, Residues 707, Estimated correctness of the model 0.0 % 8 chains (75 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25078 restraints for refining 11210 atoms. 22104 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2216 (Rfree = 0.000) for 11210 atoms. Found 44 (53 requested) and removed 57 (26 requested) atoms. Cycle 17: After refmac, R = 0.2050 (Rfree = 0.000) for 11060 atoms. Found 43 (53 requested) and removed 48 (26 requested) atoms. Cycle 18: After refmac, R = 0.1717 (Rfree = 0.000) for 10954 atoms. Found 9 (52 requested) and removed 50 (26 requested) atoms. Cycle 19: After refmac, R = 0.1822 (Rfree = 0.000) for 10867 atoms. Found 47 (51 requested) and removed 38 (25 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1860 (Rfree = 0.000) for 10834 atoms. Found 51 (51 requested) and removed 46 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 11183 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 11199 seeds are put forward Round 1: 656 peptides, 117 chains. Longest chain 16 peptides. Score 0.350 Round 2: 740 peptides, 113 chains. Longest chain 21 peptides. Score 0.436 Round 3: 709 peptides, 111 chains. Longest chain 20 peptides. Score 0.418 Round 4: 745 peptides, 107 chains. Longest chain 21 peptides. Score 0.461 Round 5: 738 peptides, 101 chains. Longest chain 30 peptides. Score 0.477 Taking the results from Round 5 Chains 102, Residues 637, Estimated correctness of the model 0.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25804 restraints for refining 11210 atoms. 23199 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2127 (Rfree = 0.000) for 11210 atoms. Found 32 (53 requested) and removed 50 (26 requested) atoms. Cycle 22: After refmac, R = 0.1904 (Rfree = 0.000) for 11083 atoms. Found 22 (53 requested) and removed 46 (26 requested) atoms. Cycle 23: After refmac, R = 0.1854 (Rfree = 0.000) for 11010 atoms. Found 39 (52 requested) and removed 48 (26 requested) atoms. Cycle 24: After refmac, R = 0.1833 (Rfree = 0.000) for 10966 atoms. Found 34 (52 requested) and removed 45 (26 requested) atoms. Cycle 25: After refmac, R = 0.1798 (Rfree = 0.000) for 10926 atoms. Found 40 (52 requested) and removed 45 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 3.47 Search for helices and strands: 0 residues in 0 chains, 11252 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 11273 seeds are put forward Round 1: 655 peptides, 133 chains. Longest chain 12 peptides. Score 0.288 Round 2: 718 peptides, 115 chains. Longest chain 16 peptides. Score 0.411 Round 3: 754 peptides, 123 chains. Longest chain 17 peptides. Score 0.412 Round 4: 740 peptides, 115 chains. Longest chain 28 peptides. Score 0.429 Round 5: 756 peptides, 117 chains. Longest chain 21 peptides. Score 0.435 Taking the results from Round 5 Chains 119, Residues 639, Estimated correctness of the model 0.0 % 9 chains (75 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25784 restraints for refining 11212 atoms. 23092 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2002 (Rfree = 0.000) for 11212 atoms. Found 43 (53 requested) and removed 58 (26 requested) atoms. Cycle 27: After refmac, R = 0.1928 (Rfree = 0.000) for 11099 atoms. Found 53 (53 requested) and removed 51 (26 requested) atoms. Cycle 28: After refmac, R = 0.1904 (Rfree = 0.000) for 11038 atoms. Found 52 (52 requested) and removed 43 (26 requested) atoms. Cycle 29: After refmac, R = 0.1880 (Rfree = 0.000) for 11009 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 30: After refmac, R = 0.1543 (Rfree = 0.000) for 10977 atoms. Found 8 (52 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 11280 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 11310 seeds are put forward Round 1: 623 peptides, 122 chains. Longest chain 11 peptides. Score 0.301 Round 2: 711 peptides, 125 chains. Longest chain 17 peptides. Score 0.368 Round 3: 725 peptides, 123 chains. Longest chain 27 peptides. Score 0.388 Round 4: 745 peptides, 117 chains. Longest chain 27 peptides. Score 0.426 Round 5: 716 peptides, 114 chains. Longest chain 20 peptides. Score 0.413 Taking the results from Round 4 Chains 117, Residues 628, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26379 restraints for refining 11213 atoms. 23927 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1925 (Rfree = 0.000) for 11213 atoms. Found 36 (53 requested) and removed 49 (26 requested) atoms. Cycle 32: After refmac, R = 0.1943 (Rfree = 0.000) for 11122 atoms. Found 53 (53 requested) and removed 56 (26 requested) atoms. Cycle 33: After refmac, R = 0.1949 (Rfree = 0.000) for 11077 atoms. Found 52 (52 requested) and removed 60 (26 requested) atoms. Cycle 34: After refmac, R = 0.1916 (Rfree = 0.000) for 11039 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 35: After refmac, R = 0.1971 (Rfree = 0.000) for 11016 atoms. Found 52 (52 requested) and removed 51 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.48 Search for helices and strands: 0 residues in 0 chains, 11437 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 11464 seeds are put forward Round 1: 562 peptides, 116 chains. Longest chain 13 peptides. Score 0.267 Round 2: 669 peptides, 117 chains. Longest chain 27 peptides. Score 0.362 Round 3: 718 peptides, 116 chains. Longest chain 22 peptides. Score 0.407 Round 4: 688 peptides, 111 chains. Longest chain 22 peptides. Score 0.401 Round 5: 701 peptides, 104 chains. Longest chain 25 peptides. Score 0.437 Taking the results from Round 5 Chains 104, Residues 597, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26458 restraints for refining 11213 atoms. 24126 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2039 (Rfree = 0.000) for 11213 atoms. Found 53 (53 requested) and removed 57 (26 requested) atoms. Cycle 37: After refmac, R = 0.1962 (Rfree = 0.000) for 11138 atoms. Found 53 (53 requested) and removed 50 (26 requested) atoms. Cycle 38: After refmac, R = 0.1636 (Rfree = 0.000) for 11093 atoms. Found 10 (52 requested) and removed 34 (26 requested) atoms. Cycle 39: After refmac, R = 0.1694 (Rfree = 0.000) for 11038 atoms. Found 23 (52 requested) and removed 47 (26 requested) atoms. Cycle 40: After refmac, R = 0.1610 (Rfree = 0.000) for 11003 atoms. Found 7 (52 requested) and removed 41 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 11309 seeds are put forward NCS extension: 41 residues added (5 deleted due to clashes), 11350 seeds are put forward Round 1: 526 peptides, 103 chains. Longest chain 18 peptides. Score 0.286 Round 2: 612 peptides, 101 chains. Longest chain 21 peptides. Score 0.373 Round 3: 649 peptides, 102 chains. Longest chain 19 peptides. Score 0.401 Round 4: 631 peptides, 100 chains. Longest chain 20 peptides. Score 0.394 Round 5: 641 peptides, 97 chains. Longest chain 24 peptides. Score 0.413 Taking the results from Round 5 Chains 99, Residues 544, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26528 restraints for refining 11213 atoms. 24357 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1927 (Rfree = 0.000) for 11213 atoms. Found 34 (53 requested) and removed 46 (26 requested) atoms. Cycle 42: After refmac, R = 0.2027 (Rfree = 0.000) for 11142 atoms. Found 53 (53 requested) and removed 52 (26 requested) atoms. Cycle 43: After refmac, R = 0.2022 (Rfree = 0.000) for 11106 atoms. Found 52 (52 requested) and removed 57 (26 requested) atoms. Cycle 44: After refmac, R = 0.1950 (Rfree = 0.000) for 11066 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 45: After refmac, R = 0.1525 (Rfree = 0.000) for 11045 atoms. Found 13 (52 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 11346 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 11371 seeds are put forward Round 1: 522 peptides, 108 chains. Longest chain 11 peptides. Score 0.261 Round 2: 562 peptides, 94 chains. Longest chain 15 peptides. Score 0.356 Round 3: 560 peptides, 96 chains. Longest chain 12 peptides. Score 0.347 Round 4: 567 peptides, 95 chains. Longest chain 15 peptides. Score 0.357 Round 5: 544 peptides, 88 chains. Longest chain 13 peptides. Score 0.364 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 88, Residues 456, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vl6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16252 reflections ( 99.83 % complete ) and 27242 restraints for refining 11210 atoms. 25506 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1900 (Rfree = 0.000) for 11210 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.1866 (Rfree = 0.000) for 11156 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2076 (Rfree = 0.000) for 11116 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2100 (Rfree = 0.000) for 11068 atoms. TimeTaking 119.35