Mon 24 Dec 07:58:01 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 1vl6-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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/1vl6-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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 07:58:06 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/1vl6-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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 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-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-4.0-parrot-noncs.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 13692 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3452 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3282 (Rfree = 0.000) for 13692 atoms. Found 65 (65 requested) and removed 64 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 3.53 Search for helices and strands: 0 residues in 0 chains, 13925 seeds are put forward NCS extension: 0 residues added, 13925 seeds are put forward Round 1: 530 peptides, 101 chains. Longest chain 12 peptides. Score 0.298 Round 2: 694 peptides, 106 chains. Longest chain 17 peptides. Score 0.424 Round 3: 747 peptides, 103 chains. Longest chain 19 peptides. Score 0.477 Round 4: 749 peptides, 99 chains. Longest chain 25 peptides. Score 0.492 Round 5: 781 peptides, 101 chains. Longest chain 25 peptides. Score 0.509 Taking the results from Round 5 Chains 104, Residues 680, Estimated correctness of the model 0.0 % 7 chains (71 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26198 restraints for refining 11210 atoms. 23342 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2587 (Rfree = 0.000) for 11210 atoms. Found 45 (53 requested) and removed 82 (26 requested) atoms. Cycle 2: After refmac, R = 0.2389 (Rfree = 0.000) for 10925 atoms. Found 51 (53 requested) and removed 51 (26 requested) atoms. Cycle 3: After refmac, R = 0.2251 (Rfree = 0.000) for 10820 atoms. Found 27 (51 requested) and removed 45 (25 requested) atoms. Cycle 4: After refmac, R = 0.2132 (Rfree = 0.000) for 10742 atoms. Found 21 (51 requested) and removed 39 (25 requested) atoms. Cycle 5: After refmac, R = 0.2166 (Rfree = 0.000) for 10684 atoms. Found 19 (50 requested) and removed 41 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 11011 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11031 seeds are put forward Round 1: 689 peptides, 116 chains. Longest chain 15 peptides. Score 0.383 Round 2: 750 peptides, 106 chains. Longest chain 21 peptides. Score 0.468 Round 3: 786 peptides, 101 chains. Longest chain 24 peptides. Score 0.512 Round 4: 776 peptides, 96 chains. Longest chain 28 peptides. Score 0.522 Round 5: 793 peptides, 91 chains. Longest chain 26 peptides. Score 0.550 Taking the results from Round 5 Chains 98, Residues 702, Estimated correctness of the model 0.0 % 6 chains (53 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25664 restraints for refining 11211 atoms. 22768 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2469 (Rfree = 0.000) for 11211 atoms. Found 53 (53 requested) and removed 91 (26 requested) atoms. Cycle 7: After refmac, R = 0.2392 (Rfree = 0.000) for 11037 atoms. Found 53 (53 requested) and removed 68 (26 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2183 (Rfree = 0.000) for 10912 atoms. Found 52 (52 requested) and removed 55 (26 requested) atoms. Cycle 9: After refmac, R = 0.1903 (Rfree = 0.000) for 10837 atoms. Found 17 (51 requested) and removed 39 (25 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1862 (Rfree = 0.000) for 10763 atoms. Found 13 (51 requested) and removed 39 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.86 3.51 Search for helices and strands: 0 residues in 0 chains, 11072 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 11084 seeds are put forward Round 1: 691 peptides, 117 chains. Longest chain 18 peptides. Score 0.381 Round 2: 774 peptides, 115 chains. Longest chain 19 peptides. Score 0.456 Round 3: 783 peptides, 99 chains. Longest chain 27 peptides. Score 0.517 Round 4: 773 peptides, 101 chains. Longest chain 20 peptides. Score 0.503 Round 5: 778 peptides, 101 chains. Longest chain 22 peptides. Score 0.507 Taking the results from Round 3 Chains 102, Residues 684, Estimated correctness of the model 0.0 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25357 restraints for refining 11209 atoms. 22505 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2074 (Rfree = 0.000) for 11209 atoms. Found 36 (53 requested) and removed 77 (26 requested) atoms. Cycle 12: After refmac, R = 0.1919 (Rfree = 0.000) for 11067 atoms. Found 11 (53 requested) and removed 49 (26 requested) atoms. Cycle 13: After refmac, R = 0.1869 (Rfree = 0.000) for 10991 atoms. Found 7 (52 requested) and removed 35 (26 requested) atoms. Cycle 14: After refmac, R = 0.1859 (Rfree = 0.000) for 10956 atoms. Found 3 (52 requested) and removed 28 (26 requested) atoms. Cycle 15: After refmac, R = 0.1862 (Rfree = 0.000) for 10927 atoms. Found 7 (51 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 11262 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 11300 seeds are put forward Round 1: 716 peptides, 115 chains. Longest chain 18 peptides. Score 0.409 Round 2: 761 peptides, 101 chains. Longest chain 24 peptides. Score 0.494 Round 3: 798 peptides, 101 chains. Longest chain 29 peptides. Score 0.521 Round 4: 803 peptides, 109 chains. Longest chain 21 peptides. Score 0.498 Round 5: 787 peptides, 103 chains. Longest chain 20 peptides. Score 0.506 Taking the results from Round 3 Chains 101, Residues 697, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26134 restraints for refining 11211 atoms. 23428 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2075 (Rfree = 0.000) for 11211 atoms. Found 31 (53 requested) and removed 52 (26 requested) atoms. Cycle 17: After refmac, R = 0.1924 (Rfree = 0.000) for 11102 atoms. Found 21 (53 requested) and removed 48 (26 requested) atoms. Cycle 18: After refmac, R = 0.1753 (Rfree = 0.000) for 11038 atoms. Found 8 (52 requested) and removed 41 (26 requested) atoms. Cycle 19: After refmac, R = 0.1753 (Rfree = 0.000) for 10990 atoms. Found 6 (52 requested) and removed 40 (26 requested) atoms. Cycle 20: After refmac, R = 0.1765 (Rfree = 0.000) for 10948 atoms. Found 3 (52 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.87 3.52 Search for helices and strands: 0 residues in 0 chains, 11344 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11364 seeds are put forward Round 1: 649 peptides, 120 chains. Longest chain 12 peptides. Score 0.333 Round 2: 748 peptides, 112 chains. Longest chain 17 peptides. Score 0.446 Round 3: 764 peptides, 110 chains. Longest chain 20 peptides. Score 0.465 Round 4: 775 peptides, 108 chains. Longest chain 20 peptides. Score 0.481 Round 5: 772 peptides, 105 chains. Longest chain 21 peptides. Score 0.489 Taking the results from Round 5 Chains 106, Residues 667, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26269 restraints for refining 11213 atoms. 23603 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2197 (Rfree = 0.000) for 11213 atoms. Found 27 (53 requested) and removed 54 (26 requested) atoms. Cycle 22: After refmac, R = 0.2074 (Rfree = 0.000) for 11121 atoms. Found 14 (53 requested) and removed 41 (26 requested) atoms. Cycle 23: After refmac, R = 0.2062 (Rfree = 0.000) for 11077 atoms. Found 12 (52 requested) and removed 36 (26 requested) atoms. Cycle 24: After refmac, R = 0.2072 (Rfree = 0.000) for 11049 atoms. Found 6 (52 requested) and removed 31 (26 requested) atoms. Cycle 25: After refmac, R = 0.2092 (Rfree = 0.000) for 11023 atoms. Found 7 (52 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.87 3.52 Search for helices and strands: 0 residues in 0 chains, 11372 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 11391 seeds are put forward Round 1: 606 peptides, 106 chains. Longest chain 13 peptides. Score 0.348 Round 2: 674 peptides, 100 chains. Longest chain 14 peptides. Score 0.429 Round 3: 673 peptides, 99 chains. Longest chain 18 peptides. Score 0.432 Round 4: 702 peptides, 100 chains. Longest chain 20 peptides. Score 0.452 Round 5: 718 peptides, 100 chains. Longest chain 16 peptides. Score 0.465 Taking the results from Round 5 Chains 100, Residues 618, Estimated correctness of the model 0.0 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26792 restraints for refining 11212 atoms. 24289 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2300 (Rfree = 0.000) for 11212 atoms. Found 48 (53 requested) and removed 48 (26 requested) atoms. Cycle 27: After refmac, R = 0.2286 (Rfree = 0.000) for 11126 atoms. Found 53 (53 requested) and removed 56 (26 requested) atoms. Cycle 28: After refmac, R = 0.2200 (Rfree = 0.000) for 11037 atoms. Found 52 (52 requested) and removed 65 (26 requested) atoms. Cycle 29: After refmac, R = 0.2142 (Rfree = 0.000) for 10932 atoms. Found 52 (52 requested) and removed 56 (26 requested) atoms. Cycle 30: After refmac, R = 0.2122 (Rfree = 0.000) for 10851 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.47 Search for helices and strands: 0 residues in 0 chains, 11277 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11294 seeds are put forward Round 1: 533 peptides, 108 chains. Longest chain 14 peptides. Score 0.272 Round 2: 637 peptides, 106 chains. Longest chain 15 peptides. Score 0.376 Round 3: 676 peptides, 104 chains. Longest chain 16 peptides. Score 0.416 Round 4: 658 peptides, 101 chains. Longest chain 17 peptides. Score 0.413 Round 5: 689 peptides, 102 chains. Longest chain 18 peptides. Score 0.434 Taking the results from Round 5 Chains 103, Residues 587, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26228 restraints for refining 11210 atoms. 23889 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2088 (Rfree = 0.000) for 11210 atoms. Found 53 (53 requested) and removed 96 (26 requested) atoms. Cycle 32: After refmac, R = 0.2094 (Rfree = 0.000) for 11070 atoms. Found 53 (53 requested) and removed 80 (26 requested) atoms. Cycle 33: After refmac, R = 0.1732 (Rfree = 0.000) for 11004 atoms. Found 15 (52 requested) and removed 54 (26 requested) atoms. Cycle 34: After refmac, R = 0.1666 (Rfree = 0.000) for 10942 atoms. Found 13 (52 requested) and removed 49 (26 requested) atoms. Cycle 35: After refmac, R = 0.1599 (Rfree = 0.000) for 10892 atoms. Found 8 (51 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 11176 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11191 seeds are put forward Round 1: 610 peptides, 120 chains. Longest chain 12 peptides. Score 0.297 Round 2: 672 peptides, 116 chains. Longest chain 16 peptides. Score 0.368 Round 3: 689 peptides, 113 chains. Longest chain 19 peptides. Score 0.394 Round 4: 668 peptides, 102 chains. Longest chain 16 peptides. Score 0.417 Round 5: 692 peptides, 101 chains. Longest chain 18 peptides. Score 0.440 Taking the results from Round 5 Chains 101, Residues 591, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26371 restraints for refining 11212 atoms. 24044 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2211 (Rfree = 0.000) for 11212 atoms. Found 53 (53 requested) and removed 57 (26 requested) atoms. Cycle 37: After refmac, R = 0.2161 (Rfree = 0.000) for 11124 atoms. Found 53 (53 requested) and removed 59 (26 requested) atoms. Cycle 38: After refmac, R = 0.2160 (Rfree = 0.000) for 11041 atoms. Found 52 (52 requested) and removed 61 (26 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2139 (Rfree = 0.000) for 10976 atoms. Found 52 (52 requested) and removed 55 (26 requested) atoms. Cycle 40: After refmac, R = 0.2065 (Rfree = 0.000) for 10921 atoms. Found 52 (52 requested) and removed 61 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 11399 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 11420 seeds are put forward Round 1: 512 peptides, 108 chains. Longest chain 11 peptides. Score 0.251 Round 2: 643 peptides, 112 chains. Longest chain 15 peptides. Score 0.358 Round 3: 630 peptides, 111 chains. Longest chain 13 peptides. Score 0.350 Round 4: 615 peptides, 101 chains. Longest chain 13 peptides. Score 0.376 Round 5: 625 peptides, 104 chains. Longest chain 13 peptides. Score 0.373 Taking the results from Round 4 Chains 102, Residues 514, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25219 restraints for refining 10834 atoms. 23196 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2119 (Rfree = 0.000) for 10834 atoms. Found 48 (51 requested) and removed 70 (25 requested) atoms. Cycle 42: After refmac, R = 0.2035 (Rfree = 0.000) for 10742 atoms. Found 51 (51 requested) and removed 52 (25 requested) atoms. Cycle 43: After refmac, R = 0.2119 (Rfree = 0.000) for 10684 atoms. Found 51 (51 requested) and removed 58 (25 requested) atoms. Cycle 44: After refmac, R = 0.2037 (Rfree = 0.000) for 10632 atoms. Found 50 (50 requested) and removed 48 (25 requested) atoms. Cycle 45: After refmac, R = 0.2067 (Rfree = 0.000) for 10608 atoms. Found 50 (50 requested) and removed 50 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.83 3.49 Search for helices and strands: 0 residues in 0 chains, 11013 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 11030 seeds are put forward Round 1: 495 peptides, 104 chains. Longest chain 14 peptides. Score 0.251 Round 2: 596 peptides, 112 chains. Longest chain 11 peptides. Score 0.316 Round 3: 615 peptides, 112 chains. Longest chain 13 peptides. Score 0.333 Round 4: 595 peptides, 97 chains. Longest chain 17 peptides. Score 0.374 Round 5: 609 peptides, 99 chains. Longest chain 17 peptides. Score 0.378 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 100, Residues 510, Estimated correctness of the model 0.0 % 5 chains (30 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vl6-4_warpNtrace.pdb as input Building loops using Loopy2018 100 chains (510 residues) following loop building 5 chains (30 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16252 reflections ( 99.83 % complete ) and 25160 restraints for refining 10941 atoms. 23145 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2124 (Rfree = 0.000) for 10941 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 47: After refmac, R = 0.2053 (Rfree = 0.000) for 10838 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2152 (Rfree = 0.000) for 10729 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 49: After refmac, R = 0.2125 (Rfree = 0.000) for 10660 atoms. TimeTaking 124.08