Mon 24 Dec 00:00:30 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 1vlu-3.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-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/1vlu-3.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-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 ============================================================ Mon 24 Dec 00:00:35 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/1vlu-3.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-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 1068 and 0 Target number of residues in the AU: 1068 Target solvent content: 0.6067 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-3.0-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7488 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: 44.569 3.000 Wilson plot Bfac: 55.41 29835 reflections ( 99.91 % complete ) and 0 restraints for refining 8316 atoms. Observations/parameters ratio is 0.90 ------------------------------------------------------ Starting model: R = 0.3552 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3238 (Rfree = 0.000) for 8316 atoms. Found 89 (89 requested) and removed 119 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 2.45 Search for helices and strands: 0 residues in 0 chains, 8480 seeds are put forward NCS extension: 0 residues added, 8480 seeds are put forward Round 1: 485 peptides, 72 chains. Longest chain 22 peptides. Score 0.421 Round 2: 577 peptides, 69 chains. Longest chain 24 peptides. Score 0.530 Round 3: 602 peptides, 66 chains. Longest chain 38 peptides. Score 0.565 Round 4: 588 peptides, 57 chains. Longest chain 42 peptides. Score 0.591 Round 5: 613 peptides, 61 chains. Longest chain 48 peptides. Score 0.596 Taking the results from Round 5 Chains 70, Residues 552, Estimated correctness of the model 51.0 % 10 chains (171 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 13048 restraints for refining 6868 atoms. 10283 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2879 (Rfree = 0.000) for 6868 atoms. Found 74 (74 requested) and removed 80 (37 requested) atoms. Cycle 2: After refmac, R = 0.2636 (Rfree = 0.000) for 6770 atoms. Found 69 (74 requested) and removed 64 (37 requested) atoms. Cycle 3: After refmac, R = 0.2443 (Rfree = 0.000) for 6737 atoms. Found 42 (73 requested) and removed 51 (36 requested) atoms. Cycle 4: After refmac, R = 0.2354 (Rfree = 0.000) for 6696 atoms. Found 32 (72 requested) and removed 37 (36 requested) atoms. Cycle 5: After refmac, R = 0.2292 (Rfree = 0.000) for 6667 atoms. Found 22 (72 requested) and removed 38 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.98 2.39 Search for helices and strands: 0 residues in 0 chains, 6915 seeds are put forward NCS extension: 39 residues added (6 deleted due to clashes), 6954 seeds are put forward Round 1: 608 peptides, 60 chains. Longest chain 46 peptides. Score 0.595 Round 2: 634 peptides, 52 chains. Longest chain 70 peptides. Score 0.648 Round 3: 636 peptides, 56 chains. Longest chain 47 peptides. Score 0.634 Round 4: 633 peptides, 56 chains. Longest chain 54 peptides. Score 0.632 Round 5: 621 peptides, 58 chains. Longest chain 45 peptides. Score 0.614 Taking the results from Round 2 Chains 56, Residues 582, Estimated correctness of the model 61.9 % 12 chains (233 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 12181 restraints for refining 6872 atoms. 9003 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2590 (Rfree = 0.000) for 6872 atoms. Found 74 (74 requested) and removed 68 (37 requested) atoms. Cycle 7: After refmac, R = 0.2349 (Rfree = 0.000) for 6834 atoms. Found 44 (74 requested) and removed 50 (37 requested) atoms. Cycle 8: After refmac, R = 0.2385 (Rfree = 0.000) for 6796 atoms. Found 49 (73 requested) and removed 50 (36 requested) atoms. Cycle 9: After refmac, R = 0.2150 (Rfree = 0.000) for 6774 atoms. Found 33 (73 requested) and removed 44 (36 requested) atoms. Cycle 10: After refmac, R = 0.2110 (Rfree = 0.000) for 6744 atoms. Found 19 (72 requested) and removed 41 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 2.39 Search for helices and strands: 0 residues in 0 chains, 6936 seeds are put forward NCS extension: 77 residues added (25 deleted due to clashes), 7013 seeds are put forward Round 1: 595 peptides, 60 chains. Longest chain 39 peptides. Score 0.584 Round 2: 630 peptides, 56 chains. Longest chain 51 peptides. Score 0.629 Round 3: 631 peptides, 53 chains. Longest chain 39 peptides. Score 0.642 Round 4: 645 peptides, 56 chains. Longest chain 44 peptides. Score 0.641 Round 5: 644 peptides, 51 chains. Longest chain 47 peptides. Score 0.659 Taking the results from Round 5 Chains 59, Residues 593, Estimated correctness of the model 64.1 % 14 chains (293 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11484 restraints for refining 6871 atoms. 8087 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2623 (Rfree = 0.000) for 6871 atoms. Found 74 (74 requested) and removed 95 (37 requested) atoms. Cycle 12: After refmac, R = 0.2463 (Rfree = 0.000) for 6799 atoms. Found 69 (73 requested) and removed 63 (36 requested) atoms. Cycle 13: After refmac, R = 0.2188 (Rfree = 0.000) for 6765 atoms. Found 33 (73 requested) and removed 48 (36 requested) atoms. Cycle 14: After refmac, R = 0.2122 (Rfree = 0.000) for 6741 atoms. Found 27 (72 requested) and removed 39 (36 requested) atoms. Cycle 15: After refmac, R = 0.2113 (Rfree = 0.000) for 6718 atoms. Found 24 (72 requested) and removed 46 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.96 2.37 Search for helices and strands: 0 residues in 0 chains, 6925 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 6961 seeds are put forward Round 1: 626 peptides, 49 chains. Longest chain 51 peptides. Score 0.653 Round 2: 635 peptides, 47 chains. Longest chain 48 peptides. Score 0.667 Round 3: 640 peptides, 52 chains. Longest chain 50 peptides. Score 0.652 Round 4: 627 peptides, 54 chains. Longest chain 49 peptides. Score 0.635 Round 5: 639 peptides, 51 chains. Longest chain 49 peptides. Score 0.655 Taking the results from Round 2 Chains 55, Residues 588, Estimated correctness of the model 65.6 % 11 chains (267 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11645 restraints for refining 6872 atoms. 8335 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2546 (Rfree = 0.000) for 6872 atoms. Found 74 (74 requested) and removed 95 (37 requested) atoms. Cycle 17: After refmac, R = 0.2405 (Rfree = 0.000) for 6804 atoms. Found 73 (73 requested) and removed 68 (36 requested) atoms. Cycle 18: After refmac, R = 0.2344 (Rfree = 0.000) for 6776 atoms. Found 73 (73 requested) and removed 66 (36 requested) atoms. Cycle 19: After refmac, R = 0.2278 (Rfree = 0.000) for 6770 atoms. Found 70 (73 requested) and removed 55 (36 requested) atoms. Cycle 20: After refmac, R = 0.2077 (Rfree = 0.000) for 6769 atoms. Found 23 (73 requested) and removed 51 (36 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 6984 seeds are put forward NCS extension: 43 residues added (12 deleted due to clashes), 7027 seeds are put forward Round 1: 623 peptides, 54 chains. Longest chain 48 peptides. Score 0.631 Round 2: 655 peptides, 54 chains. Longest chain 33 peptides. Score 0.656 Round 3: 626 peptides, 52 chains. Longest chain 43 peptides. Score 0.641 Round 4: 640 peptides, 50 chains. Longest chain 57 peptides. Score 0.660 Round 5: 652 peptides, 49 chains. Longest chain 47 peptides. Score 0.672 Taking the results from Round 5 Chains 58, Residues 603, Estimated correctness of the model 66.6 % 14 chains (295 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11335 restraints for refining 6873 atoms. 7819 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2495 (Rfree = 0.000) for 6873 atoms. Found 74 (74 requested) and removed 89 (37 requested) atoms. Cycle 22: After refmac, R = 0.2326 (Rfree = 0.000) for 6823 atoms. Found 58 (73 requested) and removed 63 (36 requested) atoms. Cycle 23: After refmac, R = 0.2251 (Rfree = 0.000) for 6799 atoms. Found 50 (73 requested) and removed 52 (36 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2222 (Rfree = 0.000) for 6789 atoms. Found 54 (73 requested) and removed 48 (36 requested) atoms. Cycle 25: After refmac, R = 0.2148 (Rfree = 0.000) for 6789 atoms. Found 49 (73 requested) and removed 45 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 7021 seeds are put forward NCS extension: 45 residues added (5 deleted due to clashes), 7066 seeds are put forward Round 1: 616 peptides, 55 chains. Longest chain 47 peptides. Score 0.622 Round 2: 639 peptides, 47 chains. Longest chain 63 peptides. Score 0.670 Round 3: 643 peptides, 56 chains. Longest chain 40 peptides. Score 0.639 Round 4: 627 peptides, 50 chains. Longest chain 44 peptides. Score 0.650 Round 5: 629 peptides, 55 chains. Longest chain 47 peptides. Score 0.632 Taking the results from Round 2 Chains 55, Residues 592, Estimated correctness of the model 66.2 % 15 chains (347 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10716 restraints for refining 6873 atoms. 7119 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2343 (Rfree = 0.000) for 6873 atoms. Found 74 (74 requested) and removed 81 (37 requested) atoms. Cycle 27: After refmac, R = 0.2189 (Rfree = 0.000) for 6823 atoms. Found 50 (74 requested) and removed 62 (37 requested) atoms. Cycle 28: After refmac, R = 0.2130 (Rfree = 0.000) for 6788 atoms. Found 45 (73 requested) and removed 48 (36 requested) atoms. Cycle 29: After refmac, R = 0.1973 (Rfree = 0.000) for 6766 atoms. Found 28 (73 requested) and removed 44 (36 requested) atoms. Cycle 30: After refmac, R = 0.1929 (Rfree = 0.000) for 6747 atoms. Found 23 (72 requested) and removed 41 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.98 2.39 Search for helices and strands: 0 residues in 0 chains, 6940 seeds are put forward NCS extension: 32 residues added (33 deleted due to clashes), 6972 seeds are put forward Round 1: 608 peptides, 51 chains. Longest chain 42 peptides. Score 0.631 Round 2: 653 peptides, 46 chains. Longest chain 51 peptides. Score 0.683 Round 3: 632 peptides, 49 chains. Longest chain 47 peptides. Score 0.657 Round 4: 634 peptides, 56 chains. Longest chain 50 peptides. Score 0.632 Round 5: 642 peptides, 54 chains. Longest chain 37 peptides. Score 0.646 Taking the results from Round 2 Chains 47, Residues 607, Estimated correctness of the model 68.6 % 14 chains (340 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10922 restraints for refining 6873 atoms. 7296 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2207 (Rfree = 0.000) for 6873 atoms. Found 54 (74 requested) and removed 64 (37 requested) atoms. Cycle 32: After refmac, R = 0.2131 (Rfree = 0.000) for 6838 atoms. Found 54 (74 requested) and removed 47 (37 requested) atoms. Cycle 33: After refmac, R = 0.2150 (Rfree = 0.000) for 6836 atoms. Found 39 (73 requested) and removed 44 (36 requested) atoms. Cycle 34: After refmac, R = 0.2104 (Rfree = 0.000) for 6823 atoms. Found 53 (73 requested) and removed 51 (36 requested) atoms. Cycle 35: After refmac, R = 0.2116 (Rfree = 0.000) for 6816 atoms. Found 55 (73 requested) and removed 48 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.99 2.40 Search for helices and strands: 0 residues in 0 chains, 7045 seeds are put forward NCS extension: 29 residues added (51 deleted due to clashes), 7074 seeds are put forward Round 1: 611 peptides, 56 chains. Longest chain 43 peptides. Score 0.614 Round 2: 623 peptides, 51 chains. Longest chain 44 peptides. Score 0.643 Round 3: 636 peptides, 51 chains. Longest chain 47 peptides. Score 0.653 Round 4: 642 peptides, 52 chains. Longest chain 51 peptides. Score 0.654 Round 5: 625 peptides, 52 chains. Longest chain 40 peptides. Score 0.641 Taking the results from Round 4 Chains 56, Residues 590, Estimated correctness of the model 63.1 % 13 chains (283 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11463 restraints for refining 6873 atoms. 8105 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2367 (Rfree = 0.000) for 6873 atoms. Found 73 (74 requested) and removed 83 (37 requested) atoms. Cycle 37: After refmac, R = 0.2289 (Rfree = 0.000) for 6829 atoms. Found 53 (74 requested) and removed 62 (37 requested) atoms. Cycle 38: After refmac, R = 0.2260 (Rfree = 0.000) for 6796 atoms. Found 67 (73 requested) and removed 48 (36 requested) atoms. Cycle 39: After refmac, R = 0.2237 (Rfree = 0.000) for 6799 atoms. Found 71 (73 requested) and removed 44 (36 requested) atoms. Cycle 40: After refmac, R = 0.1986 (Rfree = 0.000) for 6808 atoms. Found 21 (73 requested) and removed 43 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 2.39 Search for helices and strands: 0 residues in 0 chains, 6981 seeds are put forward NCS extension: 52 residues added (14 deleted due to clashes), 7033 seeds are put forward Round 1: 594 peptides, 58 chains. Longest chain 57 peptides. Score 0.592 Round 2: 629 peptides, 49 chains. Longest chain 51 peptides. Score 0.655 Round 3: 635 peptides, 49 chains. Longest chain 70 peptides. Score 0.660 Round 4: 635 peptides, 49 chains. Longest chain 40 peptides. Score 0.660 Round 5: 641 peptides, 51 chains. Longest chain 45 peptides. Score 0.657 Taking the results from Round 4 Chains 61, Residues 586, Estimated correctness of the model 64.3 % 19 chains (314 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11218 restraints for refining 6871 atoms. 7740 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2419 (Rfree = 0.000) for 6871 atoms. Found 74 (74 requested) and removed 72 (37 requested) atoms. Cycle 42: After refmac, R = 0.2316 (Rfree = 0.000) for 6830 atoms. Found 74 (74 requested) and removed 52 (37 requested) atoms. Cycle 43: After refmac, R = 0.2257 (Rfree = 0.000) for 6840 atoms. Found 71 (73 requested) and removed 55 (36 requested) atoms. Cycle 44: After refmac, R = 0.2209 (Rfree = 0.000) for 6841 atoms. Found 56 (73 requested) and removed 47 (36 requested) atoms. Cycle 45: After refmac, R = 0.1966 (Rfree = 0.000) for 6834 atoms. Found 27 (73 requested) and removed 42 (36 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 7028 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 7067 seeds are put forward Round 1: 605 peptides, 50 chains. Longest chain 45 peptides. Score 0.633 Round 2: 632 peptides, 46 chains. Longest chain 48 peptides. Score 0.668 Round 3: 627 peptides, 49 chains. Longest chain 47 peptides. Score 0.654 Round 4: 627 peptides, 56 chains. Longest chain 47 peptides. Score 0.627 Round 5: 614 peptides, 48 chains. Longest chain 46 peptides. Score 0.647 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 47, Residues 586, Estimated correctness of the model 65.8 % 17 chains (369 residues) have been docked in sequence Sequence coverage is 62 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 34 A and 37 A Built loop between residues 126 A and 129 A Built loop between residues 174 A and 177 A Built loop between residues 196 A and 201 A Built loop between residues 30 B and 35 B Built loop between residues 219 B and 223 B 41 chains (603 residues) following loop building 11 chains (386 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 29835 reflections ( 99.91 % complete ) and 10388 restraints for refining 6873 atoms. 6588 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2412 (Rfree = 0.000) for 6873 atoms. Found 0 (74 requested) and removed 37 (37 requested) atoms. Cycle 47: After refmac, R = 0.2328 (Rfree = 0.000) for 6797 atoms. Found 0 (73 requested) and removed 33 (36 requested) atoms. Cycle 48: After refmac, R = 0.2294 (Rfree = 0.000) for 6751 atoms. Found 0 (72 requested) and removed 29 (36 requested) atoms. Cycle 49: After refmac, R = 0.2221 (Rfree = 0.000) for 6706 atoms. TimeTaking 84.72