null Mon 24 Dec 08:01:04 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 2hr2-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-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/2hr2-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-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 08:01:08 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/2hr2-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-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 943 and 0 Target number of residues in the AU: 943 Target solvent content: 0.6438 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-3.4-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 7632 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: 88.085 3.400 Wilson plot Bfac: 74.08 20082 reflections ( 98.41 % complete ) and 0 restraints for refining 8446 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3246 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2910 (Rfree = 0.000) for 8446 atoms. Found 63 (63 requested) and removed 42 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 2.77 Search for helices and strands: 0 residues in 0 chains, 8758 seeds are put forward NCS extension: 0 residues added, 8758 seeds are put forward Round 1: 525 peptides, 87 chains. Longest chain 22 peptides. Score 0.396 Round 2: 610 peptides, 80 chains. Longest chain 31 peptides. Score 0.519 Round 3: 622 peptides, 78 chains. Longest chain 22 peptides. Score 0.539 Round 4: 631 peptides, 70 chains. Longest chain 24 peptides. Score 0.581 Round 5: 632 peptides, 73 chains. Longest chain 23 peptides. Score 0.570 Taking the results from Round 4 Chains 77, Residues 561, Estimated correctness of the model 22.4 % 17 chains (146 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13617 restraints for refining 6937 atoms. 10955 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2585 (Rfree = 0.000) for 6937 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 2: After refmac, R = 0.2361 (Rfree = 0.000) for 6843 atoms. Found 44 (52 requested) and removed 35 (26 requested) atoms. Cycle 3: After refmac, R = 0.2285 (Rfree = 0.000) for 6805 atoms. Found 24 (51 requested) and removed 32 (25 requested) atoms. Cycle 4: After refmac, R = 0.2208 (Rfree = 0.000) for 6774 atoms. Found 28 (51 requested) and removed 26 (25 requested) atoms. Cycle 5: After refmac, R = 0.2161 (Rfree = 0.000) for 6765 atoms. Found 18 (51 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 2.77 Search for helices and strands: 0 residues in 0 chains, 7128 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 7152 seeds are put forward Round 1: 600 peptides, 85 chains. Longest chain 25 peptides. Score 0.487 Round 2: 611 peptides, 79 chains. Longest chain 30 peptides. Score 0.525 Round 3: 600 peptides, 70 chains. Longest chain 33 peptides. Score 0.553 Round 4: 594 peptides, 65 chains. Longest chain 26 peptides. Score 0.569 Round 5: 609 peptides, 68 chains. Longest chain 25 peptides. Score 0.570 Taking the results from Round 5 Chains 74, Residues 541, Estimated correctness of the model 18.6 % 13 chains (149 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13368 restraints for refining 6939 atoms. 10718 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2595 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 60 (26 requested) atoms. Cycle 7: After refmac, R = 0.2355 (Rfree = 0.000) for 6886 atoms. Found 44 (52 requested) and removed 40 (26 requested) atoms. Cycle 8: After refmac, R = 0.2238 (Rfree = 0.000) for 6860 atoms. Found 28 (52 requested) and removed 29 (26 requested) atoms. Cycle 9: After refmac, R = 0.2160 (Rfree = 0.000) for 6849 atoms. Found 18 (51 requested) and removed 25 (25 requested) atoms. Cycle 10: After refmac, R = 0.2111 (Rfree = 0.000) for 6837 atoms. Found 14 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 2.78 Search for helices and strands: 0 residues in 0 chains, 7212 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 7238 seeds are put forward Round 1: 570 peptides, 84 chains. Longest chain 14 peptides. Score 0.460 Round 2: 612 peptides, 72 chains. Longest chain 35 peptides. Score 0.556 Round 3: 612 peptides, 71 chains. Longest chain 26 peptides. Score 0.560 Round 4: 582 peptides, 73 chains. Longest chain 28 peptides. Score 0.523 Round 5: 587 peptides, 69 chains. Longest chain 27 peptides. Score 0.545 Taking the results from Round 3 Chains 79, Residues 541, Estimated correctness of the model 15.1 % 11 chains (99 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14110 restraints for refining 6939 atoms. 11687 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2513 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 53 (26 requested) atoms. Cycle 12: After refmac, R = 0.2320 (Rfree = 0.000) for 6890 atoms. Found 31 (52 requested) and removed 35 (26 requested) atoms. Cycle 13: After refmac, R = 0.2194 (Rfree = 0.000) for 6863 atoms. Found 24 (51 requested) and removed 43 (25 requested) atoms. Cycle 14: After refmac, R = 0.2137 (Rfree = 0.000) for 6833 atoms. Found 12 (51 requested) and removed 29 (25 requested) atoms. Cycle 15: After refmac, R = 0.2089 (Rfree = 0.000) for 6806 atoms. Found 14 (51 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.76 Search for helices and strands: 0 residues in 0 chains, 7175 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 7194 seeds are put forward Round 1: 580 peptides, 88 chains. Longest chain 24 peptides. Score 0.452 Round 2: 599 peptides, 73 chains. Longest chain 26 peptides. Score 0.539 Round 3: 575 peptides, 70 chains. Longest chain 18 peptides. Score 0.530 Round 4: 584 peptides, 68 chains. Longest chain 31 peptides. Score 0.547 Round 5: 598 peptides, 69 chains. Longest chain 21 peptides. Score 0.556 Taking the results from Round 5 Chains 72, Residues 529, Estimated correctness of the model 13.7 % 9 chains (73 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14206 restraints for refining 6939 atoms. 11934 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2490 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. Cycle 17: After refmac, R = 0.2305 (Rfree = 0.000) for 6896 atoms. Found 32 (52 requested) and removed 38 (26 requested) atoms. Cycle 18: After refmac, R = 0.2204 (Rfree = 0.000) for 6858 atoms. Found 19 (52 requested) and removed 29 (26 requested) atoms. Cycle 19: After refmac, R = 0.2120 (Rfree = 0.000) for 6829 atoms. Found 31 (51 requested) and removed 30 (25 requested) atoms. Cycle 20: After refmac, R = 0.2058 (Rfree = 0.000) for 6818 atoms. Found 22 (51 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 2.77 Search for helices and strands: 0 residues in 0 chains, 7226 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 7252 seeds are put forward Round 1: 544 peptides, 79 chains. Longest chain 22 peptides. Score 0.456 Round 2: 601 peptides, 73 chains. Longest chain 20 peptides. Score 0.541 Round 3: 592 peptides, 70 chains. Longest chain 28 peptides. Score 0.546 Round 4: 584 peptides, 65 chains. Longest chain 35 peptides. Score 0.560 Round 5: 566 peptides, 72 chains. Longest chain 20 peptides. Score 0.512 Taking the results from Round 4 Chains 69, Residues 519, Estimated correctness of the model 15.1 % 7 chains (97 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14044 restraints for refining 6939 atoms. 11680 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2428 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 22: After refmac, R = 0.2247 (Rfree = 0.000) for 6901 atoms. Found 32 (52 requested) and removed 37 (26 requested) atoms. Cycle 23: After refmac, R = 0.2182 (Rfree = 0.000) for 6886 atoms. Found 22 (52 requested) and removed 32 (26 requested) atoms. Cycle 24: After refmac, R = 0.2167 (Rfree = 0.000) for 6865 atoms. Found 18 (51 requested) and removed 26 (25 requested) atoms. Cycle 25: After refmac, R = 0.2176 (Rfree = 0.000) for 6847 atoms. Found 23 (51 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.77 Search for helices and strands: 0 residues in 0 chains, 7236 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 7261 seeds are put forward Round 1: 526 peptides, 85 chains. Longest chain 15 peptides. Score 0.407 Round 2: 548 peptides, 76 chains. Longest chain 20 peptides. Score 0.475 Round 3: 558 peptides, 73 chains. Longest chain 24 peptides. Score 0.499 Round 4: 528 peptides, 70 chains. Longest chain 19 peptides. Score 0.482 Round 5: 542 peptides, 76 chains. Longest chain 25 peptides. Score 0.468 Taking the results from Round 3 Chains 73, Residues 485, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 15377 restraints for refining 6938 atoms. 13510 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2274 (Rfree = 0.000) for 6938 atoms. Found 36 (52 requested) and removed 31 (26 requested) atoms. Cycle 27: After refmac, R = 0.2168 (Rfree = 0.000) for 6921 atoms. Found 26 (52 requested) and removed 32 (26 requested) atoms. Cycle 28: After refmac, R = 0.2101 (Rfree = 0.000) for 6907 atoms. Found 14 (52 requested) and removed 28 (26 requested) atoms. Cycle 29: After refmac, R = 0.2491 (Rfree = 0.000) for 6883 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. Cycle 30: After refmac, R = 0.2032 (Rfree = 0.000) for 6882 atoms. Found 22 (52 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 2.74 Search for helices and strands: 0 residues in 0 chains, 7265 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 7294 seeds are put forward Round 1: 513 peptides, 84 chains. Longest chain 17 peptides. Score 0.397 Round 2: 578 peptides, 75 chains. Longest chain 25 peptides. Score 0.510 Round 3: 575 peptides, 76 chains. Longest chain 19 peptides. Score 0.502 Round 4: 575 peptides, 75 chains. Longest chain 20 peptides. Score 0.507 Round 5: 561 peptides, 70 chains. Longest chain 24 peptides. Score 0.516 Taking the results from Round 5 Chains 76, Residues 491, Estimated correctness of the model 0.0 % 10 chains (75 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14489 restraints for refining 6939 atoms. 12361 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2410 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 37 (26 requested) atoms. Cycle 32: After refmac, R = 0.2240 (Rfree = 0.000) for 6932 atoms. Found 30 (52 requested) and removed 37 (26 requested) atoms. Cycle 33: After refmac, R = 0.2217 (Rfree = 0.000) for 6913 atoms. Found 32 (52 requested) and removed 30 (26 requested) atoms. Cycle 34: After refmac, R = 0.2128 (Rfree = 0.000) for 6911 atoms. Found 13 (52 requested) and removed 28 (26 requested) atoms. Cycle 35: After refmac, R = 0.2071 (Rfree = 0.000) for 6889 atoms. Found 13 (52 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 2.77 Search for helices and strands: 0 residues in 0 chains, 7250 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7268 seeds are put forward Round 1: 525 peptides, 93 chains. Longest chain 14 peptides. Score 0.366 Round 2: 539 peptides, 82 chains. Longest chain 19 peptides. Score 0.436 Round 3: 554 peptides, 79 chains. Longest chain 28 peptides. Score 0.467 Round 4: 561 peptides, 83 chains. Longest chain 17 peptides. Score 0.455 Round 5: 548 peptides, 72 chains. Longest chain 22 peptides. Score 0.494 Taking the results from Round 5 Chains 75, Residues 476, Estimated correctness of the model 0.0 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 15010 restraints for refining 6939 atoms. 13049 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2383 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 35 (26 requested) atoms. Cycle 37: After refmac, R = 0.2168 (Rfree = 0.000) for 6936 atoms. Found 27 (52 requested) and removed 33 (26 requested) atoms. Cycle 38: After refmac, R = 0.2077 (Rfree = 0.000) for 6914 atoms. Found 10 (52 requested) and removed 30 (26 requested) atoms. Cycle 39: After refmac, R = 0.2015 (Rfree = 0.000) for 6882 atoms. Found 18 (52 requested) and removed 27 (26 requested) atoms. Cycle 40: After refmac, R = 0.1974 (Rfree = 0.000) for 6864 atoms. Found 13 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 2.78 Search for helices and strands: 0 residues in 0 chains, 7199 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 7218 seeds are put forward Round 1: 469 peptides, 81 chains. Longest chain 13 peptides. Score 0.361 Round 2: 516 peptides, 73 chains. Longest chain 23 peptides. Score 0.455 Round 3: 535 peptides, 72 chains. Longest chain 27 peptides. Score 0.480 Round 4: 524 peptides, 76 chains. Longest chain 21 peptides. Score 0.449 Round 5: 540 peptides, 74 chains. Longest chain 26 peptides. Score 0.476 Taking the results from Round 3 Chains 75, Residues 463, Estimated correctness of the model 0.0 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 15038 restraints for refining 6939 atoms. 13073 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2272 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 33 (26 requested) atoms. Cycle 42: After refmac, R = 0.2107 (Rfree = 0.000) for 6942 atoms. Found 22 (52 requested) and removed 27 (26 requested) atoms. Cycle 43: After refmac, R = 0.2008 (Rfree = 0.000) for 6931 atoms. Found 11 (52 requested) and removed 26 (26 requested) atoms. Cycle 44: After refmac, R = 0.1966 (Rfree = 0.000) for 6913 atoms. Found 10 (52 requested) and removed 26 (26 requested) atoms. Cycle 45: After refmac, R = 0.1945 (Rfree = 0.000) for 6895 atoms. Found 9 (52 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 2.78 Search for helices and strands: 0 residues in 0 chains, 7242 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 7264 seeds are put forward Round 1: 449 peptides, 81 chains. Longest chain 15 peptides. Score 0.337 Round 2: 524 peptides, 78 chains. Longest chain 22 peptides. Score 0.439 Round 3: 535 peptides, 82 chains. Longest chain 17 peptides. Score 0.432 Round 4: 537 peptides, 80 chains. Longest chain 20 peptides. Score 0.444 Round 5: 539 peptides, 79 chains. Longest chain 17 peptides. Score 0.451 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 79, Residues 460, Estimated correctness of the model 0.0 % 7 chains (50 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 64 C and 78 C 77 chains (467 residues) following loop building 6 chains (63 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20082 reflections ( 98.41 % complete ) and 14919 restraints for refining 6938 atoms. 12936 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2363 (Rfree = 0.000) for 6938 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2194 (Rfree = 0.000) for 6891 atoms. Found 0 (52 requested) and removed 19 (26 requested) atoms. Cycle 48: After refmac, R = 0.2131 (Rfree = 0.000) for 6861 atoms. Found 0 (51 requested) and removed 8 (25 requested) atoms. Cycle 49: After refmac, R = 0.2074 (Rfree = 0.000) for 6847 atoms. Found 0 (51 requested) and removed 3 (25 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:15:48 GMT 2018 Job finished. TimeTaking 74.73 Used memory is bytes: 8916120