null Mon 24 Dec 07:31:17 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 2hr2-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.2-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/2hr2-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.2-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 07:31:21 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/2hr2-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.2-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 956 and 0 Target number of residues in the AU: 956 Target solvent content: 0.6389 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: 2hr2-3.2-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: 2hr2-3.2-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 3.200 Wilson plot Bfac: 71.25 24032 reflections ( 98.55 % complete ) and 0 restraints for refining 8412 atoms. Observations/parameters ratio is 0.71 ------------------------------------------------------ Starting model: R = 0.3249 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2982 (Rfree = 0.000) for 8412 atoms. Found 75 (75 requested) and removed 72 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 2.68 Search for helices and strands: 0 residues in 0 chains, 8700 seeds are put forward NCS extension: 0 residues added, 8700 seeds are put forward Round 1: 574 peptides, 89 chains. Longest chain 20 peptides. Score 0.441 Round 2: 651 peptides, 87 chains. Longest chain 19 peptides. Score 0.528 Round 3: 682 peptides, 80 chains. Longest chain 30 peptides. Score 0.586 Round 4: 677 peptides, 78 chains. Longest chain 25 peptides. Score 0.589 Round 5: 666 peptides, 73 chains. Longest chain 26 peptides. Score 0.600 Taking the results from Round 5 Chains 77, Residues 593, Estimated correctness of the model 41.1 % 12 chains (180 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 12869 restraints for refining 6964 atoms. 9954 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2718 (Rfree = 0.000) for 6964 atoms. Found 62 (62 requested) and removed 61 (31 requested) atoms. Cycle 2: After refmac, R = 0.2577 (Rfree = 0.000) for 6875 atoms. Found 50 (62 requested) and removed 39 (31 requested) atoms. Cycle 3: After refmac, R = 0.2508 (Rfree = 0.000) for 6838 atoms. Found 38 (61 requested) and removed 44 (30 requested) atoms. Cycle 4: After refmac, R = 0.2425 (Rfree = 0.000) for 6798 atoms. Found 27 (61 requested) and removed 35 (30 requested) atoms. Cycle 5: After refmac, R = 0.2354 (Rfree = 0.000) for 6774 atoms. Found 16 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.21 2.65 Search for helices and strands: 0 residues in 0 chains, 7113 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 7139 seeds are put forward Round 1: 654 peptides, 84 chains. Longest chain 31 peptides. Score 0.544 Round 2: 676 peptides, 75 chains. Longest chain 33 peptides. Score 0.600 Round 3: 667 peptides, 75 chains. Longest chain 27 peptides. Score 0.593 Round 4: 673 peptides, 71 chains. Longest chain 34 peptides. Score 0.613 Round 5: 658 peptides, 70 chains. Longest chain 37 peptides. Score 0.605 Taking the results from Round 4 Chains 77, Residues 602, Estimated correctness of the model 44.5 % 20 chains (233 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 12620 restraints for refining 6966 atoms. 9444 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2613 (Rfree = 0.000) for 6966 atoms. Found 62 (62 requested) and removed 49 (31 requested) atoms. Cycle 7: After refmac, R = 0.2394 (Rfree = 0.000) for 6927 atoms. Found 34 (62 requested) and removed 45 (31 requested) atoms. Cycle 8: After refmac, R = 0.2345 (Rfree = 0.000) for 6882 atoms. Found 26 (62 requested) and removed 37 (31 requested) atoms. Cycle 9: After refmac, R = 0.2313 (Rfree = 0.000) for 6849 atoms. Found 26 (61 requested) and removed 37 (30 requested) atoms. Cycle 10: After refmac, R = 0.2229 (Rfree = 0.000) for 6817 atoms. Found 13 (61 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 2.66 Search for helices and strands: 0 residues in 0 chains, 7146 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 7174 seeds are put forward Round 1: 645 peptides, 82 chains. Longest chain 33 peptides. Score 0.544 Round 2: 678 peptides, 73 chains. Longest chain 31 peptides. Score 0.610 Round 3: 682 peptides, 75 chains. Longest chain 21 peptides. Score 0.605 Round 4: 673 peptides, 67 chains. Longest chain 31 peptides. Score 0.629 Round 5: 665 peptides, 76 chains. Longest chain 31 peptides. Score 0.587 Taking the results from Round 4 Chains 81, Residues 606, Estimated correctness of the model 48.6 % 20 chains (237 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 12236 restraints for refining 6966 atoms. 9040 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2664 (Rfree = 0.000) for 6966 atoms. Found 62 (62 requested) and removed 56 (31 requested) atoms. Cycle 12: After refmac, R = 0.2517 (Rfree = 0.000) for 6939 atoms. Found 37 (62 requested) and removed 39 (31 requested) atoms. Cycle 13: After refmac, R = 0.2449 (Rfree = 0.000) for 6910 atoms. Found 30 (62 requested) and removed 57 (31 requested) atoms. Cycle 14: After refmac, R = 0.2369 (Rfree = 0.000) for 6858 atoms. Found 31 (61 requested) and removed 45 (30 requested) atoms. Cycle 15: After refmac, R = 0.2318 (Rfree = 0.000) for 6830 atoms. Found 16 (61 requested) and removed 43 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 2.67 Search for helices and strands: 0 residues in 0 chains, 7148 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 7163 seeds are put forward Round 1: 574 peptides, 76 chains. Longest chain 25 peptides. Score 0.501 Round 2: 640 peptides, 78 chains. Longest chain 20 peptides. Score 0.556 Round 3: 638 peptides, 76 chains. Longest chain 27 peptides. Score 0.563 Round 4: 648 peptides, 74 chains. Longest chain 22 peptides. Score 0.580 Round 5: 662 peptides, 72 chains. Longest chain 28 peptides. Score 0.600 Taking the results from Round 5 Chains 78, Residues 590, Estimated correctness of the model 41.1 % 13 chains (143 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 13432 restraints for refining 6965 atoms. 10628 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2560 (Rfree = 0.000) for 6965 atoms. Found 62 (62 requested) and removed 45 (31 requested) atoms. Cycle 17: After refmac, R = 0.2376 (Rfree = 0.000) for 6954 atoms. Found 32 (62 requested) and removed 42 (31 requested) atoms. Cycle 18: After refmac, R = 0.2302 (Rfree = 0.000) for 6930 atoms. Found 26 (62 requested) and removed 37 (31 requested) atoms. Cycle 19: After refmac, R = 0.2279 (Rfree = 0.000) for 6904 atoms. Found 29 (62 requested) and removed 33 (31 requested) atoms. Cycle 20: After refmac, R = 0.2258 (Rfree = 0.000) for 6884 atoms. Found 20 (61 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 2.66 Search for helices and strands: 0 residues in 0 chains, 7179 seeds are put forward NCS extension: 18 residues added (7 deleted due to clashes), 7197 seeds are put forward Round 1: 612 peptides, 85 chains. Longest chain 21 peptides. Score 0.499 Round 2: 656 peptides, 73 chains. Longest chain 21 peptides. Score 0.591 Round 3: 671 peptides, 74 chains. Longest chain 29 peptides. Score 0.600 Round 4: 643 peptides, 72 chains. Longest chain 22 peptides. Score 0.584 Round 5: 659 peptides, 78 chains. Longest chain 26 peptides. Score 0.573 Taking the results from Round 3 Chains 80, Residues 597, Estimated correctness of the model 41.1 % 13 chains (155 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 13130 restraints for refining 6967 atoms. 10252 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2453 (Rfree = 0.000) for 6967 atoms. Found 62 (62 requested) and removed 46 (31 requested) atoms. Cycle 22: After refmac, R = 0.2255 (Rfree = 0.000) for 6965 atoms. Found 21 (62 requested) and removed 47 (31 requested) atoms. Cycle 23: After refmac, R = 0.2180 (Rfree = 0.000) for 6920 atoms. Found 22 (62 requested) and removed 41 (31 requested) atoms. Cycle 24: After refmac, R = 0.2150 (Rfree = 0.000) for 6888 atoms. Found 18 (61 requested) and removed 35 (30 requested) atoms. Cycle 25: After refmac, R = 0.2131 (Rfree = 0.000) for 6862 atoms. Found 26 (61 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 2.67 Search for helices and strands: 0 residues in 0 chains, 7194 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 7217 seeds are put forward Round 1: 605 peptides, 93 chains. Longest chain 17 peptides. Score 0.455 Round 2: 643 peptides, 80 chains. Longest chain 26 peptides. Score 0.551 Round 3: 636 peptides, 78 chains. Longest chain 24 peptides. Score 0.553 Round 4: 646 peptides, 84 chains. Longest chain 34 peptides. Score 0.536 Round 5: 633 peptides, 77 chains. Longest chain 24 peptides. Score 0.554 Taking the results from Round 5 Chains 83, Residues 556, Estimated correctness of the model 28.1 % 14 chains (129 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 13717 restraints for refining 6966 atoms. 11136 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2448 (Rfree = 0.000) for 6966 atoms. Found 62 (62 requested) and removed 36 (31 requested) atoms. Cycle 27: After refmac, R = 0.2224 (Rfree = 0.000) for 6959 atoms. Found 22 (62 requested) and removed 37 (31 requested) atoms. Cycle 28: After refmac, R = 0.2144 (Rfree = 0.000) for 6928 atoms. Found 15 (62 requested) and removed 34 (31 requested) atoms. Cycle 29: After refmac, R = 0.2107 (Rfree = 0.000) for 6896 atoms. Found 16 (62 requested) and removed 32 (31 requested) atoms. Cycle 30: After refmac, R = 0.2062 (Rfree = 0.000) for 6870 atoms. Found 15 (61 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 2.68 Search for helices and strands: 0 residues in 0 chains, 7179 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7193 seeds are put forward Round 1: 586 peptides, 84 chains. Longest chain 30 peptides. Score 0.477 Round 2: 643 peptides, 78 chains. Longest chain 22 peptides. Score 0.559 Round 3: 635 peptides, 84 chains. Longest chain 27 peptides. Score 0.526 Round 4: 654 peptides, 84 chains. Longest chain 19 peptides. Score 0.544 Round 5: 625 peptides, 77 chains. Longest chain 25 peptides. Score 0.547 Taking the results from Round 2 Chains 84, Residues 565, Estimated correctness of the model 29.5 % 15 chains (156 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 13398 restraints for refining 6967 atoms. 10681 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2406 (Rfree = 0.000) for 6967 atoms. Found 62 (62 requested) and removed 45 (31 requested) atoms. Cycle 32: After refmac, R = 0.2256 (Rfree = 0.000) for 6970 atoms. Found 24 (62 requested) and removed 33 (31 requested) atoms. Cycle 33: After refmac, R = 0.2213 (Rfree = 0.000) for 6946 atoms. Found 19 (62 requested) and removed 31 (31 requested) atoms. Cycle 34: After refmac, R = 0.2159 (Rfree = 0.000) for 6928 atoms. Found 19 (62 requested) and removed 31 (31 requested) atoms. Cycle 35: After refmac, R = 0.2097 (Rfree = 0.000) for 6909 atoms. Found 12 (62 requested) and removed 31 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.25 2.68 Search for helices and strands: 0 residues in 0 chains, 7225 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7238 seeds are put forward Round 1: 560 peptides, 86 chains. Longest chain 21 peptides. Score 0.440 Round 2: 621 peptides, 83 chains. Longest chain 22 peptides. Score 0.517 Round 3: 630 peptides, 78 chains. Longest chain 22 peptides. Score 0.547 Round 4: 625 peptides, 76 chains. Longest chain 22 peptides. Score 0.551 Round 5: 620 peptides, 77 chains. Longest chain 31 peptides. Score 0.542 Taking the results from Round 4 Chains 76, Residues 549, Estimated correctness of the model 27.2 % 6 chains (46 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 14480 restraints for refining 6964 atoms. 12192 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2386 (Rfree = 0.000) for 6964 atoms. Found 48 (62 requested) and removed 38 (31 requested) atoms. Cycle 37: After refmac, R = 0.2221 (Rfree = 0.000) for 6954 atoms. Found 23 (62 requested) and removed 34 (31 requested) atoms. Cycle 38: After refmac, R = 0.2189 (Rfree = 0.000) for 6935 atoms. Found 21 (62 requested) and removed 31 (31 requested) atoms. Cycle 39: After refmac, R = 0.2199 (Rfree = 0.000) for 6922 atoms. Found 19 (62 requested) and removed 31 (31 requested) atoms. Cycle 40: After refmac, R = 0.2127 (Rfree = 0.000) for 6903 atoms. Found 18 (62 requested) and removed 31 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.66 Search for helices and strands: 0 residues in 0 chains, 7204 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 7215 seeds are put forward Round 1: 556 peptides, 79 chains. Longest chain 36 peptides. Score 0.469 Round 2: 609 peptides, 78 chains. Longest chain 23 peptides. Score 0.527 Round 3: 626 peptides, 86 chains. Longest chain 28 peptides. Score 0.508 Round 4: 629 peptides, 84 chains. Longest chain 24 peptides. Score 0.520 Round 5: 633 peptides, 84 chains. Longest chain 37 peptides. Score 0.524 Taking the results from Round 2 Chains 88, Residues 531, Estimated correctness of the model 19.9 % 14 chains (134 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 13638 restraints for refining 6967 atoms. 11098 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2456 (Rfree = 0.000) for 6967 atoms. Found 62 (62 requested) and removed 46 (31 requested) atoms. Cycle 42: After refmac, R = 0.2321 (Rfree = 0.000) for 6971 atoms. Found 30 (62 requested) and removed 33 (31 requested) atoms. Cycle 43: After refmac, R = 0.2290 (Rfree = 0.000) for 6961 atoms. Found 16 (62 requested) and removed 31 (31 requested) atoms. Cycle 44: After refmac, R = 0.2287 (Rfree = 0.000) for 6935 atoms. Found 35 (62 requested) and removed 31 (31 requested) atoms. Cycle 45: After refmac, R = 0.2227 (Rfree = 0.000) for 6933 atoms. Found 26 (62 requested) and removed 32 (31 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.68 Search for helices and strands: 0 residues in 0 chains, 7284 seeds are put forward NCS extension: 14 residues added (9 deleted due to clashes), 7298 seeds are put forward Round 1: 538 peptides, 84 chains. Longest chain 28 peptides. Score 0.425 Round 2: 583 peptides, 78 chains. Longest chain 28 peptides. Score 0.501 Round 3: 583 peptides, 76 chains. Longest chain 33 peptides. Score 0.510 Round 4: 582 peptides, 79 chains. Longest chain 24 peptides. Score 0.496 Round 5: 596 peptides, 74 chains. Longest chain 35 peptides. Score 0.532 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 522, Estimated correctness of the model 21.4 % 12 chains (129 residues) have been docked in sequence Sequence coverage is 24 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 80 chains (522 residues) following loop building 12 chains (129 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24032 reflections ( 98.55 % complete ) and 13695 restraints for refining 6967 atoms. 11220 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2518 (Rfree = 0.000) for 6967 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Cycle 47: After refmac, R = 0.2391 (Rfree = 0.000) for 6909 atoms. Found 0 (62 requested) and removed 23 (31 requested) atoms. Cycle 48: After refmac, R = 0.2407 (Rfree = 0.000) for 6876 atoms. Found 0 (61 requested) and removed 15 (30 requested) atoms. Cycle 49: After refmac, R = 0.2324 (Rfree = 0.000) for 6852 atoms. Found 0 (61 requested) and removed 6 (30 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:55:27 GMT 2018 Job finished. TimeTaking 84.18 Used memory is bytes: 3634176