Mon 24 Dec 01:01:42 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 2hr2-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.2-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/2hr2-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.2-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 01:01:46 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/2hr2-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.2-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 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-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.80 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 8517 atoms. Observations/parameters ratio is 0.71 ------------------------------------------------------ Starting model: R = 0.3109 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2632 (Rfree = 0.000) for 8517 atoms. Found 76 (76 requested) and removed 173 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 2.67 Search for helices and strands: 0 residues in 0 chains, 8671 seeds are put forward NCS extension: 0 residues added, 8671 seeds are put forward Round 1: 572 peptides, 102 chains. Longest chain 16 peptides. Score 0.375 Round 2: 681 peptides, 94 chains. Longest chain 26 peptides. Score 0.527 Round 3: 686 peptides, 90 chains. Longest chain 17 peptides. Score 0.548 Round 4: 682 peptides, 76 chains. Longest chain 33 peptides. Score 0.601 Round 5: 700 peptides, 80 chains. Longest chain 25 peptides. Score 0.601 Taking the results from Round 5 Chains 83, Residues 620, Estimated correctness of the model 41.3 % 15 chains (150 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 13130 restraints for refining 6964 atoms. 10228 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2779 (Rfree = 0.000) for 6964 atoms. Found 62 (62 requested) and removed 77 (31 requested) atoms. Cycle 2: After refmac, R = 0.2616 (Rfree = 0.000) for 6856 atoms. Found 47 (62 requested) and removed 59 (31 requested) atoms. Cycle 3: After refmac, R = 0.2507 (Rfree = 0.000) for 6808 atoms. Found 24 (61 requested) and removed 39 (30 requested) atoms. Cycle 4: After refmac, R = 0.2452 (Rfree = 0.000) for 6763 atoms. Found 23 (60 requested) and removed 35 (30 requested) atoms. Cycle 5: After refmac, R = 0.2434 (Rfree = 0.000) for 6738 atoms. Found 21 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.66 Search for helices and strands: 0 residues in 0 chains, 7064 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 7092 seeds are put forward Round 1: 666 peptides, 80 chains. Longest chain 23 peptides. Score 0.571 Round 2: 706 peptides, 73 chains. Longest chain 33 peptides. Score 0.633 Round 3: 703 peptides, 66 chains. Longest chain 30 peptides. Score 0.656 Round 4: 695 peptides, 74 chains. Longest chain 35 peptides. Score 0.620 Round 5: 688 peptides, 74 chains. Longest chain 29 peptides. Score 0.614 Taking the results from Round 3 Chains 73, Residues 637, Estimated correctness of the model 55.3 % 20 chains (272 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 11930 restraints for refining 6967 atoms. 8464 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2756 (Rfree = 0.000) for 6967 atoms. Found 62 (62 requested) and removed 65 (31 requested) atoms. Cycle 7: After refmac, R = 0.2711 (Rfree = 0.000) for 6917 atoms. Found 62 (62 requested) and removed 61 (31 requested) atoms. Cycle 8: After refmac, R = 0.2801 (Rfree = 0.000) for 6879 atoms. Found 62 (62 requested) and removed 71 (31 requested) atoms. Cycle 9: After refmac, R = 0.2659 (Rfree = 0.000) for 6822 atoms. Found 61 (61 requested) and removed 63 (30 requested) atoms. Cycle 10: After refmac, R = 0.2663 (Rfree = 0.000) for 6767 atoms. Found 61 (61 requested) and removed 74 (30 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 2.63 Search for helices and strands: 0 residues in 0 chains, 7082 seeds are put forward NCS extension: 37 residues added (5 deleted due to clashes), 7119 seeds are put forward Round 1: 690 peptides, 80 chains. Longest chain 22 peptides. Score 0.593 Round 2: 706 peptides, 68 chains. Longest chain 31 peptides. Score 0.651 Round 3: 710 peptides, 73 chains. Longest chain 40 peptides. Score 0.636 Round 4: 702 peptides, 71 chains. Longest chain 27 peptides. Score 0.637 Round 5: 688 peptides, 70 chains. Longest chain 33 peptides. Score 0.630 Taking the results from Round 2 Chains 76, Residues 638, Estimated correctness of the model 54.1 % 17 chains (245 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 12286 restraints for refining 6965 atoms. 8927 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2581 (Rfree = 0.000) for 6965 atoms. Found 62 (62 requested) and removed 50 (31 requested) atoms. Cycle 12: After refmac, R = 0.2321 (Rfree = 0.000) for 6935 atoms. Found 29 (62 requested) and removed 47 (31 requested) atoms. Cycle 13: After refmac, R = 0.2225 (Rfree = 0.000) for 6878 atoms. Found 25 (62 requested) and removed 39 (31 requested) atoms. Cycle 14: After refmac, R = 0.2136 (Rfree = 0.000) for 6846 atoms. Found 27 (61 requested) and removed 43 (30 requested) atoms. Cycle 15: After refmac, R = 0.2076 (Rfree = 0.000) for 6821 atoms. Found 16 (61 requested) and removed 34 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 2.65 Search for helices and strands: 0 residues in 0 chains, 7107 seeds are put forward NCS extension: 6 residues added (16 deleted due to clashes), 7113 seeds are put forward Round 1: 681 peptides, 85 chains. Longest chain 27 peptides. Score 0.564 Round 2: 706 peptides, 73 chains. Longest chain 34 peptides. Score 0.633 Round 3: 721 peptides, 73 chains. Longest chain 31 peptides. Score 0.644 Round 4: 717 peptides, 75 chains. Longest chain 33 peptides. Score 0.634 Round 5: 700 peptides, 68 chains. Longest chain 28 peptides. Score 0.646 Taking the results from Round 5 Chains 75, Residues 632, Estimated correctness of the model 52.9 % 20 chains (293 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 11933 restraints for refining 6967 atoms. 8402 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2623 (Rfree = 0.000) for 6967 atoms. Found 62 (62 requested) and removed 54 (31 requested) atoms. Cycle 17: After refmac, R = 0.2617 (Rfree = 0.000) for 6936 atoms. Found 62 (62 requested) and removed 58 (31 requested) atoms. Cycle 18: After refmac, R = 0.2626 (Rfree = 0.000) for 6898 atoms. Found 62 (62 requested) and removed 51 (31 requested) atoms. Cycle 19: After refmac, R = 0.2645 (Rfree = 0.000) for 6886 atoms. Found 62 (62 requested) and removed 53 (31 requested) atoms. Cycle 20: After refmac, R = 0.2625 (Rfree = 0.000) for 6877 atoms. Found 61 (61 requested) and removed 58 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 2.64 Search for helices and strands: 0 residues in 0 chains, 7233 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 7244 seeds are put forward Round 1: 663 peptides, 78 chains. Longest chain 28 peptides. Score 0.577 Round 2: 696 peptides, 68 chains. Longest chain 39 peptides. Score 0.643 Round 3: 658 peptides, 67 chains. Longest chain 40 peptides. Score 0.617 Round 4: 658 peptides, 68 chains. Longest chain 42 peptides. Score 0.613 Round 5: 679 peptides, 64 chains. Longest chain 31 peptides. Score 0.645 Taking the results from Round 5 Chains 81, Residues 615, Estimated correctness of the model 52.6 % 26 chains (289 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 11963 restraints for refining 6966 atoms. 8554 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2629 (Rfree = 0.000) for 6966 atoms. Found 62 (62 requested) and removed 45 (31 requested) atoms. Cycle 22: After refmac, R = 0.2418 (Rfree = 0.000) for 6950 atoms. Found 37 (62 requested) and removed 44 (31 requested) atoms. Cycle 23: After refmac, R = 0.2527 (Rfree = 0.000) for 6919 atoms. Found 62 (62 requested) and removed 53 (31 requested) atoms. Cycle 24: After refmac, R = 0.2604 (Rfree = 0.000) for 6904 atoms. Found 62 (62 requested) and removed 63 (31 requested) atoms. Cycle 25: After refmac, R = 0.2565 (Rfree = 0.000) for 6889 atoms. Found 61 (61 requested) and removed 51 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.65 Search for helices and strands: 0 residues in 0 chains, 7197 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7217 seeds are put forward Round 1: 610 peptides, 76 chains. Longest chain 21 peptides. Score 0.537 Round 2: 654 peptides, 73 chains. Longest chain 21 peptides. Score 0.589 Round 3: 668 peptides, 68 chains. Longest chain 35 peptides. Score 0.621 Round 4: 643 peptides, 69 chains. Longest chain 36 peptides. Score 0.596 Round 5: 647 peptides, 68 chains. Longest chain 31 peptides. Score 0.603 Taking the results from Round 3 Chains 76, Residues 600, Estimated correctness of the model 46.6 % 16 chains (232 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 12305 restraints for refining 6967 atoms. 9109 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2605 (Rfree = 0.000) for 6967 atoms. Found 62 (62 requested) and removed 66 (31 requested) atoms. Cycle 27: After refmac, R = 0.2590 (Rfree = 0.000) for 6919 atoms. Found 62 (62 requested) and removed 54 (31 requested) atoms. Cycle 28: After refmac, R = 0.2602 (Rfree = 0.000) for 6901 atoms. Found 62 (62 requested) and removed 53 (31 requested) atoms. Cycle 29: After refmac, R = 0.2566 (Rfree = 0.000) for 6887 atoms. Found 62 (62 requested) and removed 52 (31 requested) atoms. Cycle 30: After refmac, R = 0.2513 (Rfree = 0.000) for 6879 atoms. Found 61 (61 requested) and removed 50 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.63 Search for helices and strands: 0 residues in 0 chains, 7212 seeds are put forward NCS extension: 12 residues added (14 deleted due to clashes), 7224 seeds are put forward Round 1: 625 peptides, 84 chains. Longest chain 25 peptides. Score 0.516 Round 2: 662 peptides, 72 chains. Longest chain 29 peptides. Score 0.600 Round 3: 660 peptides, 73 chains. Longest chain 27 peptides. Score 0.595 Round 4: 679 peptides, 77 chains. Longest chain 28 peptides. Score 0.595 Round 5: 677 peptides, 76 chains. Longest chain 22 peptides. Score 0.597 Taking the results from Round 2 Chains 80, Residues 590, Estimated correctness of the model 41.1 % 18 chains (201 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 12735 restraints for refining 6967 atoms. 9723 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2466 (Rfree = 0.000) for 6967 atoms. Found 62 (62 requested) and removed 51 (31 requested) atoms. Cycle 32: After refmac, R = 0.2286 (Rfree = 0.000) for 6943 atoms. Found 37 (62 requested) and removed 42 (31 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2195 (Rfree = 0.000) for 6921 atoms. Found 19 (62 requested) and removed 38 (31 requested) atoms. Cycle 34: After refmac, R = 0.2171 (Rfree = 0.000) for 6889 atoms. Found 33 (61 requested) and removed 35 (30 requested) atoms. Cycle 35: After refmac, R = 0.2118 (Rfree = 0.000) for 6870 atoms. Found 26 (61 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 2.68 Search for helices and strands: 0 residues in 0 chains, 7203 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 7222 seeds are put forward Round 1: 593 peptides, 90 chains. Longest chain 22 peptides. Score 0.456 Round 2: 651 peptides, 84 chains. Longest chain 22 peptides. Score 0.541 Round 3: 670 peptides, 80 chains. Longest chain 29 peptides. Score 0.575 Round 4: 661 peptides, 71 chains. Longest chain 47 peptides. Score 0.603 Round 5: 662 peptides, 80 chains. Longest chain 28 peptides. Score 0.568 Taking the results from Round 4 Chains 84, Residues 590, Estimated correctness of the model 41.9 % 21 chains (208 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 12799 restraints for refining 6967 atoms. 9780 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2484 (Rfree = 0.000) for 6967 atoms. Found 62 (62 requested) and removed 66 (31 requested) atoms. Cycle 37: After refmac, R = 0.2335 (Rfree = 0.000) for 6932 atoms. Found 34 (62 requested) and removed 46 (31 requested) atoms. Cycle 38: After refmac, R = 0.2270 (Rfree = 0.000) for 6906 atoms. Found 22 (62 requested) and removed 41 (31 requested) atoms. Cycle 39: After refmac, R = 0.2239 (Rfree = 0.000) for 6872 atoms. Found 34 (61 requested) and removed 39 (30 requested) atoms. Cycle 40: After refmac, R = 0.2577 (Rfree = 0.000) for 6854 atoms. Found 61 (61 requested) and removed 41 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 2.66 Search for helices and strands: 0 residues in 0 chains, 7184 seeds are put forward NCS extension: 5 residues added (9 deleted due to clashes), 7189 seeds are put forward Round 1: 582 peptides, 85 chains. Longest chain 16 peptides. Score 0.468 Round 2: 636 peptides, 76 chains. Longest chain 36 peptides. Score 0.561 Round 3: 641 peptides, 79 chains. Longest chain 28 peptides. Score 0.553 Round 4: 647 peptides, 79 chains. Longest chain 32 peptides. Score 0.558 Round 5: 664 peptides, 77 chains. Longest chain 42 peptides. Score 0.582 Taking the results from Round 5 Chains 82, Residues 587, Estimated correctness of the model 36.1 % 9 chains (107 residues) have been docked in sequence ------------------------------------------------------ 24032 reflections ( 98.55 % complete ) and 13736 restraints for refining 6966 atoms. 11059 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2505 (Rfree = 0.000) for 6966 atoms. Found 51 (62 requested) and removed 41 (31 requested) atoms. Cycle 42: After refmac, R = 0.2299 (Rfree = 0.000) for 6957 atoms. Found 20 (62 requested) and removed 40 (31 requested) atoms. Cycle 43: After refmac, R = 0.2238 (Rfree = 0.000) for 6924 atoms. Found 18 (62 requested) and removed 36 (31 requested) atoms. Cycle 44: After refmac, R = 0.2224 (Rfree = 0.000) for 6885 atoms. Found 16 (61 requested) and removed 39 (30 requested) atoms. Cycle 45: After refmac, R = 0.2171 (Rfree = 0.000) for 6849 atoms. Found 22 (61 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 2.63 Search for helices and strands: 0 residues in 0 chains, 7144 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 7172 seeds are put forward Round 1: 598 peptides, 90 chains. Longest chain 21 peptides. Score 0.462 Round 2: 645 peptides, 76 chains. Longest chain 26 peptides. Score 0.569 Round 3: 662 peptides, 76 chains. Longest chain 27 peptides. Score 0.584 Round 4: 656 peptides, 75 chains. Longest chain 28 peptides. Score 0.583 Round 5: 658 peptides, 79 chains. Longest chain 22 peptides. Score 0.568 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 83, Residues 586, Estimated correctness of the model 36.7 % 10 chains (111 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 18 B and 28 B 81 chains (589 residues) following loop building 9 chains (120 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24032 reflections ( 98.55 % complete ) and 13565 restraints for refining 6967 atoms. 10853 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2399 (Rfree = 0.000) for 6967 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Cycle 47: After refmac, R = 0.2282 (Rfree = 0.000) for 6917 atoms. Found 0 (62 requested) and removed 27 (31 requested) atoms. Cycle 48: After refmac, R = 0.2257 (Rfree = 0.000) for 6874 atoms. Found 0 (61 requested) and removed 17 (30 requested) atoms. Cycle 49: After refmac, R = 0.2216 (Rfree = 0.000) for 6853 atoms. TimeTaking 78.08