Sun 23 Dec 22:22:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vmg-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmg-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.4-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:55 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/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmg-3.4-parrot-hancs/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 103 and 0 Target number of residues in the AU: 103 Target solvent content: 0.6344 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 95 Adjusted target solvent content: 0.66 Input MTZ file: 1vmg-3.4-parrot-hancs.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: 98 Cell parameters: 79.748 79.748 95.906 90.000 90.000 90.000 Input sequence file: 1vmg-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 760 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 Loops will be built when appropriate and at the last cycle Resolution range: 61.319 3.400 Wilson plot Bfac: 67.89 2309 reflections ( 99.65 % complete ) and 0 restraints for refining 850 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3454 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3567 (Rfree = 0.000) for 850 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 2.66 Search for helices and strands: 0 residues in 0 chains, 878 seeds are put forward Round 1: 49 peptides, 8 chains. Longest chain 11 peptides. Score 0.381 Round 2: 58 peptides, 9 chains. Longest chain 9 peptides. Score 0.430 Round 3: 56 peptides, 8 chains. Longest chain 12 peptides. Score 0.455 Round 4: 53 peptides, 7 chains. Longest chain 12 peptides. Score 0.471 Round 5: 59 peptides, 8 chains. Longest chain 10 peptides. Score 0.485 Taking the results from Round 5 Chains 8, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1513 restraints for refining 691 atoms. 1317 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3247 (Rfree = 0.000) for 691 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 2: After refmac, R = 0.3200 (Rfree = 0.000) for 688 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 3: After refmac, R = 0.3347 (Rfree = 0.000) for 683 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 4: After refmac, R = 0.2890 (Rfree = 0.000) for 670 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 5: After refmac, R = 0.2693 (Rfree = 0.000) for 666 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.58 Search for helices and strands: 0 residues in 0 chains, 724 seeds are put forward Round 1: 52 peptides, 7 chains. Longest chain 13 peptides. Score 0.461 Round 2: 52 peptides, 7 chains. Longest chain 15 peptides. Score 0.461 Round 3: 56 peptides, 7 chains. Longest chain 14 peptides. Score 0.500 Round 4: 61 peptides, 7 chains. Longest chain 16 peptides. Score 0.546 Round 5: 62 peptides, 7 chains. Longest chain 18 peptides. Score 0.555 Taking the results from Round 5 Chains 7, Residues 55, Estimated correctness of the model 13.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1427 restraints for refining 687 atoms. 1214 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2731 (Rfree = 0.000) for 687 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 7: After refmac, R = 0.2457 (Rfree = 0.000) for 675 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 8: After refmac, R = 0.2629 (Rfree = 0.000) for 674 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.2145 (Rfree = 0.000) for 671 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 10: After refmac, R = 0.2869 (Rfree = 0.000) for 674 atoms. Found 5 (5 requested) and removed 14 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 2.60 Search for helices and strands: 0 residues in 0 chains, 701 seeds are put forward Round 1: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.456 Round 2: 67 peptides, 8 chains. Longest chain 15 peptides. Score 0.558 Round 3: 60 peptides, 6 chains. Longest chain 21 peptides. Score 0.578 Round 4: 65 peptides, 8 chains. Longest chain 16 peptides. Score 0.541 Round 5: 64 peptides, 6 chains. Longest chain 19 peptides. Score 0.611 Taking the results from Round 5 Chains 6, Residues 58, Estimated correctness of the model 32.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1436 restraints for refining 689 atoms. 1210 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2608 (Rfree = 0.000) for 689 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.2575 (Rfree = 0.000) for 678 atoms. Found 4 (5 requested) and removed 25 (2 requested) atoms. Cycle 13: After refmac, R = 0.2437 (Rfree = 0.000) for 654 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 14: After refmac, R = 0.2427 (Rfree = 0.000) for 653 atoms. Found 4 (4 requested) and removed 32 (2 requested) atoms. Cycle 15: After refmac, R = 0.2360 (Rfree = 0.000) for 623 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 2.61 Search for helices and strands: 0 residues in 0 chains, 671 seeds are put forward Round 1: 64 peptides, 7 chains. Longest chain 26 peptides. Score 0.572 Round 2: 66 peptides, 6 chains. Longest chain 19 peptides. Score 0.627 Round 3: 56 peptides, 8 chains. Longest chain 11 peptides. Score 0.455 Round 4: 57 peptides, 6 chains. Longest chain 16 peptides. Score 0.552 Round 5: 58 peptides, 7 chains. Longest chain 12 peptides. Score 0.519 Taking the results from Round 2 Chains 6, Residues 60, Estimated correctness of the model 37.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1235 restraints for refining 629 atoms. 1001 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2361 (Rfree = 0.000) for 629 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 17: After refmac, R = 0.2260 (Rfree = 0.000) for 631 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 18: After refmac, R = 0.2360 (Rfree = 0.000) for 630 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 19: After refmac, R = 0.2092 (Rfree = 0.000) for 627 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 20: After refmac, R = 0.2235 (Rfree = 0.000) for 628 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 2.58 Search for helices and strands: 0 residues in 0 chains, 666 seeds are put forward Round 1: 61 peptides, 7 chains. Longest chain 17 peptides. Score 0.546 Round 2: 63 peptides, 6 chains. Longest chain 20 peptides. Score 0.603 Round 3: 71 peptides, 7 chains. Longest chain 17 peptides. Score 0.628 Round 4: 65 peptides, 7 chains. Longest chain 20 peptides. Score 0.581 Round 5: 56 peptides, 7 chains. Longest chain 14 peptides. Score 0.500 Taking the results from Round 3 Chains 9, Residues 64, Estimated correctness of the model 37.5 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1163 restraints for refining 666 atoms. 874 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2437 (Rfree = 0.000) for 666 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 22: After refmac, R = 0.2385 (Rfree = 0.000) for 662 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.2369 (Rfree = 0.000) for 657 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.2839 (Rfree = 0.000) for 653 atoms. Found 4 (4 requested) and removed 31 (2 requested) atoms. Cycle 25: After refmac, R = 0.2403 (Rfree = 0.000) for 625 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 668 seeds are put forward Round 1: 65 peptides, 7 chains. Longest chain 18 peptides. Score 0.581 Round 2: 66 peptides, 7 chains. Longest chain 19 peptides. Score 0.589 Round 3: 63 peptides, 7 chains. Longest chain 17 peptides. Score 0.564 Round 4: 67 peptides, 5 chains. Longest chain 21 peptides. Score 0.670 Round 5: 63 peptides, 6 chains. Longest chain 23 peptides. Score 0.603 Taking the results from Round 4 Chains 5, Residues 62, Estimated correctness of the model 49.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1368 restraints for refining 663 atoms. 1125 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2513 (Rfree = 0.000) for 663 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 27: After refmac, R = 0.2368 (Rfree = 0.000) for 657 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 28: After refmac, R = 0.2578 (Rfree = 0.000) for 657 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.2277 (Rfree = 0.000) for 657 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.2460 (Rfree = 0.000) for 657 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 2.62 Search for helices and strands: 0 residues in 0 chains, 688 seeds are put forward Round 1: 59 peptides, 7 chains. Longest chain 12 peptides. Score 0.528 Round 2: 62 peptides, 7 chains. Longest chain 15 peptides. Score 0.555 Round 3: 70 peptides, 8 chains. Longest chain 21 peptides. Score 0.583 Round 4: 70 peptides, 6 chains. Longest chain 22 peptides. Score 0.656 Round 5: 59 peptides, 7 chains. Longest chain 19 peptides. Score 0.528 Taking the results from Round 4 Chains 6, Residues 64, Estimated correctness of the model 45.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1411 restraints for refining 679 atoms. 1161 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2986 (Rfree = 0.000) for 679 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 32: After refmac, R = 0.2618 (Rfree = 0.000) for 673 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 33: After refmac, R = 0.2589 (Rfree = 0.000) for 672 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.2363 (Rfree = 0.000) for 674 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.2184 (Rfree = 0.000) for 674 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 2.76 Search for helices and strands: 0 residues in 0 chains, 712 seeds are put forward Round 1: 64 peptides, 7 chains. Longest chain 19 peptides. Score 0.572 Round 2: 65 peptides, 5 chains. Longest chain 20 peptides. Score 0.656 Round 3: 69 peptides, 8 chains. Longest chain 24 peptides. Score 0.575 Round 4: 71 peptides, 8 chains. Longest chain 25 peptides. Score 0.592 Round 5: 67 peptides, 8 chains. Longest chain 14 peptides. Score 0.558 Taking the results from Round 2 Chains 6, Residues 60, Estimated correctness of the model 45.9 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1277 restraints for refining 691 atoms. 974 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2367 (Rfree = 0.000) for 691 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 37: After refmac, R = 0.2200 (Rfree = 0.000) for 684 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.2747 (Rfree = 0.000) for 686 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.2721 (Rfree = 0.000) for 686 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.2367 (Rfree = 0.000) for 680 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 2.61 Search for helices and strands: 0 residues in 0 chains, 714 seeds are put forward Round 1: 61 peptides, 8 chains. Longest chain 14 peptides. Score 0.504 Round 2: 66 peptides, 7 chains. Longest chain 21 peptides. Score 0.589 Round 3: 67 peptides, 7 chains. Longest chain 13 peptides. Score 0.597 Round 4: 71 peptides, 8 chains. Longest chain 13 peptides. Score 0.592 Round 5: 58 peptides, 7 chains. Longest chain 12 peptides. Score 0.519 Taking the results from Round 3 Chains 7, Residues 60, Estimated correctness of the model 27.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2309 reflections ( 99.65 % complete ) and 1451 restraints for refining 683 atoms. 1218 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2566 (Rfree = 0.000) for 683 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 42: After refmac, R = 0.2273 (Rfree = 0.000) for 679 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.2766 (Rfree = 0.000) for 677 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.2278 (Rfree = 0.000) for 675 atoms. Found 3 (5 requested) and removed 2 (2 requested) atoms. Cycle 45: After refmac, R = 0.2260 (Rfree = 0.000) for 676 atoms. Found 2 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.22 2.58 Search for helices and strands: 0 residues in 0 chains, 701 seeds are put forward Round 1: 66 peptides, 8 chains. Longest chain 12 peptides. Score 0.549 Round 2: 64 peptides, 8 chains. Longest chain 17 peptides. Score 0.532 Round 3: 66 peptides, 7 chains. Longest chain 23 peptides. Score 0.589 Round 4: 68 peptides, 6 chains. Longest chain 27 peptides. Score 0.642 Round 5: 66 peptides, 8 chains. Longest chain 11 peptides. Score 0.549 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 62, Estimated correctness of the model 41.8 % 1 chains (26 residues) have been docked in sequence Sequence coverage is 41 % Consider running further cycles of model building using 1vmg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2309 reflections ( 99.65 % complete ) and 1149 restraints for refining 691 atoms. 776 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3110 (Rfree = 0.000) for 691 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2967 (Rfree = 0.000) for 685 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2970 (Rfree = 0.000) for 681 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2957 (Rfree = 0.000) for 679 atoms. TimeTaking 23.07