Sun 23 Dec 22:22:49 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 2hr2-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-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/2hr2-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-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 22:22:58 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/2hr2-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-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 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-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.4-parrot-hancs.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 3.400 Wilson plot Bfac: 74.08 Failed to save intermediate PDB 20082 reflections ( 98.41 % complete ) and 0 restraints for refining 8423 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3134 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2845 (Rfree = 0.000) for 8423 atoms. Found 63 (63 requested) and removed 43 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 2.77 Search for helices and strands: 0 residues in 0 chains, 8723 seeds are put forward NCS extension: 0 residues added, 8723 seeds are put forward Round 1: 550 peptides, 85 chains. Longest chain 16 peptides. Score 0.434 Round 2: 626 peptides, 79 chains. Longest chain 22 peptides. Score 0.539 Round 3: 639 peptides, 76 chains. Longest chain 25 peptides. Score 0.564 Round 4: 648 peptides, 70 chains. Longest chain 33 peptides. Score 0.596 Round 5: 632 peptides, 70 chains. Longest chain 26 peptides. Score 0.582 Taking the results from Round 4 Chains 76, Residues 578, Estimated correctness of the model 27.4 % 14 chains (179 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 12998 restraints for refining 6936 atoms. 10122 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2579 (Rfree = 0.000) for 6936 atoms. Found 52 (52 requested) and removed 62 (26 requested) atoms. Cycle 2: After refmac, R = 0.2410 (Rfree = 0.000) for 6790 atoms. Found 45 (52 requested) and removed 54 (26 requested) atoms. Cycle 3: After refmac, R = 0.2319 (Rfree = 0.000) for 6715 atoms. Found 27 (51 requested) and removed 39 (25 requested) atoms. Cycle 4: After refmac, R = 0.2265 (Rfree = 0.000) for 6661 atoms. Found 25 (50 requested) and removed 36 (25 requested) atoms. Cycle 5: After refmac, R = 0.2237 (Rfree = 0.000) for 6627 atoms. Found 21 (50 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 2.74 Search for helices and strands: 0 residues in 0 chains, 7012 seeds are put forward NCS extension: 38 residues added (4 deleted due to clashes), 7050 seeds are put forward Round 1: 608 peptides, 77 chains. Longest chain 25 peptides. Score 0.530 Round 2: 638 peptides, 72 chains. Longest chain 21 peptides. Score 0.579 Round 3: 631 peptides, 72 chains. Longest chain 22 peptides. Score 0.573 Round 4: 631 peptides, 63 chains. Longest chain 29 peptides. Score 0.610 Round 5: 625 peptides, 65 chains. Longest chain 24 peptides. Score 0.597 Taking the results from Round 4 Chains 76, Residues 568, Estimated correctness of the model 31.9 % 13 chains (154 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13098 restraints for refining 6937 atoms. 10348 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2485 (Rfree = 0.000) for 6937 atoms. Found 52 (52 requested) and removed 56 (26 requested) atoms. Cycle 7: After refmac, R = 0.2272 (Rfree = 0.000) for 6888 atoms. Found 28 (52 requested) and removed 37 (26 requested) atoms. Cycle 8: After refmac, R = 0.2181 (Rfree = 0.000) for 6853 atoms. Found 21 (51 requested) and removed 27 (25 requested) atoms. Cycle 9: After refmac, R = 0.2119 (Rfree = 0.000) for 6830 atoms. Found 20 (51 requested) and removed 30 (25 requested) atoms. Cycle 10: After refmac, R = 0.2072 (Rfree = 0.000) for 6810 atoms. Found 13 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 2.75 Search for helices and strands: 0 residues in 0 chains, 7167 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 7200 seeds are put forward Round 1: 616 peptides, 88 chains. Longest chain 20 peptides. Score 0.489 Round 2: 641 peptides, 79 chains. Longest chain 28 peptides. Score 0.553 Round 3: 635 peptides, 74 chains. Longest chain 25 peptides. Score 0.568 Round 4: 647 peptides, 69 chains. Longest chain 47 peptides. Score 0.599 Round 5: 629 peptides, 72 chains. Longest chain 28 peptides. Score 0.571 Taking the results from Round 4 Chains 79, Residues 578, Estimated correctness of the model 28.3 % 11 chains (143 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13448 restraints for refining 6939 atoms. 10682 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2491 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 12: After refmac, R = 0.2329 (Rfree = 0.000) for 6914 atoms. Found 31 (52 requested) and removed 35 (26 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2215 (Rfree = 0.000) for 6886 atoms. Found 15 (52 requested) and removed 28 (26 requested) atoms. Cycle 14: After refmac, R = 0.2161 (Rfree = 0.000) for 6863 atoms. Found 12 (51 requested) and removed 25 (25 requested) atoms. Cycle 15: After refmac, R = 0.2119 (Rfree = 0.000) for 6842 atoms. Found 11 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 2.75 Search for helices and strands: 0 residues in 0 chains, 7205 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 7221 seeds are put forward Round 1: 573 peptides, 83 chains. Longest chain 18 peptides. Score 0.468 Round 2: 625 peptides, 70 chains. Longest chain 30 peptides. Score 0.576 Round 3: 647 peptides, 74 chains. Longest chain 26 peptides. Score 0.579 Round 4: 650 peptides, 75 chains. Longest chain 28 peptides. Score 0.578 Round 5: 621 peptides, 75 chains. Longest chain 25 peptides. Score 0.551 Taking the results from Round 3 Chains 80, Residues 573, Estimated correctness of the model 21.7 % 14 chains (131 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13779 restraints for refining 6939 atoms. 11120 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2485 (Rfree = 0.000) for 6939 atoms. Found 49 (52 requested) and removed 36 (26 requested) atoms. Cycle 17: After refmac, R = 0.2293 (Rfree = 0.000) for 6917 atoms. Found 23 (52 requested) and removed 32 (26 requested) atoms. Cycle 18: After refmac, R = 0.2210 (Rfree = 0.000) for 6892 atoms. Found 10 (52 requested) and removed 27 (26 requested) atoms. Cycle 19: After refmac, R = 0.2178 (Rfree = 0.000) for 6861 atoms. Found 10 (51 requested) and removed 25 (25 requested) atoms. Cycle 20: After refmac, R = 0.2168 (Rfree = 0.000) for 6840 atoms. Found 18 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.75 Search for helices and strands: 0 residues in 0 chains, 7201 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 7219 seeds are put forward Round 1: 560 peptides, 87 chains. Longest chain 32 peptides. Score 0.435 Round 2: 608 peptides, 73 chains. Longest chain 25 peptides. Score 0.548 Round 3: 617 peptides, 75 chains. Longest chain 22 peptides. Score 0.548 Round 4: 608 peptides, 70 chains. Longest chain 29 peptides. Score 0.561 Round 5: 600 peptides, 68 chains. Longest chain 23 peptides. Score 0.562 Taking the results from Round 5 Chains 74, Residues 532, Estimated correctness of the model 15.8 % 12 chains (111 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14206 restraints for refining 6939 atoms. 11772 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2537 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Cycle 22: After refmac, R = 0.2351 (Rfree = 0.000) for 6918 atoms. Found 22 (52 requested) and removed 34 (26 requested) atoms. Cycle 23: After refmac, R = 0.2250 (Rfree = 0.000) for 6888 atoms. Found 21 (52 requested) and removed 29 (26 requested) atoms. Cycle 24: After refmac, R = 0.2178 (Rfree = 0.000) for 6864 atoms. Found 11 (51 requested) and removed 26 (25 requested) atoms. Cycle 25: After refmac, R = 0.2142 (Rfree = 0.000) for 6843 atoms. Found 9 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 2.77 Search for helices and strands: 0 residues in 0 chains, 7208 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 7219 seeds are put forward Round 1: 536 peptides, 82 chains. Longest chain 14 peptides. Score 0.433 Round 2: 616 peptides, 74 chains. Longest chain 26 peptides. Score 0.551 Round 3: 612 peptides, 71 chains. Longest chain 27 peptides. Score 0.560 Round 4: 605 peptides, 67 chains. Longest chain 25 peptides. Score 0.571 Round 5: 616 peptides, 76 chains. Longest chain 27 peptides. Score 0.542 Taking the results from Round 4 Chains 74, Residues 538, Estimated correctness of the model 18.9 % 11 chains (123 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13897 restraints for refining 6939 atoms. 11354 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2475 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. Cycle 27: After refmac, R = 0.2286 (Rfree = 0.000) for 6932 atoms. Found 20 (52 requested) and removed 30 (26 requested) atoms. Cycle 28: After refmac, R = 0.2200 (Rfree = 0.000) for 6907 atoms. Found 14 (52 requested) and removed 31 (26 requested) atoms. Cycle 29: After refmac, R = 0.2148 (Rfree = 0.000) for 6882 atoms. Found 14 (52 requested) and removed 27 (26 requested) atoms. Cycle 30: After refmac, R = 0.2129 (Rfree = 0.000) for 6859 atoms. Found 16 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 2.78 Search for helices and strands: 0 residues in 0 chains, 7211 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 7233 seeds are put forward Round 1: 530 peptides, 89 chains. Longest chain 14 peptides. Score 0.392 Round 2: 577 peptides, 77 chains. Longest chain 29 peptides. Score 0.500 Round 3: 591 peptides, 74 chains. Longest chain 36 peptides. Score 0.527 Round 4: 585 peptides, 74 chains. Longest chain 20 peptides. Score 0.521 Round 5: 598 peptides, 73 chains. Longest chain 30 peptides. Score 0.538 Taking the results from Round 5 Chains 79, Residues 525, Estimated correctness of the model 7.2 % 10 chains (79 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14440 restraints for refining 6939 atoms. 12145 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2541 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 32: After refmac, R = 0.2342 (Rfree = 0.000) for 6922 atoms. Found 32 (52 requested) and removed 34 (26 requested) atoms. Cycle 33: After refmac, R = 0.2270 (Rfree = 0.000) for 6908 atoms. Found 15 (52 requested) and removed 30 (26 requested) atoms. Cycle 34: After refmac, R = 0.2219 (Rfree = 0.000) for 6888 atoms. Found 11 (52 requested) and removed 26 (26 requested) atoms. Cycle 35: After refmac, R = 0.2181 (Rfree = 0.000) for 6868 atoms. Found 8 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 2.77 Search for helices and strands: 0 residues in 0 chains, 7198 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 7211 seeds are put forward Round 1: 502 peptides, 89 chains. Longest chain 14 peptides. Score 0.359 Round 2: 557 peptides, 81 chains. Longest chain 19 peptides. Score 0.461 Round 3: 567 peptides, 79 chains. Longest chain 18 peptides. Score 0.480 Round 4: 587 peptides, 80 chains. Longest chain 18 peptides. Score 0.496 Round 5: 608 peptides, 85 chains. Longest chain 20 peptides. Score 0.495 Taking the results from Round 4 Chains 85, Residues 507, Estimated correctness of the model 0.0 % 11 chains (92 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14328 restraints for refining 6939 atoms. 12055 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2524 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Cycle 37: After refmac, R = 0.2357 (Rfree = 0.000) for 6925 atoms. Found 44 (52 requested) and removed 30 (26 requested) atoms. Cycle 38: After refmac, R = 0.2279 (Rfree = 0.000) for 6933 atoms. Found 24 (52 requested) and removed 27 (26 requested) atoms. Cycle 39: After refmac, R = 0.2231 (Rfree = 0.000) for 6921 atoms. Found 11 (52 requested) and removed 26 (26 requested) atoms. Cycle 40: After refmac, R = 0.2192 (Rfree = 0.000) for 6898 atoms. Found 13 (52 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.77 Search for helices and strands: 0 residues in 0 chains, 7207 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 7225 seeds are put forward Round 1: 451 peptides, 81 chains. Longest chain 16 peptides. Score 0.339 Round 2: 514 peptides, 79 chains. Longest chain 19 peptides. Score 0.423 Round 3: 535 peptides, 79 chains. Longest chain 21 peptides. Score 0.447 Round 4: 514 peptides, 71 chains. Longest chain 21 peptides. Score 0.463 Round 5: 523 peptides, 74 chains. Longest chain 17 peptides. Score 0.458 Taking the results from Round 4 Chains 74, Residues 443, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 15233 restraints for refining 6939 atoms. 13410 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2426 (Rfree = 0.000) for 6939 atoms. Found 52 (52 requested) and removed 34 (26 requested) atoms. Cycle 42: After refmac, R = 0.2293 (Rfree = 0.000) for 6936 atoms. Found 26 (52 requested) and removed 32 (26 requested) atoms. Cycle 43: After refmac, R = 0.2247 (Rfree = 0.000) for 6924 atoms. Found 13 (52 requested) and removed 27 (26 requested) atoms. Cycle 44: After refmac, R = 0.2218 (Rfree = 0.000) for 6907 atoms. Found 15 (52 requested) and removed 26 (26 requested) atoms. Cycle 45: After refmac, R = 0.2198 (Rfree = 0.000) for 6891 atoms. Found 6 (52 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 2.77 Search for helices and strands: 0 residues in 0 chains, 7203 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 7224 seeds are put forward Round 1: 442 peptides, 81 chains. Longest chain 14 peptides. Score 0.328 Round 2: 491 peptides, 71 chains. Longest chain 20 peptides. Score 0.438 Round 3: 501 peptides, 77 chains. Longest chain 20 peptides. Score 0.419 Round 4: 519 peptides, 71 chains. Longest chain 25 peptides. Score 0.468 Round 5: 475 peptides, 70 chains. Longest chain 16 peptides. Score 0.425 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 72, Residues 448, Estimated correctness of the model 0.0 % 7 chains (63 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 15 A and 28 A 71 chains (454 residues) following loop building 6 chains (75 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20082 reflections ( 98.41 % complete ) and 14885 restraints for refining 6936 atoms. 12968 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2492 (Rfree = 0.000) for 6936 atoms. Found 0 (52 requested) and removed 23 (26 requested) atoms. Cycle 47: After refmac, R = 0.2410 (Rfree = 0.000) for 6898 atoms. Found 0 (52 requested) and removed 9 (26 requested) atoms. Cycle 48: After refmac, R = 0.2373 (Rfree = 0.000) for 6884 atoms. Found 0 (52 requested) and removed 3 (26 requested) atoms. Cycle 49: After refmac, R = 0.2344 (Rfree = 0.000) for 6881 atoms. TimeTaking 96.43