Mon 24 Dec 07:38:43 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 2pgc-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-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/2pgc-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 07:38:47 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/2pgc-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 788 and 0 Target number of residues in the AU: 788 Target solvent content: 0.6348 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 8280 target number of atoms Had to go as low as 0.75 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: 98.043 3.200 Wilson plot Bfac: 69.11 19941 reflections ( 99.69 % complete ) and 0 restraints for refining 9164 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3360 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3116 (Rfree = 0.000) for 9164 atoms. Found 82 (82 requested) and removed 55 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.23 Search for helices and strands: 0 residues in 0 chains, 9367 seeds are put forward NCS extension: 0 residues added, 9367 seeds are put forward Round 1: 445 peptides, 77 chains. Longest chain 15 peptides. Score 0.383 Round 2: 553 peptides, 81 chains. Longest chain 15 peptides. Score 0.501 Round 3: 611 peptides, 75 chains. Longest chain 24 peptides. Score 0.596 Round 4: 638 peptides, 82 chains. Longest chain 25 peptides. Score 0.592 Round 5: 663 peptides, 80 chains. Longest chain 27 peptides. Score 0.626 Taking the results from Round 5 Chains 81, Residues 583, Estimated correctness of the model 47.9 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16534 restraints for refining 7559 atoms. 14200 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2759 (Rfree = 0.000) for 7559 atoms. Found 55 (67 requested) and removed 51 (33 requested) atoms. Cycle 2: After refmac, R = 0.2678 (Rfree = 0.000) for 7441 atoms. Found 33 (67 requested) and removed 44 (33 requested) atoms. Cycle 3: After refmac, R = 0.2643 (Rfree = 0.000) for 7382 atoms. Found 31 (66 requested) and removed 48 (33 requested) atoms. Cycle 4: After refmac, R = 0.2476 (Rfree = 0.000) for 7331 atoms. Found 31 (66 requested) and removed 41 (33 requested) atoms. Cycle 5: After refmac, R = 0.2387 (Rfree = 0.000) for 7298 atoms. Found 23 (65 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 7615 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7629 seeds are put forward Round 1: 565 peptides, 85 chains. Longest chain 18 peptides. Score 0.494 Round 2: 606 peptides, 79 chains. Longest chain 26 peptides. Score 0.572 Round 3: 651 peptides, 83 chains. Longest chain 27 peptides. Score 0.600 Round 4: 658 peptides, 74 chains. Longest chain 41 peptides. Score 0.647 Round 5: 659 peptides, 72 chains. Longest chain 41 peptides. Score 0.656 Taking the results from Round 5 Chains 78, Residues 587, Estimated correctness of the model 55.3 % 7 chains (111 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 15712 restraints for refining 7559 atoms. 13040 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2545 (Rfree = 0.000) for 7559 atoms. Found 56 (67 requested) and removed 63 (33 requested) atoms. Cycle 7: After refmac, R = 0.2546 (Rfree = 0.000) for 7506 atoms. Found 38 (67 requested) and removed 45 (33 requested) atoms. Cycle 8: After refmac, R = 0.2381 (Rfree = 0.000) for 7479 atoms. Found 27 (67 requested) and removed 44 (33 requested) atoms. Cycle 9: After refmac, R = 0.2341 (Rfree = 0.000) for 7454 atoms. Found 27 (66 requested) and removed 52 (33 requested) atoms. Cycle 10: After refmac, R = 0.2241 (Rfree = 0.000) for 7421 atoms. Found 23 (66 requested) and removed 44 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 7673 seeds are put forward NCS extension: 18 residues added (13 deleted due to clashes), 7691 seeds are put forward Round 1: 604 peptides, 85 chains. Longest chain 25 peptides. Score 0.540 Round 2: 652 peptides, 76 chains. Longest chain 32 peptides. Score 0.633 Round 3: 644 peptides, 73 chains. Longest chain 36 peptides. Score 0.638 Round 4: 666 peptides, 73 chains. Longest chain 39 peptides. Score 0.658 Round 5: 661 peptides, 68 chains. Longest chain 30 peptides. Score 0.675 Taking the results from Round 5 Chains 71, Residues 593, Estimated correctness of the model 59.7 % 4 chains (68 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 15915 restraints for refining 7558 atoms. 13349 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2657 (Rfree = 0.000) for 7558 atoms. Found 67 (67 requested) and removed 51 (33 requested) atoms. Cycle 12: After refmac, R = 0.2669 (Rfree = 0.000) for 7533 atoms. Found 67 (67 requested) and removed 48 (33 requested) atoms. Cycle 13: After refmac, R = 0.2261 (Rfree = 0.000) for 7522 atoms. Found 36 (67 requested) and removed 45 (33 requested) atoms. Cycle 14: After refmac, R = 0.2332 (Rfree = 0.000) for 7492 atoms. Found 37 (67 requested) and removed 43 (33 requested) atoms. Cycle 15: After refmac, R = 0.2132 (Rfree = 0.000) for 7460 atoms. Found 21 (67 requested) and removed 36 (33 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 7691 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 7710 seeds are put forward Round 1: 566 peptides, 78 chains. Longest chain 39 peptides. Score 0.532 Round 2: 648 peptides, 70 chains. Longest chain 27 peptides. Score 0.655 Round 3: 656 peptides, 74 chains. Longest chain 29 peptides. Score 0.645 Round 4: 636 peptides, 72 chains. Longest chain 28 peptides. Score 0.635 Round 5: 638 peptides, 71 chains. Longest chain 23 peptides. Score 0.641 Taking the results from Round 2 Chains 70, Residues 578, Estimated correctness of the model 55.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16431 restraints for refining 7560 atoms. 14110 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2407 (Rfree = 0.000) for 7560 atoms. Found 41 (67 requested) and removed 38 (33 requested) atoms. Cycle 17: After refmac, R = 0.2327 (Rfree = 0.000) for 7547 atoms. Found 25 (67 requested) and removed 40 (33 requested) atoms. Cycle 18: After refmac, R = 0.2213 (Rfree = 0.000) for 7521 atoms. Found 25 (67 requested) and removed 35 (33 requested) atoms. Cycle 19: After refmac, R = 0.2183 (Rfree = 0.000) for 7503 atoms. Found 22 (67 requested) and removed 35 (33 requested) atoms. Cycle 20: After refmac, R = 0.2154 (Rfree = 0.000) for 7481 atoms. Found 24 (67 requested) and removed 35 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.16 Search for helices and strands: 0 residues in 0 chains, 7743 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 7764 seeds are put forward Round 1: 568 peptides, 82 chains. Longest chain 19 peptides. Score 0.514 Round 2: 626 peptides, 74 chains. Longest chain 26 peptides. Score 0.616 Round 3: 614 peptides, 68 chains. Longest chain 28 peptides. Score 0.631 Round 4: 609 peptides, 73 chains. Longest chain 22 peptides. Score 0.604 Round 5: 634 peptides, 73 chains. Longest chain 43 peptides. Score 0.628 Taking the results from Round 3 Chains 71, Residues 546, Estimated correctness of the model 49.1 % 5 chains (57 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16287 restraints for refining 7558 atoms. 13991 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2409 (Rfree = 0.000) for 7558 atoms. Found 63 (67 requested) and removed 38 (33 requested) atoms. Cycle 22: After refmac, R = 0.2248 (Rfree = 0.000) for 7562 atoms. Found 35 (68 requested) and removed 42 (34 requested) atoms. Cycle 23: After refmac, R = 0.2166 (Rfree = 0.000) for 7536 atoms. Found 35 (67 requested) and removed 38 (33 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2192 (Rfree = 0.000) for 7520 atoms. Found 31 (67 requested) and removed 33 (33 requested) atoms. Cycle 25: After refmac, R = 0.2125 (Rfree = 0.000) for 7505 atoms. Found 34 (67 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.17 Search for helices and strands: 0 residues in 0 chains, 7721 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 7731 seeds are put forward Round 1: 555 peptides, 76 chains. Longest chain 20 peptides. Score 0.530 Round 2: 618 peptides, 72 chains. Longest chain 27 peptides. Score 0.617 Round 3: 616 peptides, 69 chains. Longest chain 36 peptides. Score 0.629 Round 4: 610 peptides, 71 chains. Longest chain 32 peptides. Score 0.614 Round 5: 621 peptides, 72 chains. Longest chain 28 peptides. Score 0.620 Taking the results from Round 3 Chains 74, Residues 547, Estimated correctness of the model 48.6 % 7 chains (63 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16012 restraints for refining 7560 atoms. 13683 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2332 (Rfree = 0.000) for 7560 atoms. Found 38 (67 requested) and removed 41 (33 requested) atoms. Cycle 27: After refmac, R = 0.2312 (Rfree = 0.000) for 7531 atoms. Found 35 (67 requested) and removed 36 (33 requested) atoms. Cycle 28: After refmac, R = 0.2196 (Rfree = 0.000) for 7513 atoms. Found 17 (67 requested) and removed 33 (33 requested) atoms. Cycle 29: After refmac, R = 0.2152 (Rfree = 0.000) for 7486 atoms. Found 21 (67 requested) and removed 37 (33 requested) atoms. Cycle 30: After refmac, R = 0.2072 (Rfree = 0.000) for 7457 atoms. Found 16 (67 requested) and removed 34 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.19 Search for helices and strands: 0 residues in 0 chains, 7677 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 7701 seeds are put forward Round 1: 544 peptides, 82 chains. Longest chain 21 peptides. Score 0.485 Round 2: 591 peptides, 76 chains. Longest chain 19 peptides. Score 0.570 Round 3: 605 peptides, 76 chains. Longest chain 25 peptides. Score 0.585 Round 4: 595 peptides, 66 chains. Longest chain 34 peptides. Score 0.622 Round 5: 594 peptides, 72 chains. Longest chain 34 peptides. Score 0.593 Taking the results from Round 4 Chains 68, Residues 529, Estimated correctness of the model 46.9 % 5 chains (69 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16252 restraints for refining 7558 atoms. 13962 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2373 (Rfree = 0.000) for 7558 atoms. Found 39 (67 requested) and removed 41 (33 requested) atoms. Cycle 32: After refmac, R = 0.2329 (Rfree = 0.000) for 7537 atoms. Found 31 (67 requested) and removed 37 (33 requested) atoms. Cycle 33: After refmac, R = 0.2228 (Rfree = 0.000) for 7517 atoms. Found 32 (67 requested) and removed 34 (33 requested) atoms. Cycle 34: After refmac, R = 0.2194 (Rfree = 0.000) for 7494 atoms. Found 30 (67 requested) and removed 33 (33 requested) atoms. Cycle 35: After refmac, R = 0.2178 (Rfree = 0.000) for 7481 atoms. Found 32 (67 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 7707 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 7739 seeds are put forward Round 1: 499 peptides, 75 chains. Longest chain 17 peptides. Score 0.467 Round 2: 571 peptides, 60 chains. Longest chain 26 peptides. Score 0.626 Round 3: 562 peptides, 62 chains. Longest chain 33 peptides. Score 0.607 Round 4: 543 peptides, 64 chains. Longest chain 22 peptides. Score 0.578 Round 5: 556 peptides, 66 chains. Longest chain 24 peptides. Score 0.582 Taking the results from Round 2 Chains 63, Residues 511, Estimated correctness of the model 47.9 % 4 chains (66 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16311 restraints for refining 7558 atoms. 14081 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2341 (Rfree = 0.000) for 7558 atoms. Found 43 (67 requested) and removed 38 (33 requested) atoms. Cycle 37: After refmac, R = 0.2291 (Rfree = 0.000) for 7540 atoms. Found 35 (67 requested) and removed 34 (33 requested) atoms. Cycle 38: After refmac, R = 0.2255 (Rfree = 0.000) for 7519 atoms. Found 35 (67 requested) and removed 34 (33 requested) atoms. Cycle 39: After refmac, R = 0.2207 (Rfree = 0.000) for 7504 atoms. Found 26 (67 requested) and removed 34 (33 requested) atoms. Cycle 40: After refmac, R = 0.2172 (Rfree = 0.000) for 7484 atoms. Found 23 (67 requested) and removed 33 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.27 3.18 Search for helices and strands: 0 residues in 0 chains, 7694 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 7710 seeds are put forward Round 1: 501 peptides, 68 chains. Longest chain 25 peptides. Score 0.508 Round 2: 573 peptides, 76 chains. Longest chain 35 peptides. Score 0.551 Round 3: 565 peptides, 68 chains. Longest chain 32 peptides. Score 0.582 Round 4: 560 peptides, 68 chains. Longest chain 25 peptides. Score 0.576 Round 5: 564 peptides, 67 chains. Longest chain 25 peptides. Score 0.585 Taking the results from Round 5 Chains 68, Residues 497, Estimated correctness of the model 37.0 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 19941 reflections ( 99.69 % complete ) and 16753 restraints for refining 7560 atoms. 14693 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2369 (Rfree = 0.000) for 7560 atoms. Found 56 (67 requested) and removed 38 (33 requested) atoms. Cycle 42: After refmac, R = 0.2294 (Rfree = 0.000) for 7564 atoms. Found 45 (68 requested) and removed 35 (34 requested) atoms. Cycle 43: After refmac, R = 0.2249 (Rfree = 0.000) for 7557 atoms. Found 32 (67 requested) and removed 34 (33 requested) atoms. Cycle 44: After refmac, R = 0.2220 (Rfree = 0.000) for 7538 atoms. Found 46 (67 requested) and removed 35 (33 requested) atoms. Cycle 45: After refmac, R = 0.2157 (Rfree = 0.000) for 7539 atoms. Found 40 (67 requested) and removed 36 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.20 Search for helices and strands: 0 residues in 0 chains, 7788 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 7801 seeds are put forward Round 1: 461 peptides, 70 chains. Longest chain 19 peptides. Score 0.446 Round 2: 485 peptides, 62 chains. Longest chain 19 peptides. Score 0.522 Round 3: 485 peptides, 60 chains. Longest chain 23 peptides. Score 0.533 Round 4: 505 peptides, 58 chains. Longest chain 27 peptides. Score 0.566 Round 5: 530 peptides, 62 chains. Longest chain 25 peptides. Score 0.573 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 468, Estimated correctness of the model 33.6 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2pgc-3_warpNtrace.pdb as input Building loops using Loopy2018 62 chains (468 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 19941 reflections ( 99.69 % complete ) and 16864 restraints for refining 7560 atoms. 14959 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2313 (Rfree = 0.000) for 7560 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 47: After refmac, R = 0.2341 (Rfree = 0.000) for 7506 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 48: After refmac, R = 0.2266 (Rfree = 0.000) for 7462 atoms. Found 0 (67 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.2224 (Rfree = 0.000) for 7424 atoms. TimeTaking 79.33