Mon 24 Dec 00:54:03 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 1ztc-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-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/1ztc-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-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 00:54:08 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/1ztc-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.4-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 1148 and 0 Target number of residues in the AU: 1148 Target solvent content: 0.6430 Checking the provided sequence file Detected sequence length: 221 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 884 Adjusted target solvent content: 0.73 Input MTZ file: 1ztc-3.4-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: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.10 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: 97.673 3.400 Wilson plot Bfac: 73.76 24384 reflections ( 98.85 % complete ) and 0 restraints for refining 7914 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Starting model: R = 0.3219 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2865 (Rfree = 0.000) for 7914 atoms. Found 59 (59 requested) and removed 39 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 8064 seeds are put forward NCS extension: 0 residues added, 8064 seeds are put forward Round 1: 629 peptides, 75 chains. Longest chain 23 peptides. Score 0.511 Round 2: 664 peptides, 63 chains. Longest chain 37 peptides. Score 0.583 Round 3: 669 peptides, 56 chains. Longest chain 41 peptides. Score 0.611 Round 4: 676 peptides, 58 chains. Longest chain 40 peptides. Score 0.609 Round 5: 684 peptides, 62 chains. Longest chain 33 peptides. Score 0.601 Taking the results from Round 3 Chains 59, Residues 613, Estimated correctness of the model 32.2 % 4 chains (94 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12734 restraints for refining 6618 atoms. 9928 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2592 (Rfree = 0.000) for 6618 atoms. Found 50 (50 requested) and removed 36 (25 requested) atoms. Cycle 2: After refmac, R = 0.2420 (Rfree = 0.000) for 6525 atoms. Found 50 (50 requested) and removed 37 (25 requested) atoms. Cycle 3: After refmac, R = 0.2319 (Rfree = 0.000) for 6483 atoms. Found 31 (49 requested) and removed 30 (24 requested) atoms. Cycle 4: After refmac, R = 0.2244 (Rfree = 0.000) for 6460 atoms. Found 29 (48 requested) and removed 33 (24 requested) atoms. Cycle 5: After refmac, R = 0.2181 (Rfree = 0.000) for 6438 atoms. Found 22 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 2.41 Search for helices and strands: 0 residues in 0 chains, 6651 seeds are put forward NCS extension: 29 residues added (6 deleted due to clashes), 6680 seeds are put forward Round 1: 683 peptides, 60 chains. Longest chain 45 peptides. Score 0.607 Round 2: 700 peptides, 56 chains. Longest chain 40 peptides. Score 0.632 Round 3: 694 peptides, 58 chains. Longest chain 35 peptides. Score 0.622 Round 4: 670 peptides, 60 chains. Longest chain 29 peptides. Score 0.598 Round 5: 679 peptides, 51 chains. Longest chain 46 peptides. Score 0.635 Taking the results from Round 5 Chains 58, Residues 628, Estimated correctness of the model 39.7 % 8 chains (176 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11674 restraints for refining 6429 atoms. 8464 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2530 (Rfree = 0.000) for 6429 atoms. Found 48 (48 requested) and removed 53 (24 requested) atoms. Cycle 7: After refmac, R = 0.2347 (Rfree = 0.000) for 6371 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. Cycle 8: After refmac, R = 0.2216 (Rfree = 0.000) for 6358 atoms. Found 38 (48 requested) and removed 30 (24 requested) atoms. Cycle 9: After refmac, R = 0.2126 (Rfree = 0.000) for 6353 atoms. Found 23 (48 requested) and removed 26 (24 requested) atoms. Cycle 10: After refmac, R = 0.2079 (Rfree = 0.000) for 6339 atoms. Found 14 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 2.41 Search for helices and strands: 0 residues in 0 chains, 6494 seeds are put forward NCS extension: 17 residues added (16 deleted due to clashes), 6511 seeds are put forward Round 1: 686 peptides, 62 chains. Longest chain 43 peptides. Score 0.602 Round 2: 705 peptides, 56 chains. Longest chain 33 peptides. Score 0.636 Round 3: 694 peptides, 62 chains. Longest chain 28 peptides. Score 0.608 Round 4: 685 peptides, 58 chains. Longest chain 40 peptides. Score 0.615 Round 5: 684 peptides, 56 chains. Longest chain 49 peptides. Score 0.622 Taking the results from Round 2 Chains 60, Residues 649, Estimated correctness of the model 40.0 % 6 chains (122 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 12081 restraints for refining 6429 atoms. 8998 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2605 (Rfree = 0.000) for 6429 atoms. Found 48 (48 requested) and removed 44 (24 requested) atoms. Cycle 12: After refmac, R = 0.2397 (Rfree = 0.000) for 6396 atoms. Found 48 (48 requested) and removed 37 (24 requested) atoms. Cycle 13: After refmac, R = 0.2282 (Rfree = 0.000) for 6399 atoms. Found 34 (48 requested) and removed 27 (24 requested) atoms. Cycle 14: After refmac, R = 0.2208 (Rfree = 0.000) for 6399 atoms. Found 28 (48 requested) and removed 25 (24 requested) atoms. Cycle 15: After refmac, R = 0.2162 (Rfree = 0.000) for 6390 atoms. Found 21 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 2.41 Search for helices and strands: 0 residues in 0 chains, 6572 seeds are put forward NCS extension: 18 residues added (22 deleted due to clashes), 6590 seeds are put forward Round 1: 678 peptides, 62 chains. Longest chain 37 peptides. Score 0.597 Round 2: 705 peptides, 63 chains. Longest chain 34 peptides. Score 0.612 Round 3: 702 peptides, 54 chains. Longest chain 44 peptides. Score 0.640 Round 4: 698 peptides, 51 chains. Longest chain 40 peptides. Score 0.647 Round 5: 707 peptides, 51 chains. Longest chain 54 peptides. Score 0.653 Taking the results from Round 5 Chains 55, Residues 656, Estimated correctness of the model 45.0 % 8 chains (225 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11181 restraints for refining 6429 atoms. 7664 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2581 (Rfree = 0.000) for 6429 atoms. Found 48 (48 requested) and removed 58 (24 requested) atoms. Cycle 17: After refmac, R = 0.2344 (Rfree = 0.000) for 6383 atoms. Found 48 (48 requested) and removed 38 (24 requested) atoms. Cycle 18: After refmac, R = 0.2206 (Rfree = 0.000) for 6378 atoms. Found 34 (48 requested) and removed 32 (24 requested) atoms. Cycle 19: After refmac, R = 0.2140 (Rfree = 0.000) for 6373 atoms. Found 9 (48 requested) and removed 28 (24 requested) atoms. Cycle 20: After refmac, R = 0.2109 (Rfree = 0.000) for 6346 atoms. Found 16 (47 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 6532 seeds are put forward NCS extension: 32 residues added (25 deleted due to clashes), 6564 seeds are put forward Round 1: 682 peptides, 66 chains. Longest chain 32 peptides. Score 0.585 Round 2: 721 peptides, 56 chains. Longest chain 43 peptides. Score 0.646 Round 3: 713 peptides, 53 chains. Longest chain 41 peptides. Score 0.651 Round 4: 702 peptides, 55 chains. Longest chain 37 peptides. Score 0.637 Round 5: 690 peptides, 57 chains. Longest chain 51 peptides. Score 0.622 Taking the results from Round 3 Chains 60, Residues 660, Estimated correctness of the model 44.4 % 10 chains (248 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 10753 restraints for refining 6426 atoms. 7107 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2563 (Rfree = 0.000) for 6426 atoms. Found 48 (48 requested) and removed 54 (24 requested) atoms. Cycle 22: After refmac, R = 0.2321 (Rfree = 0.000) for 6388 atoms. Found 47 (48 requested) and removed 37 (24 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2196 (Rfree = 0.000) for 6376 atoms. Found 22 (48 requested) and removed 31 (24 requested) atoms. Cycle 24: After refmac, R = 0.2140 (Rfree = 0.000) for 6355 atoms. Found 16 (48 requested) and removed 24 (24 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2094 (Rfree = 0.000) for 6343 atoms. Found 8 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 6504 seeds are put forward NCS extension: 7 residues added (45 deleted due to clashes), 6511 seeds are put forward Round 1: 662 peptides, 60 chains. Longest chain 44 peptides. Score 0.592 Round 2: 684 peptides, 53 chains. Longest chain 47 peptides. Score 0.632 Round 3: 688 peptides, 62 chains. Longest chain 45 peptides. Score 0.604 Round 4: 703 peptides, 56 chains. Longest chain 49 peptides. Score 0.634 Round 5: 699 peptides, 62 chains. Longest chain 47 peptides. Score 0.611 Taking the results from Round 4 Chains 64, Residues 647, Estimated correctness of the model 39.4 % 11 chains (227 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11156 restraints for refining 6427 atoms. 7655 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2607 (Rfree = 0.000) for 6427 atoms. Found 48 (48 requested) and removed 45 (24 requested) atoms. Cycle 27: After refmac, R = 0.2324 (Rfree = 0.000) for 6399 atoms. Found 48 (48 requested) and removed 33 (24 requested) atoms. Cycle 28: After refmac, R = 0.2210 (Rfree = 0.000) for 6386 atoms. Found 23 (48 requested) and removed 27 (24 requested) atoms. Cycle 29: After refmac, R = 0.2167 (Rfree = 0.000) for 6356 atoms. Found 26 (48 requested) and removed 26 (24 requested) atoms. Cycle 30: After refmac, R = 0.2141 (Rfree = 0.000) for 6348 atoms. Found 19 (47 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 6523 seeds are put forward NCS extension: 12 residues added (17 deleted due to clashes), 6535 seeds are put forward Round 1: 647 peptides, 61 chains. Longest chain 39 peptides. Score 0.577 Round 2: 711 peptides, 49 chains. Longest chain 51 peptides. Score 0.662 Round 3: 696 peptides, 58 chains. Longest chain 35 peptides. Score 0.623 Round 4: 700 peptides, 56 chains. Longest chain 51 peptides. Score 0.632 Round 5: 708 peptides, 53 chains. Longest chain 48 peptides. Score 0.647 Taking the results from Round 2 Chains 55, Residues 662, Estimated correctness of the model 47.6 % 12 chains (325 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 10362 restraints for refining 6478 atoms. 6366 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2433 (Rfree = 0.000) for 6478 atoms. Found 48 (48 requested) and removed 66 (24 requested) atoms. Cycle 32: After refmac, R = 0.2203 (Rfree = 0.000) for 6421 atoms. Found 42 (48 requested) and removed 46 (24 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2107 (Rfree = 0.000) for 6406 atoms. Found 25 (48 requested) and removed 32 (24 requested) atoms. Cycle 34: After refmac, R = 0.2062 (Rfree = 0.000) for 6391 atoms. Found 12 (48 requested) and removed 32 (24 requested) atoms. Cycle 35: After refmac, R = 0.2015 (Rfree = 0.000) for 6362 atoms. Found 20 (48 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 6541 seeds are put forward NCS extension: 16 residues added (40 deleted due to clashes), 6557 seeds are put forward Round 1: 676 peptides, 65 chains. Longest chain 45 peptides. Score 0.585 Round 2: 696 peptides, 55 chains. Longest chain 40 peptides. Score 0.633 Round 3: 692 peptides, 53 chains. Longest chain 43 peptides. Score 0.637 Round 4: 709 peptides, 59 chains. Longest chain 50 peptides. Score 0.628 Round 5: 714 peptides, 52 chains. Longest chain 47 peptides. Score 0.655 Taking the results from Round 5 Chains 57, Residues 662, Estimated correctness of the model 45.6 % 11 chains (253 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 10798 restraints for refining 6429 atoms. 7068 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2584 (Rfree = 0.000) for 6429 atoms. Found 48 (48 requested) and removed 59 (24 requested) atoms. Cycle 37: After refmac, R = 0.2346 (Rfree = 0.000) for 6378 atoms. Found 48 (48 requested) and removed 35 (24 requested) atoms. Cycle 38: After refmac, R = 0.2204 (Rfree = 0.000) for 6370 atoms. Found 32 (48 requested) and removed 28 (24 requested) atoms. Cycle 39: After refmac, R = 0.2126 (Rfree = 0.000) for 6357 atoms. Found 20 (48 requested) and removed 25 (24 requested) atoms. Cycle 40: After refmac, R = 0.2076 (Rfree = 0.000) for 6331 atoms. Found 16 (47 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 2.43 Search for helices and strands: 0 residues in 0 chains, 6468 seeds are put forward NCS extension: 11 residues added (42 deleted due to clashes), 6479 seeds are put forward Round 1: 661 peptides, 62 chains. Longest chain 32 peptides. Score 0.584 Round 2: 688 peptides, 54 chains. Longest chain 47 peptides. Score 0.631 Round 3: 689 peptides, 59 chains. Longest chain 77 peptides. Score 0.615 Round 4: 696 peptides, 53 chains. Longest chain 50 peptides. Score 0.640 Round 5: 699 peptides, 57 chains. Longest chain 41 peptides. Score 0.628 Taking the results from Round 4 Chains 56, Residues 643, Estimated correctness of the model 41.2 % 6 chains (175 residues) have been docked in sequence ------------------------------------------------------ 24384 reflections ( 98.85 % complete ) and 11850 restraints for refining 6428 atoms. 8586 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2499 (Rfree = 0.000) for 6428 atoms. Found 48 (48 requested) and removed 43 (24 requested) atoms. Cycle 42: After refmac, R = 0.2295 (Rfree = 0.000) for 6408 atoms. Found 48 (48 requested) and removed 29 (24 requested) atoms. Cycle 43: After refmac, R = 0.2155 (Rfree = 0.000) for 6410 atoms. Found 20 (48 requested) and removed 30 (24 requested) atoms. Cycle 44: After refmac, R = 0.2080 (Rfree = 0.000) for 6395 atoms. Found 10 (48 requested) and removed 26 (24 requested) atoms. Cycle 45: After refmac, R = 0.2051 (Rfree = 0.000) for 6375 atoms. Found 14 (48 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 6562 seeds are put forward NCS extension: 38 residues added (19 deleted due to clashes), 6600 seeds are put forward Round 1: 632 peptides, 64 chains. Longest chain 28 peptides. Score 0.555 Round 2: 681 peptides, 54 chains. Longest chain 48 peptides. Score 0.626 Round 3: 661 peptides, 57 chains. Longest chain 50 peptides. Score 0.602 Round 4: 669 peptides, 59 chains. Longest chain 50 peptides. Score 0.601 Round 5: 682 peptides, 51 chains. Longest chain 44 peptides. Score 0.637 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 631, Estimated correctness of the model 40.3 % 8 chains (175 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (631 residues) following loop building 8 chains (175 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 24384 reflections ( 98.85 % complete ) and 11626 restraints for refining 6429 atoms. 8335 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2457 (Rfree = 0.000) for 6429 atoms. Found 0 (48 requested) and removed 15 (24 requested) atoms. Cycle 47: After refmac, R = 0.2301 (Rfree = 0.000) for 6387 atoms. Found 0 (48 requested) and removed 6 (24 requested) atoms. Cycle 48: After refmac, R = 0.2233 (Rfree = 0.000) for 6375 atoms. Found 0 (48 requested) and removed 3 (24 requested) atoms. Cycle 49: After refmac, R = 0.2206 (Rfree = 0.000) for 6362 atoms. Found 0 (48 requested) and removed 2 (24 requested) atoms. Writing output files ... TimeTaking 94.83