null Mon 24 Dec 07:54:57 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 2ich-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ich-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ich-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.4-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/2ich-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.4-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 07:55:01 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/2ich-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-3.4-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 532 and 0 Target number of residues in the AU: 532 Target solvent content: 0.6089 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-3.4-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: 19 Cell parameters: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.65 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: 29.160 3.400 Wilson plot Bfac: 56.37 10621 reflections ( 99.68 % complete ) and 0 restraints for refining 5946 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3140 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3136 (Rfree = 0.000) for 5946 atoms. Found 44 (44 requested) and removed 79 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 5983 seeds are put forward NCS extension: 0 residues added, 5983 seeds are put forward Round 1: 320 peptides, 58 chains. Longest chain 16 peptides. Score 0.380 Round 2: 398 peptides, 56 chains. Longest chain 19 peptides. Score 0.552 Round 3: 424 peptides, 56 chains. Longest chain 29 peptides. Score 0.596 Round 4: 431 peptides, 49 chains. Longest chain 49 peptides. Score 0.655 Round 5: 434 peptides, 52 chains. Longest chain 24 peptides. Score 0.639 Taking the results from Round 4 Chains 55, Residues 382, Estimated correctness of the model 45.6 % 9 chains (86 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9664 restraints for refining 4872 atoms. 7847 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3052 (Rfree = 0.000) for 4872 atoms. Found 31 (36 requested) and removed 61 (18 requested) atoms. Cycle 2: After refmac, R = 0.2508 (Rfree = 0.000) for 4761 atoms. Found 18 (36 requested) and removed 32 (18 requested) atoms. Cycle 3: After refmac, R = 0.2475 (Rfree = 0.000) for 4716 atoms. Found 17 (35 requested) and removed 32 (17 requested) atoms. Cycle 4: After refmac, R = 0.2259 (Rfree = 0.000) for 4689 atoms. Found 8 (35 requested) and removed 26 (17 requested) atoms. Cycle 5: After refmac, R = 0.2292 (Rfree = 0.000) for 4661 atoms. Found 6 (35 requested) and removed 26 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 4740 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 4759 seeds are put forward Round 1: 402 peptides, 55 chains. Longest chain 26 peptides. Score 0.566 Round 2: 434 peptides, 51 chains. Longest chain 25 peptides. Score 0.646 Round 3: 428 peptides, 46 chains. Longest chain 34 peptides. Score 0.670 Round 4: 446 peptides, 45 chains. Longest chain 31 peptides. Score 0.700 Round 5: 446 peptides, 48 chains. Longest chain 34 peptides. Score 0.682 Taking the results from Round 4 Chains 50, Residues 401, Estimated correctness of the model 57.9 % 8 chains (91 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9632 restraints for refining 4873 atoms. 7727 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2728 (Rfree = 0.000) for 4873 atoms. Found 34 (36 requested) and removed 45 (18 requested) atoms. Cycle 7: After refmac, R = 0.2496 (Rfree = 0.000) for 4815 atoms. Found 20 (36 requested) and removed 35 (18 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 4777 atoms. Found 27 (36 requested) and removed 25 (18 requested) atoms. Cycle 9: After refmac, R = 0.2349 (Rfree = 0.000) for 4763 atoms. Found 20 (36 requested) and removed 29 (18 requested) atoms. Cycle 10: After refmac, R = 0.2371 (Rfree = 0.000) for 4744 atoms. Found 21 (35 requested) and removed 31 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.10 Search for helices and strands: 0 residues in 0 chains, 4823 seeds are put forward NCS extension: 41 residues added (4 deleted due to clashes), 4864 seeds are put forward Round 1: 380 peptides, 52 chains. Longest chain 19 peptides. Score 0.551 Round 2: 434 peptides, 54 chains. Longest chain 29 peptides. Score 0.625 Round 3: 449 peptides, 56 chains. Longest chain 27 peptides. Score 0.634 Round 4: 463 peptides, 52 chains. Longest chain 45 peptides. Score 0.680 Round 5: 458 peptides, 49 chains. Longest chain 38 peptides. Score 0.691 Taking the results from Round 5 Chains 53, Residues 409, Estimated correctness of the model 55.5 % 5 chains (75 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9733 restraints for refining 4874 atoms. 7841 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2836 (Rfree = 0.000) for 4874 atoms. Found 32 (36 requested) and removed 46 (18 requested) atoms. Cycle 12: After refmac, R = 0.2576 (Rfree = 0.000) for 4824 atoms. Found 25 (36 requested) and removed 35 (18 requested) atoms. Cycle 13: After refmac, R = 0.2418 (Rfree = 0.000) for 4798 atoms. Found 12 (36 requested) and removed 24 (18 requested) atoms. Cycle 14: After refmac, R = 0.2394 (Rfree = 0.000) for 4769 atoms. Found 13 (36 requested) and removed 19 (18 requested) atoms. Cycle 15: After refmac, R = 0.2652 (Rfree = 0.000) for 4757 atoms. Found 29 (35 requested) and removed 43 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 4845 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 4878 seeds are put forward Round 1: 379 peptides, 58 chains. Longest chain 14 peptides. Score 0.501 Round 2: 422 peptides, 50 chains. Longest chain 30 peptides. Score 0.635 Round 3: 423 peptides, 52 chains. Longest chain 25 peptides. Score 0.622 Round 4: 410 peptides, 47 chains. Longest chain 27 peptides. Score 0.637 Round 5: 420 peptides, 53 chains. Longest chain 25 peptides. Score 0.611 Taking the results from Round 4 Chains 51, Residues 363, Estimated correctness of the model 40.3 % 8 chains (74 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 10039 restraints for refining 4874 atoms. 8365 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2630 (Rfree = 0.000) for 4874 atoms. Found 26 (36 requested) and removed 37 (18 requested) atoms. Cycle 17: After refmac, R = 0.2543 (Rfree = 0.000) for 4843 atoms. Found 29 (36 requested) and removed 32 (18 requested) atoms. Cycle 18: After refmac, R = 0.2462 (Rfree = 0.000) for 4832 atoms. Found 20 (36 requested) and removed 42 (18 requested) atoms. Cycle 19: After refmac, R = 0.2345 (Rfree = 0.000) for 4799 atoms. Found 13 (36 requested) and removed 33 (18 requested) atoms. Cycle 20: After refmac, R = 0.2321 (Rfree = 0.000) for 4778 atoms. Found 24 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.13 Search for helices and strands: 0 residues in 0 chains, 4853 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4873 seeds are put forward Round 1: 374 peptides, 57 chains. Longest chain 19 peptides. Score 0.500 Round 2: 409 peptides, 50 chains. Longest chain 27 peptides. Score 0.615 Round 3: 414 peptides, 48 chains. Longest chain 34 peptides. Score 0.636 Round 4: 408 peptides, 53 chains. Longest chain 22 peptides. Score 0.591 Round 5: 423 peptides, 47 chains. Longest chain 21 peptides. Score 0.656 Taking the results from Round 5 Chains 54, Residues 376, Estimated correctness of the model 45.9 % 9 chains (111 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9453 restraints for refining 4874 atoms. 7567 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2682 (Rfree = 0.000) for 4874 atoms. Found 27 (36 requested) and removed 82 (18 requested) atoms. Cycle 22: After refmac, R = 0.2603 (Rfree = 0.000) for 4794 atoms. Found 34 (36 requested) and removed 31 (18 requested) atoms. Cycle 23: After refmac, R = 0.2284 (Rfree = 0.000) for 4780 atoms. Found 17 (36 requested) and removed 26 (18 requested) atoms. Cycle 24: After refmac, R = 0.2321 (Rfree = 0.000) for 4763 atoms. Found 19 (36 requested) and removed 23 (18 requested) atoms. Cycle 25: After refmac, R = 0.2161 (Rfree = 0.000) for 4755 atoms. Found 10 (35 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 4857 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4882 seeds are put forward Round 1: 369 peptides, 55 chains. Longest chain 16 peptides. Score 0.507 Round 2: 413 peptides, 50 chains. Longest chain 22 peptides. Score 0.621 Round 3: 418 peptides, 50 chains. Longest chain 30 peptides. Score 0.629 Round 4: 427 peptides, 49 chains. Longest chain 39 peptides. Score 0.649 Round 5: 421 peptides, 54 chains. Longest chain 30 peptides. Score 0.605 Taking the results from Round 4 Chains 52, Residues 378, Estimated correctness of the model 43.8 % 9 chains (85 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9676 restraints for refining 4874 atoms. 7873 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2699 (Rfree = 0.000) for 4874 atoms. Found 36 (36 requested) and removed 53 (18 requested) atoms. Cycle 27: After refmac, R = 0.2423 (Rfree = 0.000) for 4832 atoms. Found 23 (36 requested) and removed 31 (18 requested) atoms. Cycle 28: After refmac, R = 0.2425 (Rfree = 0.000) for 4791 atoms. Found 24 (36 requested) and removed 26 (18 requested) atoms. Cycle 29: After refmac, R = 0.2179 (Rfree = 0.000) for 4774 atoms. Found 12 (36 requested) and removed 27 (18 requested) atoms. Cycle 30: After refmac, R = 0.2114 (Rfree = 0.000) for 4749 atoms. Found 9 (35 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 4813 seeds are put forward NCS extension: 55 residues added (3 deleted due to clashes), 4868 seeds are put forward Round 1: 359 peptides, 58 chains. Longest chain 16 peptides. Score 0.462 Round 2: 402 peptides, 50 chains. Longest chain 39 peptides. Score 0.604 Round 3: 412 peptides, 53 chains. Longest chain 21 peptides. Score 0.598 Round 4: 419 peptides, 48 chains. Longest chain 34 peptides. Score 0.644 Round 5: 392 peptides, 50 chains. Longest chain 20 peptides. Score 0.587 Taking the results from Round 4 Chains 49, Residues 371, Estimated correctness of the model 42.4 % 8 chains (79 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9851 restraints for refining 4873 atoms. 8118 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2456 (Rfree = 0.000) for 4873 atoms. Found 34 (36 requested) and removed 42 (18 requested) atoms. Cycle 32: After refmac, R = 0.2420 (Rfree = 0.000) for 4848 atoms. Found 32 (36 requested) and removed 42 (18 requested) atoms. Cycle 33: After refmac, R = 0.2164 (Rfree = 0.000) for 4823 atoms. Found 13 (36 requested) and removed 28 (18 requested) atoms. Cycle 34: After refmac, R = 0.2076 (Rfree = 0.000) for 4798 atoms. Found 19 (36 requested) and removed 19 (18 requested) atoms. Cycle 35: After refmac, R = 0.2050 (Rfree = 0.000) for 4796 atoms. Found 11 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 4882 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 4907 seeds are put forward Round 1: 319 peptides, 52 chains. Longest chain 16 peptides. Score 0.433 Round 2: 351 peptides, 45 chains. Longest chain 30 peptides. Score 0.556 Round 3: 373 peptides, 47 chains. Longest chain 20 peptides. Score 0.578 Round 4: 379 peptides, 50 chains. Longest chain 27 peptides. Score 0.565 Round 5: 365 peptides, 48 chains. Longest chain 21 peptides. Score 0.556 Taking the results from Round 3 Chains 49, Residues 326, Estimated correctness of the model 21.3 % 9 chains (58 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 10227 restraints for refining 4874 atoms. 8762 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2520 (Rfree = 0.000) for 4874 atoms. Found 22 (36 requested) and removed 35 (18 requested) atoms. Cycle 37: After refmac, R = 0.2280 (Rfree = 0.000) for 4839 atoms. Found 17 (36 requested) and removed 31 (18 requested) atoms. Cycle 38: After refmac, R = 0.2180 (Rfree = 0.000) for 4802 atoms. Found 20 (36 requested) and removed 28 (18 requested) atoms. Cycle 39: After refmac, R = 0.2054 (Rfree = 0.000) for 4790 atoms. Found 15 (36 requested) and removed 22 (18 requested) atoms. Cycle 40: After refmac, R = 0.2093 (Rfree = 0.000) for 4778 atoms. Found 17 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 4852 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4870 seeds are put forward Round 1: 298 peptides, 49 chains. Longest chain 16 peptides. Score 0.417 Round 2: 347 peptides, 44 chains. Longest chain 25 peptides. Score 0.556 Round 3: 359 peptides, 48 chains. Longest chain 25 peptides. Score 0.546 Round 4: 346 peptides, 44 chains. Longest chain 20 peptides. Score 0.555 Round 5: 336 peptides, 42 chains. Longest chain 26 peptides. Score 0.553 Taking the results from Round 2 Chains 46, Residues 303, Estimated correctness of the model 13.7 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 10672 restraints for refining 4874 atoms. 9418 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2238 (Rfree = 0.000) for 4874 atoms. Found 30 (36 requested) and removed 27 (18 requested) atoms. Cycle 42: After refmac, R = 0.2266 (Rfree = 0.000) for 4869 atoms. Found 26 (36 requested) and removed 23 (18 requested) atoms. Cycle 43: After refmac, R = 0.2194 (Rfree = 0.000) for 4864 atoms. Found 21 (36 requested) and removed 27 (18 requested) atoms. Cycle 44: After refmac, R = 0.2301 (Rfree = 0.000) for 4852 atoms. Found 36 (36 requested) and removed 27 (18 requested) atoms. Cycle 45: After refmac, R = 0.2073 (Rfree = 0.000) for 4860 atoms. Found 6 (36 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 4919 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 4950 seeds are put forward Round 1: 314 peptides, 52 chains. Longest chain 17 peptides. Score 0.423 Round 2: 333 peptides, 47 chains. Longest chain 15 peptides. Score 0.506 Round 3: 349 peptides, 49 chains. Longest chain 20 peptides. Score 0.519 Round 4: 340 peptides, 46 chains. Longest chain 18 peptides. Score 0.527 Round 5: 333 peptides, 45 chains. Longest chain 18 peptides. Score 0.523 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 294, Estimated correctness of the model 3.1 % 7 chains (54 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (294 residues) following loop building 7 chains (54 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10621 reflections ( 99.68 % complete ) and 10430 restraints for refining 4873 atoms. 9097 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2643 (Rfree = 0.000) for 4873 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2351 (Rfree = 0.000) for 4838 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2471 (Rfree = 0.000) for 4811 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2304 (Rfree = 0.000) for 4780 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:52:08 GMT 2018 Job finished. TimeTaking 57.19 Used memory is bytes: 5326976