Mon 24 Dec 07:38:30 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ich-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ich-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-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/2ich-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-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 07:38:35 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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-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 549 and 0 Target number of residues in the AU: 549 Target solvent content: 0.5964 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-3.2-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: 19 Cell parameters: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-3.2-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 3.200 Wilson plot Bfac: 51.15 12684 reflections ( 99.73 % complete ) and 0 restraints for refining 5937 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3124 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2626 (Rfree = 0.000) for 5937 atoms. Found 40 (53 requested) and removed 64 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 2.93 Search for helices and strands: 0 residues in 0 chains, 5977 seeds are put forward NCS extension: 0 residues added, 5977 seeds are put forward Round 1: 390 peptides, 66 chains. Longest chain 15 peptides. Score 0.455 Round 2: 450 peptides, 56 chains. Longest chain 20 peptides. Score 0.636 Round 3: 468 peptides, 59 chains. Longest chain 18 peptides. Score 0.642 Round 4: 479 peptides, 56 chains. Longest chain 25 peptides. Score 0.677 Round 5: 483 peptides, 51 chains. Longest chain 30 peptides. Score 0.711 Taking the results from Round 5 Chains 58, Residues 432, Estimated correctness of the model 67.5 % 10 chains (109 residues) have been docked in sequence Building loops using Loopy2018 58 chains (432 residues) following loop building 10 chains (109 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9239 restraints for refining 4893 atoms. 7156 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2700 (Rfree = 0.000) for 4893 atoms. Found 43 (43 requested) and removed 57 (21 requested) atoms. Cycle 2: After refmac, R = 0.2515 (Rfree = 0.000) for 4827 atoms. Found 19 (42 requested) and removed 31 (21 requested) atoms. Cycle 3: After refmac, R = 0.2452 (Rfree = 0.000) for 4797 atoms. Found 11 (41 requested) and removed 24 (21 requested) atoms. Cycle 4: After refmac, R = 0.2442 (Rfree = 0.000) for 4772 atoms. Found 14 (39 requested) and removed 22 (21 requested) atoms. Cycle 5: After refmac, R = 0.2383 (Rfree = 0.000) for 4755 atoms. Found 6 (39 requested) and removed 23 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.02 2.98 Search for helices and strands: 0 residues in 0 chains, 4847 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 4862 seeds are put forward Round 1: 448 peptides, 56 chains. Longest chain 24 peptides. Score 0.633 Round 2: 481 peptides, 46 chains. Longest chain 30 peptides. Score 0.736 Round 3: 486 peptides, 48 chains. Longest chain 38 peptides. Score 0.731 Round 4: 484 peptides, 46 chains. Longest chain 29 peptides. Score 0.740 Round 5: 492 peptides, 49 chains. Longest chain 31 peptides. Score 0.733 Taking the results from Round 4 Chains 49, Residues 438, Estimated correctness of the model 73.2 % 8 chains (124 residues) have been docked in sequence Building loops using Loopy2018 49 chains (438 residues) following loop building 8 chains (124 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9287 restraints for refining 4894 atoms. 7080 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2670 (Rfree = 0.000) for 4894 atoms. Found 39 (39 requested) and removed 33 (21 requested) atoms. Cycle 7: After refmac, R = 0.2456 (Rfree = 0.000) for 4875 atoms. Found 27 (38 requested) and removed 33 (21 requested) atoms. Cycle 8: After refmac, R = 0.2364 (Rfree = 0.000) for 4851 atoms. Found 15 (37 requested) and removed 22 (21 requested) atoms. Cycle 9: After refmac, R = 0.2315 (Rfree = 0.000) for 4835 atoms. Found 13 (36 requested) and removed 21 (21 requested) atoms. Cycle 10: After refmac, R = 0.2274 (Rfree = 0.000) for 4820 atoms. Found 13 (35 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 2.98 Search for helices and strands: 0 residues in 0 chains, 4899 seeds are put forward NCS extension: 35 residues added (5 deleted due to clashes), 4934 seeds are put forward Round 1: 437 peptides, 49 chains. Longest chain 30 peptides. Score 0.663 Round 2: 474 peptides, 44 chains. Longest chain 34 peptides. Score 0.739 Round 3: 487 peptides, 42 chains. Longest chain 48 peptides. Score 0.763 Round 4: 497 peptides, 43 chains. Longest chain 56 peptides. Score 0.769 Round 5: 493 peptides, 45 chains. Longest chain 35 peptides. Score 0.754 Taking the results from Round 4 Chains 51, Residues 454, Estimated correctness of the model 78.4 % 8 chains (136 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 303 A and 314 A 49 chains (454 residues) following loop building 7 chains (146 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8831 restraints for refining 4894 atoms. 6488 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2747 (Rfree = 0.000) for 4894 atoms. Found 34 (34 requested) and removed 48 (21 requested) atoms. Cycle 12: After refmac, R = 0.2537 (Rfree = 0.000) for 4849 atoms. Found 17 (34 requested) and removed 26 (21 requested) atoms. Cycle 13: After refmac, R = 0.2470 (Rfree = 0.000) for 4829 atoms. Found 13 (33 requested) and removed 27 (21 requested) atoms. Cycle 14: After refmac, R = 0.2399 (Rfree = 0.000) for 4811 atoms. Found 9 (32 requested) and removed 21 (21 requested) atoms. Cycle 15: After refmac, R = 0.2319 (Rfree = 0.000) for 4798 atoms. Found 6 (31 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 2.97 Search for helices and strands: 0 residues in 0 chains, 4884 seeds are put forward NCS extension: 26 residues added (24 deleted due to clashes), 4910 seeds are put forward Round 1: 463 peptides, 59 chains. Longest chain 30 peptides. Score 0.635 Round 2: 491 peptides, 48 chains. Longest chain 40 peptides. Score 0.737 Round 3: 489 peptides, 56 chains. Longest chain 57 peptides. Score 0.690 Round 4: 492 peptides, 50 chains. Longest chain 37 peptides. Score 0.727 Round 5: 487 peptides, 48 chains. Longest chain 26 peptides. Score 0.732 Taking the results from Round 2 Chains 55, Residues 443, Estimated correctness of the model 72.6 % 9 chains (142 residues) have been docked in sequence Building loops using Loopy2018 55 chains (443 residues) following loop building 9 chains (142 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 8977 restraints for refining 4893 atoms. 6650 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2609 (Rfree = 0.000) for 4893 atoms. Found 30 (30 requested) and removed 49 (21 requested) atoms. Cycle 17: After refmac, R = 0.2441 (Rfree = 0.000) for 4857 atoms. Found 17 (29 requested) and removed 28 (21 requested) atoms. Cycle 18: After refmac, R = 0.2402 (Rfree = 0.000) for 4841 atoms. Found 7 (28 requested) and removed 22 (21 requested) atoms. Cycle 19: After refmac, R = 0.2332 (Rfree = 0.000) for 4816 atoms. Found 10 (28 requested) and removed 25 (21 requested) atoms. Cycle 20: After refmac, R = 0.2296 (Rfree = 0.000) for 4796 atoms. Found 5 (27 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 2.97 Search for helices and strands: 0 residues in 0 chains, 4874 seeds are put forward NCS extension: 25 residues added (21 deleted due to clashes), 4899 seeds are put forward Round 1: 421 peptides, 52 chains. Longest chain 30 peptides. Score 0.619 Round 2: 459 peptides, 51 chains. Longest chain 31 peptides. Score 0.681 Round 3: 459 peptides, 48 chains. Longest chain 40 peptides. Score 0.699 Round 4: 456 peptides, 45 chains. Longest chain 43 peptides. Score 0.712 Round 5: 455 peptides, 49 chains. Longest chain 45 peptides. Score 0.687 Taking the results from Round 4 Chains 49, Residues 411, Estimated correctness of the model 67.7 % 8 chains (111 residues) have been docked in sequence Building loops using Loopy2018 49 chains (411 residues) following loop building 7 chains (111 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9406 restraints for refining 4893 atoms. 7323 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2656 (Rfree = 0.000) for 4893 atoms. Found 26 (26 requested) and removed 61 (21 requested) atoms. Cycle 22: After refmac, R = 0.2470 (Rfree = 0.000) for 4842 atoms. Found 24 (25 requested) and removed 26 (21 requested) atoms. Cycle 23: After refmac, R = 0.2369 (Rfree = 0.000) for 4838 atoms. Found 11 (24 requested) and removed 23 (21 requested) atoms. Cycle 24: After refmac, R = 0.2309 (Rfree = 0.000) for 4823 atoms. Found 7 (23 requested) and removed 21 (21 requested) atoms. Cycle 25: After refmac, R = 0.2268 (Rfree = 0.000) for 4804 atoms. Found 12 (22 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.04 3.00 Search for helices and strands: 0 residues in 0 chains, 4885 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 4919 seeds are put forward Round 1: 412 peptides, 52 chains. Longest chain 34 peptides. Score 0.605 Round 2: 456 peptides, 49 chains. Longest chain 32 peptides. Score 0.689 Round 3: 459 peptides, 53 chains. Longest chain 24 peptides. Score 0.668 Round 4: 455 peptides, 48 chains. Longest chain 40 peptides. Score 0.693 Round 5: 460 peptides, 46 chains. Longest chain 26 peptides. Score 0.712 Taking the results from Round 5 Chains 52, Residues 414, Estimated correctness of the model 67.7 % 9 chains (103 residues) have been docked in sequence Building loops using Loopy2018 52 chains (414 residues) following loop building 9 chains (103 residues) in sequence following loop building ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9631 restraints for refining 4894 atoms. 7635 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2629 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 37 (21 requested) atoms. Cycle 27: After refmac, R = 0.2433 (Rfree = 0.000) for 4873 atoms. Found 19 (21 requested) and removed 22 (21 requested) atoms. Cycle 28: After refmac, R = 0.2357 (Rfree = 0.000) for 4864 atoms. Found 15 (21 requested) and removed 22 (21 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2313 (Rfree = 0.000) for 4847 atoms. Found 10 (21 requested) and removed 22 (21 requested) atoms. Cycle 30: After refmac, R = 0.2286 (Rfree = 0.000) for 4832 atoms. Found 6 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.01 2.97 Search for helices and strands: 0 residues in 0 chains, 4911 seeds are put forward NCS extension: 16 residues added (7 deleted due to clashes), 4927 seeds are put forward Round 1: 445 peptides, 58 chains. Longest chain 37 peptides. Score 0.615 Round 2: 460 peptides, 54 chains. Longest chain 35 peptides. Score 0.663 Round 3: 464 peptides, 56 chains. Longest chain 30 peptides. Score 0.656 Round 4: 440 peptides, 52 chains. Longest chain 34 peptides. Score 0.648 Round 5: 457 peptides, 50 chains. Longest chain 32 peptides. Score 0.684 Taking the results from Round 5 Chains 54, Residues 407, Estimated correctness of the model 61.7 % 8 chains (118 residues) have been docked in sequence ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9233 restraints for refining 4894 atoms. 7119 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2591 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 45 (21 requested) atoms. Cycle 32: After refmac, R = 0.2422 (Rfree = 0.000) for 4855 atoms. Found 21 (21 requested) and removed 27 (21 requested) atoms. Cycle 33: After refmac, R = 0.2363 (Rfree = 0.000) for 4840 atoms. Found 14 (21 requested) and removed 23 (21 requested) atoms. Cycle 34: After refmac, R = 0.2327 (Rfree = 0.000) for 4826 atoms. Found 14 (21 requested) and removed 23 (21 requested) atoms. Cycle 35: After refmac, R = 0.2291 (Rfree = 0.000) for 4815 atoms. Found 10 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 2.96 Search for helices and strands: 0 residues in 0 chains, 4868 seeds are put forward NCS extension: 23 residues added (12 deleted due to clashes), 4891 seeds are put forward Round 1: 398 peptides, 59 chains. Longest chain 18 peptides. Score 0.528 Round 2: 439 peptides, 57 chains. Longest chain 24 peptides. Score 0.612 Round 3: 455 peptides, 51 chains. Longest chain 37 peptides. Score 0.675 Round 4: 442 peptides, 53 chains. Longest chain 22 peptides. Score 0.644 Round 5: 456 peptides, 54 chains. Longest chain 38 peptides. Score 0.658 Taking the results from Round 3 Chains 53, Residues 404, Estimated correctness of the model 59.7 % 4 chains (59 residues) have been docked in sequence ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9875 restraints for refining 4894 atoms. 8064 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2480 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 33 (21 requested) atoms. Cycle 37: After refmac, R = 0.2340 (Rfree = 0.000) for 4873 atoms. Found 21 (21 requested) and removed 24 (21 requested) atoms. Cycle 38: After refmac, R = 0.2277 (Rfree = 0.000) for 4863 atoms. Found 10 (21 requested) and removed 23 (21 requested) atoms. Cycle 39: After refmac, R = 0.2252 (Rfree = 0.000) for 4845 atoms. Found 7 (21 requested) and removed 21 (21 requested) atoms. Cycle 40: After refmac, R = 0.2210 (Rfree = 0.000) for 4828 atoms. Found 8 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.02 2.98 Search for helices and strands: 0 residues in 0 chains, 4866 seeds are put forward NCS extension: 53 residues added (0 deleted due to clashes), 4919 seeds are put forward Round 1: 413 peptides, 59 chains. Longest chain 22 peptides. Score 0.555 Round 2: 423 peptides, 52 chains. Longest chain 22 peptides. Score 0.622 Round 3: 439 peptides, 51 chains. Longest chain 25 peptides. Score 0.653 Round 4: 444 peptides, 51 chains. Longest chain 39 peptides. Score 0.660 Round 5: 434 peptides, 53 chains. Longest chain 23 peptides. Score 0.632 Taking the results from Round 4 Chains 54, Residues 393, Estimated correctness of the model 56.2 % 7 chains (109 residues) have been docked in sequence ------------------------------------------------------ 12684 reflections ( 99.73 % complete ) and 9303 restraints for refining 4894 atoms. 7282 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2490 (Rfree = 0.000) for 4894 atoms. Found 21 (21 requested) and removed 47 (21 requested) atoms. Cycle 42: After refmac, R = 0.2343 (Rfree = 0.000) for 4856 atoms. Found 21 (21 requested) and removed 24 (21 requested) atoms. Cycle 43: After refmac, R = 0.2283 (Rfree = 0.000) for 4851 atoms. Found 10 (21 requested) and removed 22 (21 requested) atoms. Cycle 44: After refmac, R = 0.2233 (Rfree = 0.000) for 4832 atoms. Found 9 (21 requested) and removed 22 (21 requested) atoms. Cycle 45: After refmac, R = 0.2226 (Rfree = 0.000) for 4813 atoms. Found 5 (21 requested) and removed 21 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.00 2.96 Search for helices and strands: 0 residues in 0 chains, 4883 seeds are put forward NCS extension: 37 residues added (5 deleted due to clashes), 4920 seeds are put forward Round 1: 339 peptides, 48 chains. Longest chain 22 peptides. Score 0.509 Round 2: 381 peptides, 45 chains. Longest chain 24 peptides. Score 0.606 Round 3: 385 peptides, 49 chains. Longest chain 22 peptides. Score 0.583 Round 4: 386 peptides, 47 chains. Longest chain 22 peptides. Score 0.600 Round 5: 395 peptides, 50 chains. Longest chain 24 peptides. Score 0.592 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 336, Estimated correctness of the model 42.7 % 7 chains (62 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 50 chains (336 residues) following loop building 7 chains (62 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12684 reflections ( 99.73 % complete ) and 10299 restraints for refining 4894 atoms. 8771 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2377 (Rfree = 0.000) for 4894 atoms. Found 0 (21 requested) and removed 15 (21 requested) atoms. Cycle 47: After refmac, R = 0.2345 (Rfree = 0.000) for 4870 atoms. Found 0 (21 requested) and removed 9 (21 requested) atoms. Cycle 48: After refmac, R = 0.2321 (Rfree = 0.000) for 4860 atoms. Found 0 (21 requested) and removed 14 (21 requested) atoms. Cycle 49: After refmac, R = 0.2286 (Rfree = 0.000) for 4843 atoms. TimeTaking 59.88