Sun 23 Dec 22:22:59 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 2ich-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ich-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ich-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-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/2ich-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-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 22:23:07 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/2ich-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-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 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-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: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.70 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 5980 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3027 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3203 (Rfree = 0.000) for 5980 atoms. Found 45 (45 requested) and removed 84 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 6028 seeds are put forward NCS extension: 0 residues added, 6028 seeds are put forward Round 1: 356 peptides, 66 chains. Longest chain 12 peptides. Score 0.385 Round 2: 425 peptides, 57 chains. Longest chain 17 peptides. Score 0.590 Round 3: 437 peptides, 57 chains. Longest chain 26 peptides. Score 0.609 Round 4: 439 peptides, 49 chains. Longest chain 20 peptides. Score 0.666 Round 5: 445 peptides, 49 chains. Longest chain 27 peptides. Score 0.674 Taking the results from Round 5 Chains 54, Residues 396, Estimated correctness of the model 50.9 % 10 chains (117 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9224 restraints for refining 4873 atoms. 7220 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2770 (Rfree = 0.000) for 4873 atoms. Found 36 (36 requested) and removed 66 (18 requested) atoms. Cycle 2: After refmac, R = 0.2689 (Rfree = 0.000) for 4798 atoms. Found 19 (36 requested) and removed 46 (18 requested) atoms. Cycle 3: After refmac, R = 0.2670 (Rfree = 0.000) for 4748 atoms. Found 20 (36 requested) and removed 35 (18 requested) atoms. Cycle 4: After refmac, R = 0.2526 (Rfree = 0.000) for 4713 atoms. Found 8 (35 requested) and removed 26 (17 requested) atoms. Cycle 5: After refmac, R = 0.2510 (Rfree = 0.000) for 4673 atoms. Found 14 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 4773 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 4803 seeds are put forward Round 1: 411 peptides, 61 chains. Longest chain 20 peptides. Score 0.536 Round 2: 455 peptides, 53 chains. Longest chain 30 peptides. Score 0.663 Round 3: 464 peptides, 54 chains. Longest chain 21 peptides. Score 0.669 Round 4: 480 peptides, 50 chains. Longest chain 34 peptides. Score 0.713 Round 5: 469 peptides, 46 chains. Longest chain 44 peptides. Score 0.722 Taking the results from Round 5 Chains 52, Residues 423, Estimated correctness of the model 63.4 % 10 chains (111 residues) have been docked in sequence Building loops using Loopy2018 52 chains (423 residues) following loop building 10 chains (111 residues) in sequence following loop building ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9463 restraints for refining 4874 atoms. 7378 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2821 (Rfree = 0.000) for 4874 atoms. Found 36 (36 requested) and removed 46 (18 requested) atoms. Cycle 7: After refmac, R = 0.2709 (Rfree = 0.000) for 4819 atoms. Found 24 (35 requested) and removed 43 (18 requested) atoms. Cycle 8: After refmac, R = 0.2568 (Rfree = 0.000) for 4778 atoms. Found 14 (35 requested) and removed 41 (18 requested) atoms. Cycle 9: After refmac, R = 0.2492 (Rfree = 0.000) for 4746 atoms. Found 18 (33 requested) and removed 29 (17 requested) atoms. Cycle 10: After refmac, R = 0.2362 (Rfree = 0.000) for 4722 atoms. Found 25 (32 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 4792 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 4801 seeds are put forward Round 1: 400 peptides, 56 chains. Longest chain 19 peptides. Score 0.555 Round 2: 452 peptides, 49 chains. Longest chain 29 peptides. Score 0.683 Round 3: 447 peptides, 47 chains. Longest chain 34 peptides. Score 0.689 Round 4: 460 peptides, 50 chains. Longest chain 30 peptides. Score 0.688 Round 5: 460 peptides, 52 chains. Longest chain 23 peptides. Score 0.676 Taking the results from Round 3 Chains 52, Residues 400, Estimated correctness of the model 55.0 % 5 chains (72 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9887 restraints for refining 4872 atoms. 8063 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2680 (Rfree = 0.000) for 4872 atoms. Found 23 (32 requested) and removed 59 (18 requested) atoms. Cycle 12: After refmac, R = 0.2481 (Rfree = 0.000) for 4818 atoms. Found 20 (32 requested) and removed 39 (18 requested) atoms. Cycle 13: After refmac, R = 0.2430 (Rfree = 0.000) for 4796 atoms. Found 22 (32 requested) and removed 40 (18 requested) atoms. Cycle 14: After refmac, R = 0.2352 (Rfree = 0.000) for 4773 atoms. Found 28 (32 requested) and removed 28 (18 requested) atoms. Cycle 15: After refmac, R = 0.2270 (Rfree = 0.000) for 4769 atoms. Found 15 (32 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.10 Search for helices and strands: 0 residues in 0 chains, 4834 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 4864 seeds are put forward Round 1: 387 peptides, 58 chains. Longest chain 19 peptides. Score 0.516 Round 2: 416 peptides, 48 chains. Longest chain 29 peptides. Score 0.639 Round 3: 431 peptides, 50 chains. Longest chain 42 peptides. Score 0.648 Round 4: 430 peptides, 47 chains. Longest chain 29 peptides. Score 0.666 Round 5: 450 peptides, 51 chains. Longest chain 32 peptides. Score 0.668 Taking the results from Round 5 Chains 57, Residues 399, Estimated correctness of the model 49.3 % 9 chains (122 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10621 reflections ( 99.68 % complete ) and 9087 restraints for refining 4873 atoms. 7061 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2680 (Rfree = 0.000) for 4873 atoms. Found 31 (32 requested) and removed 67 (18 requested) atoms. Cycle 17: After refmac, R = 0.2545 (Rfree = 0.000) for 4821 atoms. Found 26 (32 requested) and removed 42 (18 requested) atoms. Cycle 18: After refmac, R = 0.2474 (Rfree = 0.000) for 4797 atoms. Found 17 (32 requested) and removed 33 (18 requested) atoms. Cycle 19: After refmac, R = 0.2519 (Rfree = 0.000) for 4778 atoms. Found 24 (32 requested) and removed 33 (18 requested) atoms. Cycle 20: After refmac, R = 0.2427 (Rfree = 0.000) for 4758 atoms. Found 21 (32 requested) and removed 43 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 4847 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4863 seeds are put forward Round 1: 389 peptides, 60 chains. Longest chain 24 peptides. Score 0.503 Round 2: 427 peptides, 51 chains. Longest chain 25 peptides. Score 0.635 Round 3: 432 peptides, 52 chains. Longest chain 25 peptides. Score 0.636 Round 4: 444 peptides, 52 chains. Longest chain 28 peptides. Score 0.654 Round 5: 417 peptides, 51 chains. Longest chain 35 peptides. Score 0.620 Taking the results from Round 4 Chains 58, Residues 392, Estimated correctness of the model 45.3 % 9 chains (91 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9773 restraints for refining 4874 atoms. 7920 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2626 (Rfree = 0.000) for 4874 atoms. Found 32 (32 requested) and removed 41 (18 requested) atoms. Cycle 22: After refmac, R = 0.2447 (Rfree = 0.000) for 4834 atoms. Found 25 (32 requested) and removed 36 (18 requested) atoms. Cycle 23: After refmac, R = 0.2358 (Rfree = 0.000) for 4808 atoms. Found 14 (32 requested) and removed 23 (18 requested) atoms. Cycle 24: After refmac, R = 0.2279 (Rfree = 0.000) for 4789 atoms. Found 19 (32 requested) and removed 24 (18 requested) atoms. Cycle 25: After refmac, R = 0.2272 (Rfree = 0.000) for 4774 atoms. Found 26 (32 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 4863 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 4882 seeds are put forward Round 1: 362 peptides, 56 chains. Longest chain 15 peptides. Score 0.485 Round 2: 404 peptides, 47 chains. Longest chain 43 peptides. Score 0.628 Round 3: 411 peptides, 45 chains. Longest chain 31 peptides. Score 0.652 Round 4: 403 peptides, 50 chains. Longest chain 22 peptides. Score 0.605 Round 5: 408 peptides, 48 chains. Longest chain 24 peptides. Score 0.627 Taking the results from Round 3 Chains 50, Residues 366, Estimated correctness of the model 44.7 % 5 chains (64 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10621 reflections ( 99.68 % complete ) and 9970 restraints for refining 4873 atoms. 8293 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2526 (Rfree = 0.000) for 4873 atoms. Found 29 (32 requested) and removed 38 (18 requested) atoms. Cycle 27: After refmac, R = 0.2334 (Rfree = 0.000) for 4847 atoms. Found 22 (32 requested) and removed 24 (18 requested) atoms. Cycle 28: After refmac, R = 0.2214 (Rfree = 0.000) for 4835 atoms. Found 16 (32 requested) and removed 20 (18 requested) atoms. Cycle 29: After refmac, R = 0.2203 (Rfree = 0.000) for 4826 atoms. Found 20 (32 requested) and removed 23 (18 requested) atoms. Cycle 30: After refmac, R = 0.2155 (Rfree = 0.000) for 4814 atoms. Found 25 (32 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 4882 seeds are put forward NCS extension: 31 residues added (6 deleted due to clashes), 4913 seeds are put forward Round 1: 378 peptides, 59 chains. Longest chain 25 peptides. Score 0.491 Round 2: 402 peptides, 50 chains. Longest chain 28 peptides. Score 0.604 Round 3: 412 peptides, 51 chains. Longest chain 34 peptides. Score 0.612 Round 4: 403 peptides, 50 chains. Longest chain 32 peptides. Score 0.605 Round 5: 408 peptides, 51 chains. Longest chain 30 peptides. Score 0.606 Taking the results from Round 3 Chains 53, Residues 361, Estimated correctness of the model 32.5 % 9 chains (73 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10621 reflections ( 99.68 % complete ) and 9870 restraints for refining 4873 atoms. 8219 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2556 (Rfree = 0.000) for 4873 atoms. Found 32 (32 requested) and removed 43 (18 requested) atoms. Cycle 32: After refmac, R = 0.2164 (Rfree = 0.000) for 4837 atoms. Found 24 (32 requested) and removed 24 (18 requested) atoms. Cycle 33: After refmac, R = 0.2273 (Rfree = 0.000) for 4828 atoms. Found 29 (32 requested) and removed 31 (18 requested) atoms. Cycle 34: After refmac, R = 0.2158 (Rfree = 0.000) for 4821 atoms. Found 21 (32 requested) and removed 26 (18 requested) atoms. Cycle 35: After refmac, R = 0.2065 (Rfree = 0.000) for 4811 atoms. Found 17 (32 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 4895 seeds are put forward NCS extension: 36 residues added (7 deleted due to clashes), 4931 seeds are put forward Round 1: 364 peptides, 54 chains. Longest chain 26 peptides. Score 0.506 Round 2: 397 peptides, 49 chains. Longest chain 27 peptides. Score 0.603 Round 3: 398 peptides, 50 chains. Longest chain 22 peptides. Score 0.597 Round 4: 398 peptides, 48 chains. Longest chain 40 peptides. Score 0.612 Round 5: 404 peptides, 49 chains. Longest chain 27 peptides. Score 0.614 Taking the results from Round 5 Chains 53, Residues 355, Estimated correctness of the model 33.2 % 10 chains (90 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9547 restraints for refining 4873 atoms. 7802 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2484 (Rfree = 0.000) for 4873 atoms. Found 32 (32 requested) and removed 33 (18 requested) atoms. Cycle 37: After refmac, R = 0.2322 (Rfree = 0.000) for 4839 atoms. Found 21 (32 requested) and removed 28 (18 requested) atoms. Cycle 38: After refmac, R = 0.2224 (Rfree = 0.000) for 4817 atoms. Found 27 (32 requested) and removed 27 (18 requested) atoms. Cycle 39: After refmac, R = 0.2185 (Rfree = 0.000) for 4810 atoms. Found 19 (32 requested) and removed 23 (18 requested) atoms. Cycle 40: After refmac, R = 0.2155 (Rfree = 0.000) for 4793 atoms. Found 28 (32 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 4868 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 4901 seeds are put forward Round 1: 329 peptides, 52 chains. Longest chain 23 peptides. Score 0.454 Round 2: 379 peptides, 48 chains. Longest chain 21 peptides. Score 0.581 Round 3: 387 peptides, 44 chains. Longest chain 28 peptides. Score 0.623 Round 4: 386 peptides, 46 chains. Longest chain 28 peptides. Score 0.607 Round 5: 370 peptides, 43 chains. Longest chain 28 peptides. Score 0.603 Taking the results from Round 3 Chains 50, Residues 343, Estimated correctness of the model 36.0 % 7 chains (74 residues) have been docked in sequence ------------------------------------------------------ 10621 reflections ( 99.68 % complete ) and 9772 restraints for refining 4874 atoms. 8122 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2455 (Rfree = 0.000) for 4874 atoms. Found 27 (32 requested) and removed 32 (18 requested) atoms. Cycle 42: After refmac, R = 0.2308 (Rfree = 0.000) for 4848 atoms. Found 23 (32 requested) and removed 23 (18 requested) atoms. Cycle 43: After refmac, R = 0.2332 (Rfree = 0.000) for 4830 atoms. Found 28 (32 requested) and removed 27 (18 requested) atoms. Cycle 44: After refmac, R = 0.2066 (Rfree = 0.000) for 4819 atoms. Found 12 (32 requested) and removed 20 (18 requested) atoms. Cycle 45: After refmac, R = 0.2028 (Rfree = 0.000) for 4806 atoms. Found 14 (32 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.16 3.12 Search for helices and strands: 0 residues in 0 chains, 4910 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 4940 seeds are put forward Round 1: 341 peptides, 52 chains. Longest chain 17 peptides. Score 0.478 Round 2: 377 peptides, 50 chains. Longest chain 27 peptides. Score 0.562 Round 3: 380 peptides, 49 chains. Longest chain 20 peptides. Score 0.575 Round 4: 375 peptides, 48 chains. Longest chain 29 peptides. Score 0.574 Round 5: 389 peptides, 52 chains. Longest chain 17 peptides. Score 0.567 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 331, Estimated correctness of the model 20.3 % 4 chains (40 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2ich-3_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (331 residues) following loop building 4 chains (40 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10621 reflections ( 99.68 % complete ) and 10349 restraints for refining 4874 atoms. 8931 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2303 (Rfree = 0.000) for 4874 atoms. Found 0 (32 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2453 (Rfree = 0.000) for 4849 atoms. Found 0 (32 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2280 (Rfree = 0.000) for 4824 atoms. Found 0 (32 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2042 (Rfree = 0.000) for 4799 atoms. Found 0 (32 requested) and removed 18 (18 requested) atoms. Writing output files ... TimeTaking 72.55