Mon 24 Dec 07:56:19 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 2hr2-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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/2hr2-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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 07:56:24 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/2hr2-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.6-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 927 and 0 Target number of residues in the AU: 927 Target solvent content: 0.6498 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-3.6-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: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.85 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: 88.085 3.600 Wilson plot Bfac: 77.86 16963 reflections ( 98.21 % complete ) and 0 restraints for refining 8458 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3278 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3131 (Rfree = 0.000) for 8458 atoms. Found 54 (54 requested) and removed 48 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 2.93 Search for helices and strands: 0 residues in 0 chains, 8776 seeds are put forward NCS extension: 0 residues added, 8776 seeds are put forward Round 1: 472 peptides, 80 chains. Longest chain 16 peptides. Score 0.370 Round 2: 550 peptides, 72 chains. Longest chain 17 peptides. Score 0.496 Round 3: 554 peptides, 62 chains. Longest chain 24 peptides. Score 0.545 Round 4: 567 peptides, 62 chains. Longest chain 25 peptides. Score 0.557 Round 5: 559 peptides, 61 chains. Longest chain 25 peptides. Score 0.554 Taking the results from Round 4 Chains 71, Residues 505, Estimated correctness of the model 0.0 % 9 chains (90 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14417 restraints for refining 6913 atoms. 12164 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2522 (Rfree = 0.000) for 6913 atoms. Found 39 (44 requested) and removed 45 (22 requested) atoms. Cycle 2: After refmac, R = 0.2336 (Rfree = 0.000) for 6803 atoms. Found 28 (44 requested) and removed 42 (22 requested) atoms. Cycle 3: After refmac, R = 0.2342 (Rfree = 0.000) for 6753 atoms. Found 27 (43 requested) and removed 49 (21 requested) atoms. Cycle 4: After refmac, R = 0.2264 (Rfree = 0.000) for 6691 atoms. Found 34 (43 requested) and removed 30 (21 requested) atoms. Cycle 5: After refmac, R = 0.2250 (Rfree = 0.000) for 6673 atoms. Found 29 (42 requested) and removed 36 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 2.86 Search for helices and strands: 0 residues in 0 chains, 7103 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7116 seeds are put forward Round 1: 523 peptides, 75 chains. Longest chain 23 peptides. Score 0.453 Round 2: 562 peptides, 66 chains. Longest chain 24 peptides. Score 0.535 Round 3: 568 peptides, 67 chains. Longest chain 23 peptides. Score 0.536 Round 4: 567 peptides, 70 chains. Longest chain 21 peptides. Score 0.522 Round 5: 570 peptides, 67 chains. Longest chain 24 peptides. Score 0.538 Taking the results from Round 5 Chains 72, Residues 503, Estimated correctness of the model 0.0 % 13 chains (91 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14349 restraints for refining 6919 atoms. 12128 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2479 (Rfree = 0.000) for 6919 atoms. Found 44 (44 requested) and removed 52 (22 requested) atoms. Cycle 7: After refmac, R = 0.2300 (Rfree = 0.000) for 6847 atoms. Found 22 (44 requested) and removed 41 (22 requested) atoms. Cycle 8: After refmac, R = 0.2249 (Rfree = 0.000) for 6810 atoms. Found 16 (43 requested) and removed 36 (21 requested) atoms. Cycle 9: After refmac, R = 0.2167 (Rfree = 0.000) for 6778 atoms. Found 22 (43 requested) and removed 30 (21 requested) atoms. Cycle 10: After refmac, R = 0.2144 (Rfree = 0.000) for 6749 atoms. Found 16 (43 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.86 Search for helices and strands: 0 residues in 0 chains, 7130 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 7152 seeds are put forward Round 1: 529 peptides, 73 chains. Longest chain 37 peptides. Score 0.469 Round 2: 555 peptides, 59 chains. Longest chain 34 peptides. Score 0.559 Round 3: 575 peptides, 63 chains. Longest chain 40 peptides. Score 0.560 Round 4: 569 peptides, 62 chains. Longest chain 27 peptides. Score 0.559 Round 5: 571 peptides, 68 chains. Longest chain 19 peptides. Score 0.535 Taking the results from Round 3 Chains 72, Residues 512, Estimated correctness of the model 0.0 % 10 chains (98 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14152 restraints for refining 6919 atoms. 11835 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2418 (Rfree = 0.000) for 6919 atoms. Found 44 (44 requested) and removed 39 (22 requested) atoms. Cycle 12: After refmac, R = 0.2262 (Rfree = 0.000) for 6876 atoms. Found 27 (44 requested) and removed 33 (22 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2211 (Rfree = 0.000) for 6839 atoms. Found 34 (44 requested) and removed 33 (22 requested) atoms. Cycle 14: After refmac, R = 0.2166 (Rfree = 0.000) for 6825 atoms. Found 32 (43 requested) and removed 33 (21 requested) atoms. Cycle 15: After refmac, R = 0.2138 (Rfree = 0.000) for 6812 atoms. Found 24 (43 requested) and removed 24 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 2.87 Search for helices and strands: 0 residues in 0 chains, 7203 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 7221 seeds are put forward Round 1: 525 peptides, 78 chains. Longest chain 21 peptides. Score 0.440 Round 2: 564 peptides, 67 chains. Longest chain 26 peptides. Score 0.532 Round 3: 562 peptides, 70 chains. Longest chain 28 peptides. Score 0.517 Round 4: 577 peptides, 68 chains. Longest chain 23 peptides. Score 0.540 Round 5: 556 peptides, 68 chains. Longest chain 23 peptides. Score 0.520 Taking the results from Round 4 Chains 70, Residues 509, Estimated correctness of the model 0.0 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14572 restraints for refining 6919 atoms. 12396 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2298 (Rfree = 0.000) for 6919 atoms. Found 44 (44 requested) and removed 45 (22 requested) atoms. Cycle 17: After refmac, R = 0.2123 (Rfree = 0.000) for 6878 atoms. Found 24 (44 requested) and removed 42 (22 requested) atoms. Cycle 18: After refmac, R = 0.2082 (Rfree = 0.000) for 6829 atoms. Found 25 (44 requested) and removed 35 (22 requested) atoms. Cycle 19: After refmac, R = 0.1996 (Rfree = 0.000) for 6799 atoms. Found 24 (43 requested) and removed 31 (21 requested) atoms. Cycle 20: After refmac, R = 0.1976 (Rfree = 0.000) for 6773 atoms. Found 22 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 2.86 Search for helices and strands: 0 residues in 0 chains, 7164 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 7181 seeds are put forward Round 1: 513 peptides, 73 chains. Longest chain 22 peptides. Score 0.452 Round 2: 563 peptides, 69 chains. Longest chain 23 peptides. Score 0.522 Round 3: 551 peptides, 64 chains. Longest chain 39 peptides. Score 0.533 Round 4: 569 peptides, 68 chains. Longest chain 32 peptides. Score 0.533 Round 5: 548 peptides, 67 chains. Longest chain 18 peptides. Score 0.517 Taking the results from Round 4 Chains 70, Residues 501, Estimated correctness of the model 0.0 % 4 chains (61 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14598 restraints for refining 6916 atoms. 12432 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2313 (Rfree = 0.000) for 6916 atoms. Found 44 (44 requested) and removed 35 (22 requested) atoms. Cycle 22: After refmac, R = 0.2154 (Rfree = 0.000) for 6878 atoms. Found 36 (44 requested) and removed 29 (22 requested) atoms. Cycle 23: After refmac, R = 0.2082 (Rfree = 0.000) for 6868 atoms. Found 27 (44 requested) and removed 32 (22 requested) atoms. Cycle 24: After refmac, R = 0.2029 (Rfree = 0.000) for 6841 atoms. Found 26 (44 requested) and removed 32 (22 requested) atoms. Cycle 25: After refmac, R = 0.2044 (Rfree = 0.000) for 6814 atoms. Found 33 (43 requested) and removed 30 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 2.86 Search for helices and strands: 0 residues in 0 chains, 7227 seeds are put forward NCS extension: 36 residues added (6 deleted due to clashes), 7263 seeds are put forward Round 1: 497 peptides, 80 chains. Longest chain 16 peptides. Score 0.399 Round 2: 527 peptides, 68 chains. Longest chain 22 peptides. Score 0.491 Round 3: 548 peptides, 74 chains. Longest chain 16 peptides. Score 0.484 Round 4: 523 peptides, 69 chains. Longest chain 17 peptides. Score 0.482 Round 5: 535 peptides, 72 chains. Longest chain 18 peptides. Score 0.480 Taking the results from Round 2 Chains 69, Residues 459, Estimated correctness of the model 0.0 % 9 chains (56 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14842 restraints for refining 6918 atoms. 12891 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2214 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 37 (22 requested) atoms. Cycle 27: After refmac, R = 0.2108 (Rfree = 0.000) for 6891 atoms. Found 23 (44 requested) and removed 28 (22 requested) atoms. Cycle 28: After refmac, R = 0.2096 (Rfree = 0.000) for 6870 atoms. Found 28 (44 requested) and removed 28 (22 requested) atoms. Cycle 29: After refmac, R = 0.2038 (Rfree = 0.000) for 6862 atoms. Found 28 (44 requested) and removed 29 (22 requested) atoms. Cycle 30: After refmac, R = 0.2021 (Rfree = 0.000) for 6847 atoms. Found 26 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 2.87 Search for helices and strands: 0 residues in 0 chains, 7211 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 7236 seeds are put forward Round 1: 479 peptides, 82 chains. Longest chain 13 peptides. Score 0.368 Round 2: 524 peptides, 73 chains. Longest chain 19 peptides. Score 0.464 Round 3: 535 peptides, 68 chains. Longest chain 25 peptides. Score 0.499 Round 4: 502 peptides, 69 chains. Longest chain 17 peptides. Score 0.460 Round 5: 544 peptides, 70 chains. Longest chain 25 peptides. Score 0.499 Taking the results from Round 5 Chains 78, Residues 474, Estimated correctness of the model 0.0 % 8 chains (82 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14781 restraints for refining 6918 atoms. 12686 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2395 (Rfree = 0.000) for 6918 atoms. Found 44 (44 requested) and removed 52 (22 requested) atoms. Cycle 32: After refmac, R = 0.2240 (Rfree = 0.000) for 6875 atoms. Found 36 (44 requested) and removed 40 (22 requested) atoms. Cycle 33: After refmac, R = 0.2195 (Rfree = 0.000) for 6857 atoms. Found 30 (44 requested) and removed 36 (22 requested) atoms. Cycle 34: After refmac, R = 0.2113 (Rfree = 0.000) for 6842 atoms. Found 22 (43 requested) and removed 30 (21 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2063 (Rfree = 0.000) for 6829 atoms. Found 20 (43 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 2.86 Search for helices and strands: 0 residues in 0 chains, 7207 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 7237 seeds are put forward Round 1: 466 peptides, 79 chains. Longest chain 14 peptides. Score 0.368 Round 2: 503 peptides, 66 chains. Longest chain 23 peptides. Score 0.475 Round 3: 497 peptides, 67 chains. Longest chain 18 peptides. Score 0.464 Round 4: 503 peptides, 66 chains. Longest chain 36 peptides. Score 0.475 Round 5: 511 peptides, 67 chains. Longest chain 21 peptides. Score 0.479 Taking the results from Round 5 Chains 69, Residues 444, Estimated correctness of the model 0.0 % 8 chains (74 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14865 restraints for refining 6918 atoms. 12909 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2373 (Rfree = 0.000) for 6918 atoms. Found 39 (44 requested) and removed 43 (22 requested) atoms. Cycle 37: After refmac, R = 0.2183 (Rfree = 0.000) for 6880 atoms. Found 35 (44 requested) and removed 34 (22 requested) atoms. Cycle 38: After refmac, R = 0.2164 (Rfree = 0.000) for 6863 atoms. Found 30 (44 requested) and removed 33 (22 requested) atoms. Cycle 39: After refmac, R = 0.2071 (Rfree = 0.000) for 6854 atoms. Found 25 (44 requested) and removed 35 (22 requested) atoms. Cycle 40: After refmac, R = 0.2083 (Rfree = 0.000) for 6837 atoms. Found 16 (43 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 7203 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 7219 seeds are put forward Round 1: 463 peptides, 83 chains. Longest chain 15 peptides. Score 0.343 Round 2: 512 peptides, 77 chains. Longest chain 13 peptides. Score 0.431 Round 3: 498 peptides, 73 chains. Longest chain 16 peptides. Score 0.435 Round 4: 509 peptides, 74 chains. Longest chain 18 peptides. Score 0.443 Round 5: 485 peptides, 73 chains. Longest chain 17 peptides. Score 0.421 Taking the results from Round 4 Chains 78, Residues 435, Estimated correctness of the model 0.0 % 9 chains (71 residues) have been docked in sequence ------------------------------------------------------ 16963 reflections ( 98.21 % complete ) and 14916 restraints for refining 6919 atoms. 13030 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2358 (Rfree = 0.000) for 6919 atoms. Found 44 (44 requested) and removed 40 (22 requested) atoms. Cycle 42: After refmac, R = 0.2256 (Rfree = 0.000) for 6894 atoms. Found 17 (44 requested) and removed 30 (22 requested) atoms. Cycle 43: After refmac, R = 0.2253 (Rfree = 0.000) for 6864 atoms. Found 29 (44 requested) and removed 33 (22 requested) atoms. Cycle 44: After refmac, R = 0.2209 (Rfree = 0.000) for 6848 atoms. Found 35 (44 requested) and removed 36 (22 requested) atoms. Cycle 45: After refmac, R = 0.2161 (Rfree = 0.000) for 6839 atoms. Found 18 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 2.85 Search for helices and strands: 0 residues in 0 chains, 7169 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7181 seeds are put forward Round 1: 415 peptides, 79 chains. Longest chain 12 peptides. Score 0.305 Round 2: 459 peptides, 72 chains. Longest chain 20 peptides. Score 0.396 Round 3: 466 peptides, 71 chains. Longest chain 16 peptides. Score 0.410 Round 4: 476 peptides, 70 chains. Longest chain 19 peptides. Score 0.426 Round 5: 490 peptides, 71 chains. Longest chain 16 peptides. Score 0.437 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 419, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 71 chains (419 residues) following loop building 2 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16963 reflections ( 98.21 % complete ) and 15471 restraints for refining 6919 atoms. 13813 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2366 (Rfree = 0.000) for 6919 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2330 (Rfree = 0.000) for 6857 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2286 (Rfree = 0.000) for 6813 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 49: After refmac, R = 0.2191 (Rfree = 0.000) for 6780 atoms. TimeTaking 75.97