null Mon 24 Dec 07:34:25 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 2g0t-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2g0t-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2g0t-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-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/2g0t-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-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 07:34:30 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/2g0t-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-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 897 and 0 Target number of residues in the AU: 897 Target solvent content: 0.5857 Checking the provided sequence file Detected sequence length: 350 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 700 Adjusted target solvent content: 0.68 Input MTZ file: 2g0t-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: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 1.00 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: 29.560 3.601 Wilson plot Bfac: 47.03 14436 reflections ( 99.70 % complete ) and 0 restraints for refining 6190 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3246 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3041 (Rfree = 0.000) for 6190 atoms. Found 39 (39 requested) and removed 69 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 2.45 Search for helices and strands: 0 residues in 0 chains, 6302 seeds are put forward NCS extension: 0 residues added, 6302 seeds are put forward Round 1: 403 peptides, 70 chains. Longest chain 14 peptides. Score 0.365 Round 2: 451 peptides, 62 chains. Longest chain 19 peptides. Score 0.479 Round 3: 476 peptides, 60 chains. Longest chain 18 peptides. Score 0.521 Round 4: 485 peptides, 59 chains. Longest chain 19 peptides. Score 0.537 Round 5: 491 peptides, 55 chains. Longest chain 27 peptides. Score 0.565 Taking the results from Round 5 Chains 60, Residues 436, Estimated correctness of the model 0.4 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10143 restraints for refining 5074 atoms. 8309 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2771 (Rfree = 0.000) for 5074 atoms. Found 32 (32 requested) and removed 37 (16 requested) atoms. Cycle 2: After refmac, R = 0.2855 (Rfree = 0.000) for 5003 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 3: After refmac, R = 0.2539 (Rfree = 0.000) for 4953 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. Cycle 4: After refmac, R = 0.2477 (Rfree = 0.000) for 4923 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 5: After refmac, R = 0.2506 (Rfree = 0.000) for 4906 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.09 2.40 Search for helices and strands: 0 residues in 0 chains, 5107 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 5132 seeds are put forward Round 1: 482 peptides, 67 chains. Longest chain 23 peptides. Score 0.490 Round 2: 502 peptides, 60 chains. Longest chain 36 peptides. Score 0.552 Round 3: 480 peptides, 53 chains. Longest chain 33 peptides. Score 0.563 Round 4: 494 peptides, 60 chains. Longest chain 31 peptides. Score 0.542 Round 5: 480 peptides, 53 chains. Longest chain 35 peptides. Score 0.563 Taking the results from Round 5 Chains 60, Residues 427, Estimated correctness of the model 0.0 % 5 chains (65 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10127 restraints for refining 5074 atoms. 8231 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2828 (Rfree = 0.000) for 5074 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 7: After refmac, R = 0.2579 (Rfree = 0.000) for 5023 atoms. Found 32 (32 requested) and removed 37 (16 requested) atoms. Cycle 8: After refmac, R = 0.2444 (Rfree = 0.000) for 4999 atoms. Found 23 (32 requested) and removed 31 (16 requested) atoms. Cycle 9: After refmac, R = 0.2382 (Rfree = 0.000) for 4975 atoms. Found 23 (31 requested) and removed 27 (15 requested) atoms. Cycle 10: After refmac, R = 0.2319 (Rfree = 0.000) for 4962 atoms. Found 24 (31 requested) and removed 32 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 2.41 Search for helices and strands: 0 residues in 0 chains, 5159 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 5191 seeds are put forward Round 1: 445 peptides, 61 chains. Longest chain 25 peptides. Score 0.477 Round 2: 479 peptides, 59 chains. Longest chain 24 peptides. Score 0.530 Round 3: 482 peptides, 53 chains. Longest chain 31 peptides. Score 0.566 Round 4: 492 peptides, 52 chains. Longest chain 33 peptides. Score 0.582 Round 5: 481 peptides, 54 chains. Longest chain 36 peptides. Score 0.559 Taking the results from Round 4 Chains 56, Residues 440, Estimated correctness of the model 7.4 % 7 chains (102 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9549 restraints for refining 5076 atoms. 7480 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2717 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 45 (16 requested) atoms. Cycle 12: After refmac, R = 0.2574 (Rfree = 0.000) for 5024 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 13: After refmac, R = 0.2458 (Rfree = 0.000) for 5006 atoms. Found 31 (32 requested) and removed 32 (16 requested) atoms. Cycle 14: After refmac, R = 0.2412 (Rfree = 0.000) for 4995 atoms. Found 15 (32 requested) and removed 26 (16 requested) atoms. Cycle 15: After refmac, R = 0.2422 (Rfree = 0.000) for 4971 atoms. Found 27 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 2.44 Search for helices and strands: 0 residues in 0 chains, 5170 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 5208 seeds are put forward Round 1: 437 peptides, 60 chains. Longest chain 26 peptides. Score 0.473 Round 2: 465 peptides, 50 chains. Longest chain 25 peptides. Score 0.562 Round 3: 462 peptides, 50 chains. Longest chain 45 peptides. Score 0.559 Round 4: 474 peptides, 52 chains. Longest chain 31 peptides. Score 0.562 Round 5: 461 peptides, 46 chains. Longest chain 45 peptides. Score 0.579 Taking the results from Round 5 Chains 51, Residues 415, Estimated correctness of the model 6.2 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10406 restraints for refining 5076 atoms. 8591 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2917 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 17: After refmac, R = 0.2866 (Rfree = 0.000) for 5028 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. Cycle 18: After refmac, R = 0.2514 (Rfree = 0.000) for 4992 atoms. Found 31 (32 requested) and removed 30 (16 requested) atoms. Cycle 19: After refmac, R = 0.2503 (Rfree = 0.000) for 4982 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 20: After refmac, R = 0.2321 (Rfree = 0.000) for 4968 atoms. Found 19 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.40 Search for helices and strands: 0 residues in 0 chains, 5151 seeds are put forward NCS extension: 29 residues added (15 deleted due to clashes), 5180 seeds are put forward Round 1: 421 peptides, 63 chains. Longest chain 15 peptides. Score 0.434 Round 2: 451 peptides, 53 chains. Longest chain 24 peptides. Score 0.530 Round 3: 469 peptides, 63 chains. Longest chain 23 peptides. Score 0.496 Round 4: 473 peptides, 55 chains. Longest chain 25 peptides. Score 0.545 Round 5: 480 peptides, 59 chains. Longest chain 29 peptides. Score 0.531 Taking the results from Round 4 Chains 56, Residues 418, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10749 restraints for refining 5076 atoms. 9068 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2667 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 22: After refmac, R = 0.2537 (Rfree = 0.000) for 5049 atoms. Found 31 (32 requested) and removed 33 (16 requested) atoms. Cycle 23: After refmac, R = 0.2452 (Rfree = 0.000) for 5031 atoms. Found 26 (32 requested) and removed 34 (16 requested) atoms. Cycle 24: After refmac, R = 0.2389 (Rfree = 0.000) for 5006 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 25: After refmac, R = 0.2312 (Rfree = 0.000) for 4991 atoms. Found 26 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 2.40 Search for helices and strands: 0 residues in 0 chains, 5198 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5214 seeds are put forward Round 1: 423 peptides, 59 chains. Longest chain 25 peptides. Score 0.461 Round 2: 488 peptides, 55 chains. Longest chain 32 peptides. Score 0.562 Round 3: 481 peptides, 51 chains. Longest chain 28 peptides. Score 0.575 Round 4: 466 peptides, 55 chains. Longest chain 20 peptides. Score 0.537 Round 5: 491 peptides, 48 chains. Longest chain 34 peptides. Score 0.601 Taking the results from Round 5 Chains 49, Residues 443, Estimated correctness of the model 15.0 % 5 chains (102 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9587 restraints for refining 5076 atoms. 7439 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2661 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 27: After refmac, R = 0.2481 (Rfree = 0.000) for 5028 atoms. Found 30 (32 requested) and removed 24 (16 requested) atoms. Cycle 28: After refmac, R = 0.2364 (Rfree = 0.000) for 5014 atoms. Found 16 (32 requested) and removed 32 (16 requested) atoms. Cycle 29: After refmac, R = 0.2299 (Rfree = 0.000) for 4989 atoms. Found 22 (32 requested) and removed 25 (16 requested) atoms. Cycle 30: After refmac, R = 0.2222 (Rfree = 0.000) for 4980 atoms. Found 10 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5140 seeds are put forward NCS extension: 32 residues added (8 deleted due to clashes), 5172 seeds are put forward Round 1: 465 peptides, 62 chains. Longest chain 19 peptides. Score 0.497 Round 2: 490 peptides, 55 chains. Longest chain 27 peptides. Score 0.564 Round 3: 489 peptides, 52 chains. Longest chain 34 peptides. Score 0.579 Round 4: 506 peptides, 54 chains. Longest chain 32 peptides. Score 0.587 Round 5: 486 peptides, 51 chains. Longest chain 34 peptides. Score 0.581 Taking the results from Round 4 Chains 55, Residues 452, Estimated correctness of the model 9.4 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10145 restraints for refining 5075 atoms. 8215 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2595 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 32: After refmac, R = 0.2386 (Rfree = 0.000) for 5051 atoms. Found 15 (32 requested) and removed 22 (16 requested) atoms. Cycle 33: After refmac, R = 0.2282 (Rfree = 0.000) for 5032 atoms. Found 12 (32 requested) and removed 26 (16 requested) atoms. Cycle 34: After refmac, R = 0.2228 (Rfree = 0.000) for 5010 atoms. Found 5 (32 requested) and removed 23 (16 requested) atoms. Cycle 35: After refmac, R = 0.2193 (Rfree = 0.000) for 4985 atoms. Found 9 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 2.37 Search for helices and strands: 0 residues in 0 chains, 5142 seeds are put forward NCS extension: 26 residues added (5 deleted due to clashes), 5168 seeds are put forward Round 1: 433 peptides, 59 chains. Longest chain 28 peptides. Score 0.474 Round 2: 464 peptides, 58 chains. Longest chain 31 peptides. Score 0.518 Round 3: 473 peptides, 60 chains. Longest chain 32 peptides. Score 0.518 Round 4: 463 peptides, 58 chains. Longest chain 23 peptides. Score 0.517 Round 5: 466 peptides, 57 chains. Longest chain 28 peptides. Score 0.526 Taking the results from Round 5 Chains 59, Residues 409, Estimated correctness of the model 0.0 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10748 restraints for refining 5076 atoms. 9078 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2584 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 37: After refmac, R = 0.2378 (Rfree = 0.000) for 5062 atoms. Found 17 (32 requested) and removed 26 (16 requested) atoms. Cycle 38: After refmac, R = 0.2307 (Rfree = 0.000) for 5043 atoms. Found 15 (32 requested) and removed 26 (16 requested) atoms. Cycle 39: After refmac, R = 0.2262 (Rfree = 0.000) for 5030 atoms. Found 12 (32 requested) and removed 22 (16 requested) atoms. Cycle 40: After refmac, R = 0.2246 (Rfree = 0.000) for 5018 atoms. Found 11 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 2.40 Search for helices and strands: 0 residues in 0 chains, 5183 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 5212 seeds are put forward Round 1: 414 peptides, 66 chains. Longest chain 18 peptides. Score 0.406 Round 2: 440 peptides, 53 chains. Longest chain 25 peptides. Score 0.517 Round 3: 472 peptides, 56 chains. Longest chain 20 peptides. Score 0.538 Round 4: 440 peptides, 52 chains. Longest chain 17 peptides. Score 0.522 Round 5: 453 peptides, 56 chains. Longest chain 20 peptides. Score 0.516 Taking the results from Round 3 Chains 57, Residues 416, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10668 restraints for refining 5075 atoms. 8994 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2566 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 42: After refmac, R = 0.2465 (Rfree = 0.000) for 5046 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 43: After refmac, R = 0.2311 (Rfree = 0.000) for 5041 atoms. Found 18 (32 requested) and removed 25 (16 requested) atoms. Cycle 44: After refmac, R = 0.2270 (Rfree = 0.000) for 5026 atoms. Found 15 (32 requested) and removed 22 (16 requested) atoms. Cycle 45: After refmac, R = 0.2237 (Rfree = 0.000) for 5013 atoms. Found 13 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.40 Search for helices and strands: 0 residues in 0 chains, 5182 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 5212 seeds are put forward Round 1: 408 peptides, 61 chains. Longest chain 15 peptides. Score 0.428 Round 2: 442 peptides, 53 chains. Longest chain 23 peptides. Score 0.519 Round 3: 454 peptides, 55 chains. Longest chain 21 peptides. Score 0.522 Round 4: 467 peptides, 53 chains. Longest chain 21 peptides. Score 0.549 Round 5: 437 peptides, 52 chains. Longest chain 23 peptides. Score 0.519 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 414, Estimated correctness of the model 0.0 % 4 chains (49 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (414 residues) following loop building 4 chains (49 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14436 reflections ( 99.70 % complete ) and 10273 restraints for refining 5075 atoms. 8489 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2581 (Rfree = 0.000) for 5075 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2452 (Rfree = 0.000) for 5032 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2432 (Rfree = 0.000) for 5004 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2411 (Rfree = 0.000) for 4980 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:24:58 GMT 2018 Job finished. TimeTaking 170.56 Used memory is bytes: 2882144