Mon 24 Dec 00:11:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2g0t-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.8-parrot-mrncs ############### 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 00:11:33 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/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.8-parrot-mrncs/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 853 and 0 Target number of residues in the AU: 853 Target solvent content: 0.6060 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-3.8-parrot-mrncs.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-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 0.95 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 3.800 Wilson plot Bfac: 55.01 12351 reflections ( 99.65 % complete ) and 0 restraints for refining 6210 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3248 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3286 (Rfree = 0.000) for 6210 atoms. Found 34 (34 requested) and removed 43 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.59 Search for helices and strands: 0 residues in 0 chains, 6319 seeds are put forward NCS extension: 0 residues added, 6319 seeds are put forward Round 1: 375 peptides, 61 chains. Longest chain 14 peptides. Score 0.382 Round 2: 441 peptides, 56 chains. Longest chain 28 peptides. Score 0.501 Round 3: 455 peptides, 56 chains. Longest chain 28 peptides. Score 0.518 Round 4: 460 peptides, 51 chains. Longest chain 34 peptides. Score 0.551 Round 5: 459 peptides, 53 chains. Longest chain 25 peptides. Score 0.539 Taking the results from Round 4 Chains 55, Residues 409, Estimated correctness of the model 0.0 % 7 chains (43 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10713 restraints for refining 5063 atoms. 9004 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2933 (Rfree = 0.000) for 5063 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 2: After refmac, R = 0.2678 (Rfree = 0.000) for 5006 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 3: After refmac, R = 0.2545 (Rfree = 0.000) for 4977 atoms. Found 20 (27 requested) and removed 35 (13 requested) atoms. Cycle 4: After refmac, R = 0.2360 (Rfree = 0.000) for 4945 atoms. Found 17 (27 requested) and removed 32 (13 requested) atoms. Cycle 5: After refmac, R = 0.2337 (Rfree = 0.000) for 4915 atoms. Found 14 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 5113 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 5142 seeds are put forward Round 1: 439 peptides, 64 chains. Longest chain 23 peptides. Score 0.452 Round 2: 474 peptides, 55 chains. Longest chain 21 peptides. Score 0.546 Round 3: 461 peptides, 55 chains. Longest chain 29 peptides. Score 0.531 Round 4: 467 peptides, 54 chains. Longest chain 32 peptides. Score 0.543 Round 5: 478 peptides, 56 chains. Longest chain 32 peptides. Score 0.545 Taking the results from Round 2 Chains 58, Residues 419, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10633 restraints for refining 5063 atoms. 8893 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2580 (Rfree = 0.000) for 5063 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 7: After refmac, R = 0.2413 (Rfree = 0.000) for 5024 atoms. Found 26 (27 requested) and removed 25 (13 requested) atoms. Cycle 8: After refmac, R = 0.2340 (Rfree = 0.000) for 5011 atoms. Found 9 (27 requested) and removed 25 (13 requested) atoms. Cycle 9: After refmac, R = 0.2303 (Rfree = 0.000) for 4981 atoms. Found 10 (27 requested) and removed 26 (13 requested) atoms. Cycle 10: After refmac, R = 0.2323 (Rfree = 0.000) for 4955 atoms. Found 11 (27 requested) and removed 37 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.56 Search for helices and strands: 0 residues in 0 chains, 5134 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5150 seeds are put forward Round 1: 427 peptides, 63 chains. Longest chain 28 peptides. Score 0.442 Round 2: 459 peptides, 58 chains. Longest chain 24 peptides. Score 0.512 Round 3: 448 peptides, 58 chains. Longest chain 21 peptides. Score 0.498 Round 4: 454 peptides, 56 chains. Longest chain 26 peptides. Score 0.517 Round 5: 457 peptides, 57 chains. Longest chain 21 peptides. Score 0.515 Taking the results from Round 4 Chains 57, Residues 398, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10922 restraints for refining 5065 atoms. 9354 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2851 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 12: After refmac, R = 0.2489 (Rfree = 0.000) for 5024 atoms. Found 23 (27 requested) and removed 38 (13 requested) atoms. Cycle 13: After refmac, R = 0.2414 (Rfree = 0.000) for 4989 atoms. Found 10 (27 requested) and removed 35 (13 requested) atoms. Cycle 14: After refmac, R = 0.2386 (Rfree = 0.000) for 4957 atoms. Found 19 (27 requested) and removed 27 (13 requested) atoms. Cycle 15: After refmac, R = 0.2351 (Rfree = 0.000) for 4939 atoms. Found 13 (27 requested) and removed 31 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 2.54 Search for helices and strands: 0 residues in 0 chains, 5126 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 5158 seeds are put forward Round 1: 414 peptides, 58 chains. Longest chain 17 peptides. Score 0.455 Round 2: 437 peptides, 50 chains. Longest chain 40 peptides. Score 0.530 Round 3: 448 peptides, 57 chains. Longest chain 27 peptides. Score 0.504 Round 4: 452 peptides, 55 chains. Longest chain 26 peptides. Score 0.520 Round 5: 459 peptides, 61 chains. Longest chain 21 peptides. Score 0.495 Taking the results from Round 2 Chains 52, Residues 387, Estimated correctness of the model 0.0 % 6 chains (93 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12351 reflections ( 99.65 % complete ) and 10083 restraints for refining 5065 atoms. 8214 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2850 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 38 (13 requested) atoms. Cycle 17: After refmac, R = 0.2587 (Rfree = 0.000) for 5035 atoms. Found 16 (27 requested) and removed 35 (13 requested) atoms. Cycle 18: After refmac, R = 0.2550 (Rfree = 0.000) for 5004 atoms. Found 14 (27 requested) and removed 36 (13 requested) atoms. Cycle 19: After refmac, R = 0.2463 (Rfree = 0.000) for 4968 atoms. Found 14 (27 requested) and removed 27 (13 requested) atoms. Cycle 20: After refmac, R = 0.2412 (Rfree = 0.000) for 4941 atoms. Found 17 (27 requested) and removed 39 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 5107 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 5118 seeds are put forward Round 1: 422 peptides, 62 chains. Longest chain 22 peptides. Score 0.441 Round 2: 449 peptides, 58 chains. Longest chain 23 peptides. Score 0.499 Round 3: 459 peptides, 53 chains. Longest chain 25 peptides. Score 0.539 Round 4: 438 peptides, 49 chains. Longest chain 27 peptides. Score 0.537 Round 5: 447 peptides, 47 chains. Longest chain 25 peptides. Score 0.558 Taking the results from Round 5 Chains 49, Residues 400, Estimated correctness of the model 0.0 % 6 chains (81 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10294 restraints for refining 5065 atoms. 8431 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2831 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 22: After refmac, R = 0.2537 (Rfree = 0.000) for 5028 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 23: After refmac, R = 0.2389 (Rfree = 0.000) for 5013 atoms. Found 16 (27 requested) and removed 29 (13 requested) atoms. Cycle 24: After refmac, R = 0.2347 (Rfree = 0.000) for 4989 atoms. Found 14 (27 requested) and removed 26 (13 requested) atoms. Cycle 25: After refmac, R = 0.2313 (Rfree = 0.000) for 4972 atoms. Found 9 (27 requested) and removed 33 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.25 2.53 Search for helices and strands: 0 residues in 0 chains, 5143 seeds are put forward NCS extension: 16 residues added (10 deleted due to clashes), 5159 seeds are put forward Round 1: 396 peptides, 58 chains. Longest chain 19 peptides. Score 0.431 Round 2: 420 peptides, 56 chains. Longest chain 26 peptides. Score 0.474 Round 3: 437 peptides, 48 chains. Longest chain 25 peptides. Score 0.541 Round 4: 439 peptides, 51 chains. Longest chain 25 peptides. Score 0.527 Round 5: 432 peptides, 54 chains. Longest chain 22 peptides. Score 0.501 Taking the results from Round 3 Chains 53, Residues 389, Estimated correctness of the model 0.0 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10799 restraints for refining 5065 atoms. 9190 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2554 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 27: After refmac, R = 0.2403 (Rfree = 0.000) for 5034 atoms. Found 18 (27 requested) and removed 27 (13 requested) atoms. Cycle 28: After refmac, R = 0.2335 (Rfree = 0.000) for 5018 atoms. Found 12 (27 requested) and removed 23 (13 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2310 (Rfree = 0.000) for 5004 atoms. Found 12 (27 requested) and removed 31 (13 requested) atoms. Cycle 30: After refmac, R = 0.2296 (Rfree = 0.000) for 4981 atoms. Found 12 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 2.57 Search for helices and strands: 0 residues in 0 chains, 5178 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 5193 seeds are put forward Round 1: 399 peptides, 57 chains. Longest chain 27 peptides. Score 0.441 Round 2: 432 peptides, 49 chains. Longest chain 28 peptides. Score 0.530 Round 3: 447 peptides, 50 chains. Longest chain 27 peptides. Score 0.542 Round 4: 436 peptides, 49 chains. Longest chain 32 peptides. Score 0.534 Round 5: 443 peptides, 49 chains. Longest chain 32 peptides. Score 0.543 Taking the results from Round 5 Chains 51, Residues 394, Estimated correctness of the model 0.0 % 5 chains (82 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12351 reflections ( 99.65 % complete ) and 10147 restraints for refining 5066 atoms. 8292 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2729 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 32: After refmac, R = 0.2570 (Rfree = 0.000) for 5034 atoms. Found 14 (27 requested) and removed 23 (13 requested) atoms. Cycle 33: After refmac, R = 0.2469 (Rfree = 0.000) for 5012 atoms. Found 14 (27 requested) and removed 30 (13 requested) atoms. Cycle 34: After refmac, R = 0.2384 (Rfree = 0.000) for 4982 atoms. Found 9 (27 requested) and removed 23 (13 requested) atoms. Cycle 35: After refmac, R = 0.2337 (Rfree = 0.000) for 4956 atoms. Found 8 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 5156 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 5179 seeds are put forward Round 1: 385 peptides, 63 chains. Longest chain 14 peptides. Score 0.384 Round 2: 424 peptides, 50 chains. Longest chain 23 peptides. Score 0.514 Round 3: 415 peptides, 51 chains. Longest chain 23 peptides. Score 0.497 Round 4: 409 peptides, 47 chains. Longest chain 27 peptides. Score 0.513 Round 5: 422 peptides, 49 chains. Longest chain 23 peptides. Score 0.518 Taking the results from Round 5 Chains 51, Residues 373, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 11119 restraints for refining 5066 atoms. 9631 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2727 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 37: After refmac, R = 0.2464 (Rfree = 0.000) for 5041 atoms. Found 12 (27 requested) and removed 24 (13 requested) atoms. Cycle 38: After refmac, R = 0.2389 (Rfree = 0.000) for 5014 atoms. Found 12 (27 requested) and removed 24 (13 requested) atoms. Cycle 39: After refmac, R = 0.2325 (Rfree = 0.000) for 4997 atoms. Found 7 (27 requested) and removed 24 (13 requested) atoms. Cycle 40: After refmac, R = 0.2296 (Rfree = 0.000) for 4973 atoms. Found 6 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5160 seeds are put forward Round 1: 376 peptides, 60 chains. Longest chain 18 peptides. Score 0.390 Round 2: 405 peptides, 52 chains. Longest chain 32 peptides. Score 0.479 Round 3: 413 peptides, 53 chains. Longest chain 25 peptides. Score 0.483 Round 4: 417 peptides, 53 chains. Longest chain 25 peptides. Score 0.488 Round 5: 421 peptides, 58 chains. Longest chain 23 peptides. Score 0.464 Taking the results from Round 4 Chains 55, Residues 364, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10884 restraints for refining 5066 atoms. 9392 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2990 (Rfree = 0.000) for 5066 atoms. Found 25 (27 requested) and removed 27 (13 requested) atoms. Cycle 42: After refmac, R = 0.2727 (Rfree = 0.000) for 5042 atoms. Found 13 (27 requested) and removed 22 (13 requested) atoms. Cycle 43: After refmac, R = 0.2619 (Rfree = 0.000) for 5015 atoms. Found 9 (27 requested) and removed 20 (13 requested) atoms. Cycle 44: After refmac, R = 0.2558 (Rfree = 0.000) for 4991 atoms. Found 12 (27 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.2590 (Rfree = 0.000) for 4974 atoms. Found 7 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 5135 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5156 seeds are put forward Round 1: 377 peptides, 62 chains. Longest chain 17 peptides. Score 0.379 Round 2: 387 peptides, 55 chains. Longest chain 19 peptides. Score 0.437 Round 3: 406 peptides, 56 chains. Longest chain 21 peptides. Score 0.456 Round 4: 427 peptides, 56 chains. Longest chain 20 peptides. Score 0.483 Round 5: 417 peptides, 57 chains. Longest chain 18 peptides. Score 0.465 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 371, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 56 chains (371 residues) following loop building 4 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12351 reflections ( 99.65 % complete ) and 10867 restraints for refining 5066 atoms. 9360 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3066 (Rfree = 0.000) for 5066 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2615 (Rfree = 0.000) for 5021 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2495 (Rfree = 0.000) for 4997 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2477 (Rfree = 0.000) for 4975 atoms. TimeTaking 145.82