Mon 24 Dec 00:27:52 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-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 00:27:57 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-4.0-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 824 and 0 Target number of residues in the AU: 824 Target solvent content: 0.6194 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-4.0-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-4.0-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 4.001 Wilson plot Bfac: 61.14 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 10611 reflections ( 99.60 % complete ) and 0 restraints for refining 6238 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3319 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3863 (Rfree = 0.000) for 6238 atoms. Found 29 (29 requested) and removed 29 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 2.71 Search for helices and strands: 0 residues in 0 chains, 6362 seeds are put forward NCS extension: 0 residues added, 6362 seeds are put forward Round 1: 348 peptides, 60 chains. Longest chain 12 peptides. Score 0.349 Round 2: 405 peptides, 50 chains. Longest chain 23 peptides. Score 0.491 Round 3: 431 peptides, 47 chains. Longest chain 27 peptides. Score 0.540 Round 4: 405 peptides, 47 chains. Longest chain 21 peptides. Score 0.508 Round 5: 417 peptides, 49 chains. Longest chain 26 peptides. Score 0.511 Taking the results from Round 3 Chains 52, Residues 384, Estimated correctness of the model 0.0 % 8 chains (81 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10383 restraints for refining 5055 atoms. 8605 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3314 (Rfree = 0.000) for 5055 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 2: After refmac, R = 0.3012 (Rfree = 0.000) for 4949 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 3: After refmac, R = 0.2850 (Rfree = 0.000) for 4896 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 4: After refmac, R = 0.2763 (Rfree = 0.000) for 4865 atoms. Found 21 (23 requested) and removed 31 (11 requested) atoms. Cycle 5: After refmac, R = 0.2773 (Rfree = 0.000) for 4830 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 2.66 Search for helices and strands: 0 residues in 0 chains, 5051 seeds are put forward NCS extension: 32 residues added (7 deleted due to clashes), 5083 seeds are put forward Round 1: 431 peptides, 64 chains. Longest chain 19 peptides. Score 0.441 Round 2: 455 peptides, 53 chains. Longest chain 23 peptides. Score 0.535 Round 3: 446 peptides, 50 chains. Longest chain 25 peptides. Score 0.541 Round 4: 429 peptides, 48 chains. Longest chain 26 peptides. Score 0.532 Round 5: 444 peptides, 55 chains. Longest chain 25 peptides. Score 0.510 Taking the results from Round 3 Chains 50, Residues 396, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 11039 restraints for refining 5058 atoms. 9474 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3064 (Rfree = 0.000) for 5058 atoms. Found 24 (24 requested) and removed 43 (12 requested) atoms. Cycle 7: After refmac, R = 0.2832 (Rfree = 0.000) for 5003 atoms. Found 14 (23 requested) and removed 37 (11 requested) atoms. Cycle 8: After refmac, R = 0.2738 (Rfree = 0.000) for 4948 atoms. Found 15 (23 requested) and removed 31 (11 requested) atoms. Cycle 9: After refmac, R = 0.2488 (Rfree = 0.000) for 4910 atoms. Found 10 (23 requested) and removed 37 (11 requested) atoms. Cycle 10: After refmac, R = 0.2423 (Rfree = 0.000) for 4872 atoms. Found 14 (23 requested) and removed 31 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.67 Search for helices and strands: 0 residues in 0 chains, 5035 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 5058 seeds are put forward Round 1: 424 peptides, 54 chains. Longest chain 19 peptides. Score 0.491 Round 2: 441 peptides, 53 chains. Longest chain 26 peptides. Score 0.518 Round 3: 445 peptides, 53 chains. Longest chain 25 peptides. Score 0.523 Round 4: 443 peptides, 50 chains. Longest chain 27 peptides. Score 0.537 Round 5: 446 peptides, 46 chains. Longest chain 35 peptides. Score 0.562 Taking the results from Round 5 Chains 46, Residues 400, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10944 restraints for refining 5056 atoms. 9363 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3193 (Rfree = 0.000) for 5056 atoms. Found 24 (24 requested) and removed 30 (12 requested) atoms. Cycle 12: After refmac, R = 0.2989 (Rfree = 0.000) for 4996 atoms. Found 23 (23 requested) and removed 36 (11 requested) atoms. Cycle 13: After refmac, R = 0.2910 (Rfree = 0.000) for 4949 atoms. Found 21 (23 requested) and removed 34 (11 requested) atoms. Cycle 14: After refmac, R = 0.2795 (Rfree = 0.000) for 4918 atoms. Found 15 (23 requested) and removed 20 (11 requested) atoms. Cycle 15: After refmac, R = 0.2827 (Rfree = 0.000) for 4894 atoms. Found 21 (23 requested) and removed 30 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 2.70 Search for helices and strands: 0 residues in 0 chains, 5107 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 5139 seeds are put forward Round 1: 421 peptides, 57 chains. Longest chain 18 peptides. Score 0.470 Round 2: 434 peptides, 52 chains. Longest chain 17 peptides. Score 0.515 Round 3: 433 peptides, 48 chains. Longest chain 24 peptides. Score 0.536 Round 4: 417 peptides, 46 chains. Longest chain 24 peptides. Score 0.529 Round 5: 425 peptides, 47 chains. Longest chain 45 peptides. Score 0.533 Taking the results from Round 3 Chains 53, Residues 385, Estimated correctness of the model 0.0 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10594 restraints for refining 5058 atoms. 8870 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3269 (Rfree = 0.000) for 5058 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 17: After refmac, R = 0.3024 (Rfree = 0.000) for 5010 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 18: After refmac, R = 0.2912 (Rfree = 0.000) for 4978 atoms. Found 14 (23 requested) and removed 27 (11 requested) atoms. Cycle 19: After refmac, R = 0.2955 (Rfree = 0.000) for 4942 atoms. Found 17 (23 requested) and removed 29 (11 requested) atoms. Cycle 20: After refmac, R = 0.2837 (Rfree = 0.000) for 4912 atoms. Found 19 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.70 Search for helices and strands: 0 residues in 0 chains, 5092 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 5119 seeds are put forward Round 1: 388 peptides, 52 chains. Longest chain 19 peptides. Score 0.457 Round 2: 408 peptides, 49 chains. Longest chain 23 peptides. Score 0.500 Round 3: 422 peptides, 52 chains. Longest chain 30 peptides. Score 0.500 Round 4: 429 peptides, 49 chains. Longest chain 22 peptides. Score 0.526 Round 5: 415 peptides, 50 chains. Longest chain 23 peptides. Score 0.503 Taking the results from Round 4 Chains 52, Residues 380, Estimated correctness of the model 0.0 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10762 restraints for refining 5055 atoms. 9157 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3061 (Rfree = 0.000) for 5055 atoms. Found 22 (24 requested) and removed 44 (12 requested) atoms. Cycle 22: After refmac, R = 0.2949 (Rfree = 0.000) for 4988 atoms. Found 12 (23 requested) and removed 32 (11 requested) atoms. Cycle 23: After refmac, R = 0.2869 (Rfree = 0.000) for 4950 atoms. Found 18 (23 requested) and removed 39 (11 requested) atoms. Cycle 24: After refmac, R = 0.2860 (Rfree = 0.000) for 4918 atoms. Found 22 (23 requested) and removed 31 (11 requested) atoms. Cycle 25: After refmac, R = 0.2976 (Rfree = 0.000) for 4900 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 2.68 Search for helices and strands: 0 residues in 0 chains, 5096 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5114 seeds are put forward Round 1: 376 peptides, 60 chains. Longest chain 14 peptides. Score 0.390 Round 2: 395 peptides, 55 chains. Longest chain 16 peptides. Score 0.448 Round 3: 428 peptides, 57 chains. Longest chain 31 peptides. Score 0.479 Round 4: 419 peptides, 54 chains. Longest chain 23 peptides. Score 0.485 Round 5: 418 peptides, 53 chains. Longest chain 21 peptides. Score 0.489 Taking the results from Round 5 Chains 55, Residues 365, Estimated correctness of the model 0.0 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 10803 restraints for refining 5057 atoms. 9250 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3163 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 27: After refmac, R = 0.2990 (Rfree = 0.000) for 5015 atoms. Found 23 (23 requested) and removed 36 (11 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2970 (Rfree = 0.000) for 4977 atoms. Found 23 (23 requested) and removed 50 (11 requested) atoms. Cycle 29: After refmac, R = 0.2950 (Rfree = 0.000) for 4928 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 30: After refmac, R = 0.2908 (Rfree = 0.000) for 4904 atoms. Found 23 (23 requested) and removed 53 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 2.72 Search for helices and strands: 0 residues in 0 chains, 5038 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 5062 seeds are put forward Round 1: 331 peptides, 61 chains. Longest chain 9 peptides. Score 0.316 Round 2: 386 peptides, 60 chains. Longest chain 14 peptides. Score 0.404 Round 3: 392 peptides, 60 chains. Longest chain 20 peptides. Score 0.413 Round 4: 378 peptides, 54 chains. Longest chain 18 peptides. Score 0.431 Round 5: 365 peptides, 54 chains. Longest chain 14 peptides. Score 0.413 Taking the results from Round 4 Chains 54, Residues 324, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 11569 restraints for refining 5057 atoms. 10327 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2660 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 48 (12 requested) atoms. Cycle 32: After refmac, R = 0.2466 (Rfree = 0.000) for 4991 atoms. Found 13 (23 requested) and removed 30 (11 requested) atoms. Cycle 33: After refmac, R = 0.2383 (Rfree = 0.000) for 4962 atoms. Found 12 (23 requested) and removed 35 (11 requested) atoms. Cycle 34: After refmac, R = 0.2352 (Rfree = 0.000) for 4922 atoms. Found 14 (23 requested) and removed 27 (11 requested) atoms. Cycle 35: After refmac, R = 0.2218 (Rfree = 0.000) for 4902 atoms. Found 5 (23 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 2.68 Search for helices and strands: 0 residues in 0 chains, 5075 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5096 seeds are put forward Round 1: 355 peptides, 64 chains. Longest chain 16 peptides. Score 0.333 Round 2: 386 peptides, 59 chains. Longest chain 16 peptides. Score 0.410 Round 3: 401 peptides, 53 chains. Longest chain 20 peptides. Score 0.468 Round 4: 380 peptides, 54 chains. Longest chain 22 peptides. Score 0.433 Round 5: 367 peptides, 51 chains. Longest chain 20 peptides. Score 0.434 Taking the results from Round 3 Chains 54, Residues 348, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 11260 restraints for refining 5057 atoms. 9868 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2870 (Rfree = 0.000) for 5057 atoms. Found 19 (24 requested) and removed 90 (12 requested) atoms. Cycle 37: After refmac, R = 0.2462 (Rfree = 0.000) for 4963 atoms. Found 21 (23 requested) and removed 33 (11 requested) atoms. Cycle 38: After refmac, R = 0.2403 (Rfree = 0.000) for 4935 atoms. Found 17 (23 requested) and removed 28 (11 requested) atoms. Cycle 39: After refmac, R = 0.2331 (Rfree = 0.000) for 4913 atoms. Found 8 (23 requested) and removed 25 (11 requested) atoms. Cycle 40: After refmac, R = 0.2307 (Rfree = 0.000) for 4887 atoms. Found 9 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 2.67 Search for helices and strands: 0 residues in 0 chains, 5035 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 5058 seeds are put forward Round 1: 342 peptides, 60 chains. Longest chain 15 peptides. Score 0.340 Round 2: 361 peptides, 56 chains. Longest chain 16 peptides. Score 0.394 Round 3: 386 peptides, 57 chains. Longest chain 18 peptides. Score 0.423 Round 4: 375 peptides, 53 chains. Longest chain 19 peptides. Score 0.433 Round 5: 366 peptides, 49 chains. Longest chain 25 peptides. Score 0.446 Taking the results from Round 5 Chains 50, Residues 317, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 10611 reflections ( 99.60 % complete ) and 11320 restraints for refining 5057 atoms. 10051 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2582 (Rfree = 0.000) for 5057 atoms. Found 24 (24 requested) and removed 43 (12 requested) atoms. Cycle 42: After refmac, R = 0.2372 (Rfree = 0.000) for 5005 atoms. Found 13 (23 requested) and removed 30 (11 requested) atoms. Cycle 43: After refmac, R = 0.2288 (Rfree = 0.000) for 4980 atoms. Found 13 (23 requested) and removed 28 (11 requested) atoms. Cycle 44: After refmac, R = 0.2205 (Rfree = 0.000) for 4957 atoms. Found 7 (23 requested) and removed 24 (11 requested) atoms. Cycle 45: After refmac, R = 0.2135 (Rfree = 0.000) for 4935 atoms. Found 7 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 2.68 Search for helices and strands: 0 residues in 0 chains, 5102 seeds are put forward NCS extension: 40 residues added (2 deleted due to clashes), 5142 seeds are put forward Round 1: 324 peptides, 60 chains. Longest chain 10 peptides. Score 0.312 Round 2: 387 peptides, 59 chains. Longest chain 22 peptides. Score 0.412 Round 3: 381 peptides, 57 chains. Longest chain 21 peptides. Score 0.416 Round 4: 388 peptides, 55 chains. Longest chain 19 peptides. Score 0.438 Round 5: 362 peptides, 51 chains. Longest chain 18 peptides. Score 0.427 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 55, Residues 333, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2g0t-4_warpNtrace.pdb as input Building loops using Loopy2018 55 chains (333 residues) following loop building 5 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 10611 reflections ( 99.60 % complete ) and 11224 restraints for refining 5057 atoms. 9900 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2519 (Rfree = 0.000) for 5057 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2338 (Rfree = 0.000) for 5020 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2251 (Rfree = 0.000) for 4993 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2180 (Rfree = 0.000) for 4973 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... TimeTaking 164.75