Mon 24 Dec 07:30:23 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 2go7-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2go7-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2go7-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-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/2go7-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-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 07:30:28 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/2go7-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-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 786 and 0 Target number of residues in the AU: 786 Target solvent content: 0.6532 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 828 Adjusted target solvent content: 0.63 Input MTZ file: 2go7-3.8-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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.15 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: 134.234 3.800 Wilson plot Bfac: 80.22 Failed to save intermediate PDB 12049 reflections ( 99.74 % complete ) and 0 restraints for refining 7327 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3657 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3148 (Rfree = 0.000) for 7327 atoms. Found 38 (40 requested) and removed 29 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.06 Search for helices and strands: 0 residues in 0 chains, 7514 seeds are put forward NCS extension: 0 residues added, 7514 seeds are put forward Round 1: 336 peptides, 63 chains. Longest chain 15 peptides. Score 0.306 Round 2: 458 peptides, 65 chains. Longest chain 29 peptides. Score 0.461 Round 3: 491 peptides, 64 chains. Longest chain 18 peptides. Score 0.506 Round 4: 477 peptides, 55 chains. Longest chain 20 peptides. Score 0.538 Round 5: 479 peptides, 60 chains. Longest chain 22 peptides. Score 0.514 Taking the results from Round 4 Chains 57, Residues 422, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13491 restraints for refining 5987 atoms. 11820 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2780 (Rfree = 0.000) for 5987 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 2: After refmac, R = 0.2586 (Rfree = 0.000) for 5885 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 3: After refmac, R = 0.2495 (Rfree = 0.000) for 5844 atoms. Found 16 (32 requested) and removed 48 (16 requested) atoms. Cycle 4: After refmac, R = 0.2366 (Rfree = 0.000) for 5777 atoms. Found 16 (31 requested) and removed 30 (15 requested) atoms. Cycle 5: After refmac, R = 0.2259 (Rfree = 0.000) for 5739 atoms. Found 15 (31 requested) and removed 32 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 2.98 Search for helices and strands: 0 residues in 0 chains, 5968 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 5987 seeds are put forward Round 1: 448 peptides, 70 chains. Longest chain 17 peptides. Score 0.420 Round 2: 505 peptides, 66 chains. Longest chain 22 peptides. Score 0.512 Round 3: 485 peptides, 60 chains. Longest chain 26 peptides. Score 0.521 Round 4: 488 peptides, 63 chains. Longest chain 23 peptides. Score 0.508 Round 5: 492 peptides, 58 chains. Longest chain 23 peptides. Score 0.539 Taking the results from Round 5 Chains 58, Residues 434, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13403 restraints for refining 5990 atoms. 11725 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2383 (Rfree = 0.000) for 5990 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 7: After refmac, R = 0.2260 (Rfree = 0.000) for 5920 atoms. Found 18 (32 requested) and removed 30 (16 requested) atoms. Cycle 8: After refmac, R = 0.2150 (Rfree = 0.000) for 5881 atoms. Found 13 (32 requested) and removed 26 (16 requested) atoms. Cycle 9: After refmac, R = 0.2093 (Rfree = 0.000) for 5844 atoms. Found 18 (32 requested) and removed 23 (16 requested) atoms. Cycle 10: After refmac, R = 0.1975 (Rfree = 0.000) for 5821 atoms. Found 10 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.56 2.98 Search for helices and strands: 0 residues in 0 chains, 6070 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 6101 seeds are put forward Round 1: 438 peptides, 74 chains. Longest chain 15 peptides. Score 0.383 Round 2: 491 peptides, 64 chains. Longest chain 21 peptides. Score 0.506 Round 3: 481 peptides, 64 chains. Longest chain 27 peptides. Score 0.495 Round 4: 486 peptides, 59 chains. Longest chain 28 peptides. Score 0.527 Round 5: 490 peptides, 68 chains. Longest chain 19 peptides. Score 0.484 Taking the results from Round 4 Chains 64, Residues 427, Estimated correctness of the model 0.0 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 12844 restraints for refining 5991 atoms. 11062 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2481 (Rfree = 0.000) for 5991 atoms. Found 32 (32 requested) and removed 51 (16 requested) atoms. Cycle 12: After refmac, R = 0.2180 (Rfree = 0.000) for 5925 atoms. Found 24 (32 requested) and removed 36 (16 requested) atoms. Cycle 13: After refmac, R = 0.2101 (Rfree = 0.000) for 5889 atoms. Found 14 (32 requested) and removed 26 (16 requested) atoms. Cycle 14: After refmac, R = 0.2060 (Rfree = 0.000) for 5865 atoms. Found 10 (32 requested) and removed 29 (16 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2008 (Rfree = 0.000) for 5839 atoms. Found 6 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.01 Search for helices and strands: 0 residues in 0 chains, 6019 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 6056 seeds are put forward Round 1: 441 peptides, 70 chains. Longest chain 17 peptides. Score 0.411 Round 2: 473 peptides, 63 chains. Longest chain 24 peptides. Score 0.491 Round 3: 494 peptides, 65 chains. Longest chain 24 peptides. Score 0.505 Round 4: 486 peptides, 64 chains. Longest chain 25 peptides. Score 0.501 Round 5: 482 peptides, 61 chains. Longest chain 29 peptides. Score 0.512 Taking the results from Round 5 Chains 61, Residues 421, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13298 restraints for refining 5992 atoms. 11646 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2556 (Rfree = 0.000) for 5992 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 17: After refmac, R = 0.2354 (Rfree = 0.000) for 5917 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 18: After refmac, R = 0.2009 (Rfree = 0.000) for 5879 atoms. Found 14 (32 requested) and removed 24 (16 requested) atoms. Cycle 19: After refmac, R = 0.2047 (Rfree = 0.000) for 5855 atoms. Found 30 (32 requested) and removed 27 (16 requested) atoms. Cycle 20: After refmac, R = 0.1996 (Rfree = 0.000) for 5848 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.01 Search for helices and strands: 0 residues in 0 chains, 6094 seeds are put forward NCS extension: 38 residues added (3 deleted due to clashes), 6132 seeds are put forward Round 1: 416 peptides, 72 chains. Longest chain 13 peptides. Score 0.365 Round 2: 476 peptides, 70 chains. Longest chain 19 peptides. Score 0.456 Round 3: 469 peptides, 68 chains. Longest chain 18 peptides. Score 0.458 Round 4: 475 peptides, 62 chains. Longest chain 18 peptides. Score 0.498 Round 5: 479 peptides, 67 chains. Longest chain 19 peptides. Score 0.476 Taking the results from Round 4 Chains 62, Residues 413, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13279 restraints for refining 5990 atoms. 11689 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2402 (Rfree = 0.000) for 5990 atoms. Found 32 (32 requested) and removed 46 (16 requested) atoms. Cycle 22: After refmac, R = 0.2201 (Rfree = 0.000) for 5918 atoms. Found 29 (32 requested) and removed 47 (16 requested) atoms. Cycle 23: After refmac, R = 0.2129 (Rfree = 0.000) for 5860 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 24: After refmac, R = 0.1949 (Rfree = 0.000) for 5834 atoms. Found 18 (32 requested) and removed 44 (16 requested) atoms. Cycle 25: After refmac, R = 0.1925 (Rfree = 0.000) for 5798 atoms. Found 22 (31 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.03 Search for helices and strands: 0 residues in 0 chains, 6035 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 6050 seeds are put forward Round 1: 377 peptides, 69 chains. Longest chain 12 peptides. Score 0.328 Round 2: 429 peptides, 63 chains. Longest chain 16 peptides. Score 0.436 Round 3: 442 peptides, 66 chains. Longest chain 15 peptides. Score 0.435 Round 4: 448 peptides, 60 chains. Longest chain 15 peptides. Score 0.477 Round 5: 444 peptides, 62 chains. Longest chain 18 peptides. Score 0.461 Taking the results from Round 4 Chains 60, Residues 388, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13469 restraints for refining 5990 atoms. 11977 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2321 (Rfree = 0.000) for 5990 atoms. Found 32 (32 requested) and removed 54 (16 requested) atoms. Cycle 27: After refmac, R = 0.2068 (Rfree = 0.000) for 5927 atoms. Found 23 (32 requested) and removed 32 (16 requested) atoms. Cycle 28: After refmac, R = 0.2006 (Rfree = 0.000) for 5899 atoms. Found 19 (32 requested) and removed 32 (16 requested) atoms. Cycle 29: After refmac, R = 0.1943 (Rfree = 0.000) for 5875 atoms. Found 11 (32 requested) and removed 35 (16 requested) atoms. Cycle 30: After refmac, R = 0.1914 (Rfree = 0.000) for 5836 atoms. Found 17 (32 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 2.99 Search for helices and strands: 0 residues in 0 chains, 6097 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6112 seeds are put forward Round 1: 408 peptides, 78 chains. Longest chain 14 peptides. Score 0.317 Round 2: 444 peptides, 69 chains. Longest chain 22 peptides. Score 0.421 Round 3: 451 peptides, 70 chains. Longest chain 17 peptides. Score 0.424 Round 4: 472 peptides, 72 chains. Longest chain 14 peptides. Score 0.440 Round 5: 473 peptides, 70 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 5 Chains 70, Residues 403, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13360 restraints for refining 5991 atoms. 11818 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2455 (Rfree = 0.000) for 5991 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 32: After refmac, R = 0.2203 (Rfree = 0.000) for 5960 atoms. Found 17 (32 requested) and removed 20 (16 requested) atoms. Cycle 33: After refmac, R = 0.2165 (Rfree = 0.000) for 5943 atoms. Found 17 (32 requested) and removed 31 (16 requested) atoms. Cycle 34: After refmac, R = 0.1973 (Rfree = 0.000) for 5922 atoms. Found 7 (32 requested) and removed 30 (16 requested) atoms. Cycle 35: After refmac, R = 0.1936 (Rfree = 0.000) for 5889 atoms. Found 10 (32 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 2.99 Search for helices and strands: 0 residues in 0 chains, 6074 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 6098 seeds are put forward Round 1: 365 peptides, 68 chains. Longest chain 14 peptides. Score 0.317 Round 2: 418 peptides, 66 chains. Longest chain 15 peptides. Score 0.404 Round 3: 447 peptides, 66 chains. Longest chain 15 peptides. Score 0.442 Round 4: 435 peptides, 64 chains. Longest chain 19 peptides. Score 0.438 Round 5: 430 peptides, 63 chains. Longest chain 14 peptides. Score 0.437 Taking the results from Round 3 Chains 66, Residues 381, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13189 restraints for refining 5991 atoms. 11693 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2231 (Rfree = 0.000) for 5991 atoms. Found 30 (32 requested) and removed 23 (16 requested) atoms. Cycle 37: After refmac, R = 0.2015 (Rfree = 0.000) for 5970 atoms. Found 13 (32 requested) and removed 20 (16 requested) atoms. Cycle 38: After refmac, R = 0.1981 (Rfree = 0.000) for 5954 atoms. Found 6 (32 requested) and removed 35 (16 requested) atoms. Cycle 39: After refmac, R = 0.1941 (Rfree = 0.000) for 5916 atoms. Found 3 (32 requested) and removed 29 (16 requested) atoms. Cycle 40: After refmac, R = 0.1897 (Rfree = 0.000) for 5881 atoms. Found 8 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.02 Search for helices and strands: 0 residues in 0 chains, 6074 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6096 seeds are put forward Round 1: 373 peptides, 67 chains. Longest chain 11 peptides. Score 0.335 Round 2: 411 peptides, 66 chains. Longest chain 15 peptides. Score 0.394 Round 3: 420 peptides, 64 chains. Longest chain 16 peptides. Score 0.418 Round 4: 427 peptides, 66 chains. Longest chain 14 peptides. Score 0.416 Round 5: 421 peptides, 61 chains. Longest chain 15 peptides. Score 0.437 Taking the results from Round 5 Chains 61, Residues 360, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13655 restraints for refining 5991 atoms. 12276 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2425 (Rfree = 0.000) for 5991 atoms. Found 26 (32 requested) and removed 31 (16 requested) atoms. Cycle 42: After refmac, R = 0.2164 (Rfree = 0.000) for 5952 atoms. Found 11 (32 requested) and removed 22 (16 requested) atoms. Cycle 43: After refmac, R = 0.2150 (Rfree = 0.000) for 5934 atoms. Found 8 (32 requested) and removed 23 (16 requested) atoms. Cycle 44: After refmac, R = 0.2113 (Rfree = 0.000) for 5916 atoms. Found 10 (32 requested) and removed 21 (16 requested) atoms. Cycle 45: After refmac, R = 0.2097 (Rfree = 0.000) for 5903 atoms. Found 8 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.00 Search for helices and strands: 0 residues in 0 chains, 6089 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6110 seeds are put forward Round 1: 339 peptides, 66 chains. Longest chain 10 peptides. Score 0.291 Round 2: 405 peptides, 67 chains. Longest chain 14 peptides. Score 0.380 Round 3: 400 peptides, 58 chains. Longest chain 13 peptides. Score 0.428 Round 4: 402 peptides, 62 chains. Longest chain 15 peptides. Score 0.406 Round 5: 392 peptides, 58 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 342, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2go7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12049 reflections ( 99.74 % complete ) and 13689 restraints for refining 5992 atoms. 12379 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2254 (Rfree = 0.000) for 5992 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2137 (Rfree = 0.000) for 5960 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2127 (Rfree = 0.000) for 5941 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2099 (Rfree = 0.000) for 5922 atoms. TimeTaking 67.03