Mon 24 Dec 00:18:07 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 2go7-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2go7-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-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/2go7-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-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 00:18:12 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/2go7-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-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 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-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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.10 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 12049 reflections ( 99.74 % complete ) and 0 restraints for refining 7392 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3454 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3371 (Rfree = 0.000) for 7392 atoms. Found 40 (40 requested) and removed 38 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.04 Search for helices and strands: 0 residues in 0 chains, 7548 seeds are put forward NCS extension: 0 residues added, 7548 seeds are put forward Round 1: 380 peptides, 73 chains. Longest chain 11 peptides. Score 0.307 Round 2: 474 peptides, 66 chains. Longest chain 23 peptides. Score 0.475 Round 3: 495 peptides, 60 chains. Longest chain 25 peptides. Score 0.532 Round 4: 508 peptides, 56 chains. Longest chain 24 peptides. Score 0.567 Round 5: 516 peptides, 61 chains. Longest chain 22 peptides. Score 0.550 Taking the results from Round 4 Chains 60, Residues 452, Estimated correctness of the model 0.0 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 12769 restraints for refining 5992 atoms. 10820 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2620 (Rfree = 0.000) for 5992 atoms. Found 31 (32 requested) and removed 41 (16 requested) atoms. Cycle 2: After refmac, R = 0.2386 (Rfree = 0.000) for 5867 atoms. Found 26 (32 requested) and removed 27 (16 requested) atoms. Cycle 3: After refmac, R = 0.2210 (Rfree = 0.000) for 5790 atoms. Found 25 (32 requested) and removed 18 (16 requested) atoms. Cycle 4: After refmac, R = 0.2141 (Rfree = 0.000) for 5761 atoms. Found 17 (31 requested) and removed 21 (15 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2076 (Rfree = 0.000) for 5728 atoms. Found 15 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 2.99 Search for helices and strands: 0 residues in 0 chains, 6048 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 6067 seeds are put forward Round 1: 476 peptides, 69 chains. Longest chain 19 peptides. Score 0.461 Round 2: 514 peptides, 60 chains. Longest chain 25 peptides. Score 0.553 Round 3: 522 peptides, 58 chains. Longest chain 43 peptides. Score 0.572 Round 4: 521 peptides, 57 chains. Longest chain 24 peptides. Score 0.576 Round 5: 517 peptides, 63 chains. Longest chain 25 peptides. Score 0.541 Taking the results from Round 4 Chains 60, Residues 464, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 12965 restraints for refining 5991 atoms. 11059 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2618 (Rfree = 0.000) for 5991 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 7: After refmac, R = 0.2411 (Rfree = 0.000) for 5944 atoms. Found 18 (32 requested) and removed 31 (16 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2309 (Rfree = 0.000) for 5916 atoms. Found 19 (32 requested) and removed 31 (16 requested) atoms. Cycle 9: After refmac, R = 0.2378 (Rfree = 0.000) for 5889 atoms. Found 25 (32 requested) and removed 25 (16 requested) atoms. Cycle 10: After refmac, R = 0.2183 (Rfree = 0.000) for 5869 atoms. Found 17 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 6116 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 6135 seeds are put forward Round 1: 467 peptides, 74 chains. Longest chain 12 peptides. Score 0.422 Round 2: 504 peptides, 61 chains. Longest chain 22 peptides. Score 0.537 Round 3: 505 peptides, 62 chains. Longest chain 28 peptides. Score 0.533 Round 4: 508 peptides, 58 chains. Longest chain 28 peptides. Score 0.557 Round 5: 510 peptides, 57 chains. Longest chain 25 peptides. Score 0.564 Taking the results from Round 5 Chains 59, Residues 453, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13252 restraints for refining 5991 atoms. 11445 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2568 (Rfree = 0.000) for 5991 atoms. Found 29 (32 requested) and removed 39 (16 requested) atoms. Cycle 12: After refmac, R = 0.2376 (Rfree = 0.000) for 5927 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 13: After refmac, R = 0.2066 (Rfree = 0.000) for 5902 atoms. Found 11 (32 requested) and removed 30 (16 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1990 (Rfree = 0.000) for 5851 atoms. Found 19 (32 requested) and removed 26 (16 requested) atoms. Cycle 15: After refmac, R = 0.1934 (Rfree = 0.000) for 5837 atoms. Found 8 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.00 Search for helices and strands: 0 residues in 0 chains, 6110 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6134 seeds are put forward Round 1: 462 peptides, 71 chains. Longest chain 18 peptides. Score 0.432 Round 2: 509 peptides, 68 chains. Longest chain 18 peptides. Score 0.506 Round 3: 480 peptides, 62 chains. Longest chain 16 peptides. Score 0.504 Round 4: 499 peptides, 63 chains. Longest chain 25 peptides. Score 0.521 Round 5: 508 peptides, 64 chains. Longest chain 19 peptides. Score 0.526 Taking the results from Round 5 Chains 64, Residues 444, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13368 restraints for refining 5991 atoms. 11656 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2246 (Rfree = 0.000) for 5991 atoms. Found 19 (32 requested) and removed 34 (16 requested) atoms. Cycle 17: After refmac, R = 0.2195 (Rfree = 0.000) for 5942 atoms. Found 11 (32 requested) and removed 26 (16 requested) atoms. Cycle 18: After refmac, R = 0.2154 (Rfree = 0.000) for 5913 atoms. Found 6 (32 requested) and removed 23 (16 requested) atoms. Cycle 19: After refmac, R = 0.2027 (Rfree = 0.000) for 5889 atoms. Found 5 (32 requested) and removed 18 (16 requested) atoms. Cycle 20: After refmac, R = 0.2078 (Rfree = 0.000) for 5869 atoms. Found 10 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.03 Search for helices and strands: 0 residues in 0 chains, 6105 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6124 seeds are put forward Round 1: 459 peptides, 83 chains. Longest chain 12 peptides. Score 0.359 Round 2: 473 peptides, 69 chains. Longest chain 19 peptides. Score 0.458 Round 3: 477 peptides, 62 chains. Longest chain 20 peptides. Score 0.501 Round 4: 495 peptides, 66 chains. Longest chain 22 peptides. Score 0.501 Round 5: 481 peptides, 63 chains. Longest chain 22 peptides. Score 0.500 Taking the results from Round 4 Chains 66, Residues 429, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13321 restraints for refining 5991 atoms. 11671 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2543 (Rfree = 0.000) for 5991 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 22: After refmac, R = 0.2422 (Rfree = 0.000) for 5957 atoms. Found 17 (32 requested) and removed 25 (16 requested) atoms. Cycle 23: After refmac, R = 0.2394 (Rfree = 0.000) for 5936 atoms. Found 21 (32 requested) and removed 30 (16 requested) atoms. Cycle 24: After refmac, R = 0.2292 (Rfree = 0.000) for 5910 atoms. Found 23 (32 requested) and removed 30 (16 requested) atoms. Cycle 25: After refmac, R = 0.2225 (Rfree = 0.000) for 5888 atoms. Found 8 (32 requested) and removed 29 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.02 Search for helices and strands: 0 residues in 0 chains, 6100 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6122 seeds are put forward Round 1: 435 peptides, 75 chains. Longest chain 15 peptides. Score 0.373 Round 2: 476 peptides, 65 chains. Longest chain 19 peptides. Score 0.483 Round 3: 465 peptides, 59 chains. Longest chain 27 peptides. Score 0.503 Round 4: 476 peptides, 58 chains. Longest chain 21 peptides. Score 0.521 Round 5: 484 peptides, 66 chains. Longest chain 23 peptides. Score 0.487 Taking the results from Round 4 Chains 63, Residues 418, Estimated correctness of the model 0.0 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13084 restraints for refining 5992 atoms. 11297 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2583 (Rfree = 0.000) for 5992 atoms. Found 25 (32 requested) and removed 26 (16 requested) atoms. Cycle 27: After refmac, R = 0.2293 (Rfree = 0.000) for 5949 atoms. Found 17 (32 requested) and removed 22 (16 requested) atoms. Cycle 28: After refmac, R = 0.2187 (Rfree = 0.000) for 5932 atoms. Found 4 (32 requested) and removed 17 (16 requested) atoms. Cycle 29: After refmac, R = 0.2106 (Rfree = 0.000) for 5908 atoms. Found 6 (32 requested) and removed 19 (16 requested) atoms. Cycle 30: After refmac, R = 0.2230 (Rfree = 0.000) for 5893 atoms. Found 19 (32 requested) and removed 97 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.01 Search for helices and strands: 0 residues in 0 chains, 5962 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 5981 seeds are put forward Round 1: 330 peptides, 72 chains. Longest chain 8 peptides. Score 0.237 Round 2: 368 peptides, 70 chains. Longest chain 14 peptides. Score 0.309 Round 3: 376 peptides, 69 chains. Longest chain 15 peptides. Score 0.327 Round 4: 398 peptides, 72 chains. Longest chain 18 peptides. Score 0.340 Round 5: 398 peptides, 69 chains. Longest chain 18 peptides. Score 0.358 Taking the results from Round 5 Chains 69, Residues 329, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 14124 restraints for refining 5991 atoms. 12857 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2750 (Rfree = 0.000) for 5991 atoms. Found 32 (32 requested) and removed 46 (16 requested) atoms. Cycle 32: After refmac, R = 0.2390 (Rfree = 0.000) for 5930 atoms. Found 32 (32 requested) and removed 63 (16 requested) atoms. Cycle 33: After refmac, R = 0.2126 (Rfree = 0.000) for 5876 atoms. Found 9 (32 requested) and removed 33 (16 requested) atoms. Cycle 34: After refmac, R = 0.2094 (Rfree = 0.000) for 5839 atoms. Found 2 (32 requested) and removed 24 (16 requested) atoms. Cycle 35: After refmac, R = 0.2136 (Rfree = 0.000) for 5813 atoms. Found 6 (31 requested) and removed 36 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.02 Search for helices and strands: 0 residues in 0 chains, 6039 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 6066 seeds are put forward Round 1: 350 peptides, 72 chains. Longest chain 11 peptides. Score 0.268 Round 2: 429 peptides, 75 chains. Longest chain 16 peptides. Score 0.365 Round 3: 405 peptides, 66 chains. Longest chain 18 peptides. Score 0.386 Round 4: 422 peptides, 67 chains. Longest chain 18 peptides. Score 0.403 Round 5: 433 peptides, 65 chains. Longest chain 18 peptides. Score 0.429 Taking the results from Round 5 Chains 66, Residues 368, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13549 restraints for refining 5992 atoms. 12061 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2577 (Rfree = 0.000) for 5992 atoms. Found 22 (32 requested) and removed 24 (16 requested) atoms. Cycle 37: After refmac, R = 0.2561 (Rfree = 0.000) for 5956 atoms. Found 13 (32 requested) and removed 24 (16 requested) atoms. Cycle 38: After refmac, R = 0.2448 (Rfree = 0.000) for 5930 atoms. Found 8 (32 requested) and removed 29 (16 requested) atoms. Cycle 39: After refmac, R = 0.2238 (Rfree = 0.000) for 5899 atoms. Found 12 (32 requested) and removed 18 (16 requested) atoms. Cycle 40: After refmac, R = 0.2302 (Rfree = 0.000) for 5881 atoms. Found 12 (32 requested) and removed 47 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.00 Search for helices and strands: 0 residues in 0 chains, 6097 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 6120 seeds are put forward Round 1: 374 peptides, 71 chains. Longest chain 11 peptides. Score 0.311 Round 2: 402 peptides, 66 chains. Longest chain 15 peptides. Score 0.382 Round 3: 388 peptides, 59 chains. Longest chain 14 peptides. Score 0.405 Round 4: 427 peptides, 62 chains. Longest chain 24 peptides. Score 0.439 Round 5: 439 peptides, 67 chains. Longest chain 17 peptides. Score 0.426 Taking the results from Round 4 Chains 62, Residues 365, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13508 restraints for refining 5990 atoms. 12110 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2602 (Rfree = 0.000) for 5990 atoms. Found 31 (32 requested) and removed 26 (16 requested) atoms. Cycle 42: After refmac, R = 0.2346 (Rfree = 0.000) for 5969 atoms. Found 9 (32 requested) and removed 27 (16 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2281 (Rfree = 0.000) for 5934 atoms. Found 8 (32 requested) and removed 27 (16 requested) atoms. Cycle 44: After refmac, R = 0.2282 (Rfree = 0.000) for 5909 atoms. Found 13 (32 requested) and removed 44 (16 requested) atoms. Cycle 45: After refmac, R = 0.2184 (Rfree = 0.000) for 5874 atoms. Found 6 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.01 Search for helices and strands: 0 residues in 0 chains, 6070 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 6099 seeds are put forward Round 1: 364 peptides, 71 chains. Longest chain 11 peptides. Score 0.296 Round 2: 401 peptides, 61 chains. Longest chain 17 peptides. Score 0.411 Round 3: 387 peptides, 59 chains. Longest chain 18 peptides. Score 0.404 Round 4: 378 peptides, 57 chains. Longest chain 13 peptides. Score 0.404 Round 5: 383 peptides, 57 chains. Longest chain 26 peptides. Score 0.411 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 326, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2go7-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (326 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12049 reflections ( 99.74 % complete ) and 13893 restraints for refining 5992 atoms. 12601 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2868 (Rfree = 0.000) for 5992 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2873 (Rfree = 0.000) for 5956 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2716 (Rfree = 0.000) for 5929 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2584 (Rfree = 0.000) for 5897 atoms. TimeTaking 79.23