Sun 23 Dec 22:22:42 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2go7-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2go7-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2go7-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:44 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/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.8-parrot-hancs/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-hancs.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-hancs.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 Failed to save intermediate PDB 12049 reflections ( 99.74 % complete ) and 0 restraints for refining 7392 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3591 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3346 (Rfree = 0.000) for 7392 atoms. Found 40 (40 requested) and removed 42 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 7561 seeds are put forward NCS extension: 0 residues added, 7561 seeds are put forward Round 1: 345 peptides, 67 chains. Longest chain 11 peptides. Score 0.293 Round 2: 446 peptides, 68 chains. Longest chain 18 peptides. Score 0.429 Round 3: 494 peptides, 66 chains. Longest chain 18 peptides. Score 0.499 Round 4: 486 peptides, 60 chains. Longest chain 25 peptides. Score 0.522 Round 5: 491 peptides, 51 chains. Longest chain 37 peptides. Score 0.574 Taking the results from Round 5 Chains 57, Residues 440, Estimated correctness of the model 0.0 % 4 chains (53 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 12857 restraints for refining 5992 atoms. 10950 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2770 (Rfree = 0.000) for 5992 atoms. Found 25 (32 requested) and removed 29 (16 requested) atoms. Cycle 2: After refmac, R = 0.2590 (Rfree = 0.000) for 5866 atoms. Found 24 (32 requested) and removed 22 (16 requested) atoms. Cycle 3: After refmac, R = 0.2480 (Rfree = 0.000) for 5827 atoms. Found 13 (32 requested) and removed 24 (16 requested) atoms. Cycle 4: After refmac, R = 0.2450 (Rfree = 0.000) for 5789 atoms. Found 7 (31 requested) and removed 17 (15 requested) atoms. Cycle 5: After refmac, R = 0.2416 (Rfree = 0.000) for 5758 atoms. Found 10 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 6005 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 6026 seeds are put forward Round 1: 432 peptides, 70 chains. Longest chain 17 peptides. Score 0.399 Round 2: 469 peptides, 60 chains. Longest chain 25 peptides. Score 0.502 Round 3: 490 peptides, 62 chains. Longest chain 20 peptides. Score 0.516 Round 4: 518 peptides, 61 chains. Longest chain 22 peptides. Score 0.552 Round 5: 521 peptides, 61 chains. Longest chain 19 peptides. Score 0.556 Taking the results from Round 5 Chains 63, Residues 460, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 12917 restraints for refining 5991 atoms. 11054 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2658 (Rfree = 0.000) for 5991 atoms. Found 29 (32 requested) and removed 284 (16 requested) atoms. Cycle 7: After refmac, R = 0.2459 (Rfree = 0.000) for 5650 atoms. Found 30 (31 requested) and removed 26 (15 requested) atoms. Cycle 8: After refmac, R = 0.2403 (Rfree = 0.000) for 5622 atoms. Found 6 (31 requested) and removed 22 (15 requested) atoms. Cycle 9: After refmac, R = 0.2388 (Rfree = 0.000) for 5588 atoms. Found 9 (30 requested) and removed 17 (15 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2350 (Rfree = 0.000) for 5573 atoms. Found 18 (30 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.00 Search for helices and strands: 0 residues in 0 chains, 5833 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 5860 seeds are put forward Round 1: 458 peptides, 65 chains. Longest chain 19 peptides. Score 0.461 Round 2: 510 peptides, 65 chains. Longest chain 21 peptides. Score 0.523 Round 3: 515 peptides, 60 chains. Longest chain 21 peptides. Score 0.554 Round 4: 530 peptides, 63 chains. Longest chain 19 peptides. Score 0.555 Round 5: 533 peptides, 61 chains. Longest chain 21 peptides. Score 0.569 Taking the results from Round 5 Chains 61, Residues 472, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 12959 restraints for refining 5991 atoms. 11132 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2664 (Rfree = 0.000) for 5991 atoms. Found 32 (32 requested) and removed 224 (16 requested) atoms. Cycle 12: After refmac, R = 0.2440 (Rfree = 0.000) for 5748 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 13: After refmac, R = 0.2323 (Rfree = 0.000) for 5720 atoms. Found 16 (31 requested) and removed 23 (15 requested) atoms. Cycle 14: After refmac, R = 0.2268 (Rfree = 0.000) for 5697 atoms. Found 8 (31 requested) and removed 19 (15 requested) atoms. Cycle 15: After refmac, R = 0.2242 (Rfree = 0.000) for 5672 atoms. Found 13 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.00 Search for helices and strands: 0 residues in 0 chains, 5893 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5915 seeds are put forward Round 1: 438 peptides, 68 chains. Longest chain 17 peptides. Score 0.419 Round 2: 482 peptides, 59 chains. Longest chain 24 peptides. Score 0.523 Round 3: 481 peptides, 59 chains. Longest chain 29 peptides. Score 0.521 Round 4: 502 peptides, 62 chains. Longest chain 26 peptides. Score 0.530 Round 5: 499 peptides, 59 chains. Longest chain 27 peptides. Score 0.542 Taking the results from Round 5 Chains 61, Residues 440, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13164 restraints for refining 5992 atoms. 11395 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2564 (Rfree = 0.000) for 5992 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 17: After refmac, R = 0.2332 (Rfree = 0.000) for 5933 atoms. Found 15 (32 requested) and removed 39 (16 requested) atoms. Cycle 18: After refmac, R = 0.2272 (Rfree = 0.000) for 5884 atoms. Found 13 (32 requested) and removed 30 (16 requested) atoms. Cycle 19: After refmac, R = 0.2156 (Rfree = 0.000) for 5841 atoms. Found 14 (32 requested) and removed 26 (16 requested) atoms. Cycle 20: After refmac, R = 0.2135 (Rfree = 0.000) for 5813 atoms. Found 12 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 6034 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6052 seeds are put forward Round 1: 420 peptides, 75 chains. Longest chain 14 peptides. Score 0.353 Round 2: 469 peptides, 69 chains. Longest chain 21 peptides. Score 0.453 Round 3: 477 peptides, 67 chains. Longest chain 23 peptides. Score 0.474 Round 4: 493 peptides, 69 chains. Longest chain 25 peptides. Score 0.482 Round 5: 496 peptides, 65 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 5 Chains 65, Residues 431, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13324 restraints for refining 5992 atoms. 11665 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2581 (Rfree = 0.000) for 5992 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. Cycle 22: After refmac, R = 0.2312 (Rfree = 0.000) for 5964 atoms. Found 7 (32 requested) and removed 24 (16 requested) atoms. Cycle 23: After refmac, R = 0.2263 (Rfree = 0.000) for 5931 atoms. Found 9 (32 requested) and removed 19 (16 requested) atoms. Cycle 24: After refmac, R = 0.2240 (Rfree = 0.000) for 5918 atoms. Found 6 (32 requested) and removed 18 (16 requested) atoms. Cycle 25: After refmac, R = 0.2201 (Rfree = 0.000) for 5903 atoms. Found 7 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 6121 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 6154 seeds are put forward Round 1: 413 peptides, 72 chains. Longest chain 19 peptides. Score 0.361 Round 2: 462 peptides, 66 chains. Longest chain 19 peptides. Score 0.461 Round 3: 467 peptides, 67 chains. Longest chain 22 peptides. Score 0.461 Round 4: 470 peptides, 62 chains. Longest chain 22 peptides. Score 0.492 Round 5: 472 peptides, 62 chains. Longest chain 22 peptides. Score 0.495 Taking the results from Round 5 Chains 64, Residues 410, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13399 restraints for refining 5990 atoms. 11750 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2734 (Rfree = 0.000) for 5990 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 27: After refmac, R = 0.2524 (Rfree = 0.000) for 5954 atoms. Found 31 (32 requested) and removed 32 (16 requested) atoms. Cycle 28: After refmac, R = 0.2433 (Rfree = 0.000) for 5938 atoms. Found 16 (32 requested) and removed 19 (16 requested) atoms. Cycle 29: After refmac, R = 0.2376 (Rfree = 0.000) for 5923 atoms. Found 7 (32 requested) and removed 16 (16 requested) atoms. Cycle 30: After refmac, R = 0.2373 (Rfree = 0.000) for 5908 atoms. Found 7 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.01 Search for helices and strands: 0 residues in 0 chains, 6095 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 6126 seeds are put forward Round 1: 426 peptides, 72 chains. Longest chain 21 peptides. Score 0.379 Round 2: 452 peptides, 71 chains. Longest chain 19 peptides. Score 0.419 Round 3: 466 peptides, 66 chains. Longest chain 21 peptides. Score 0.466 Round 4: 479 peptides, 66 chains. Longest chain 19 peptides. Score 0.481 Round 5: 484 peptides, 62 chains. Longest chain 23 peptides. Score 0.509 Taking the results from Round 5 Chains 65, Residues 422, Estimated correctness of the model 0.0 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13018 restraints for refining 5989 atoms. 11190 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2725 (Rfree = 0.000) for 5989 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 32: After refmac, R = 0.2469 (Rfree = 0.000) for 5955 atoms. Found 11 (32 requested) and removed 21 (16 requested) atoms. Cycle 33: After refmac, R = 0.2417 (Rfree = 0.000) for 5930 atoms. Found 5 (32 requested) and removed 19 (16 requested) atoms. Cycle 34: After refmac, R = 0.2381 (Rfree = 0.000) for 5910 atoms. Found 4 (32 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.2375 (Rfree = 0.000) for 5893 atoms. Found 8 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.02 Search for helices and strands: 0 residues in 0 chains, 6091 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 6112 seeds are put forward Round 1: 400 peptides, 69 chains. Longest chain 15 peptides. Score 0.361 Round 2: 452 peptides, 69 chains. Longest chain 21 peptides. Score 0.431 Round 3: 450 peptides, 64 chains. Longest chain 21 peptides. Score 0.457 Round 4: 464 peptides, 66 chains. Longest chain 21 peptides. Score 0.463 Round 5: 459 peptides, 64 chains. Longest chain 16 peptides. Score 0.468 Taking the results from Round 5 Chains 66, Residues 395, Estimated correctness of the model 0.0 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13310 restraints for refining 5991 atoms. 11676 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2589 (Rfree = 0.000) for 5991 atoms. Found 23 (32 requested) and removed 23 (16 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2347 (Rfree = 0.000) for 5948 atoms. Found 18 (32 requested) and removed 21 (16 requested) atoms. Cycle 38: After refmac, R = 0.2260 (Rfree = 0.000) for 5925 atoms. Found 10 (32 requested) and removed 31 (16 requested) atoms. Cycle 39: After refmac, R = 0.2232 (Rfree = 0.000) for 5892 atoms. Found 6 (32 requested) and removed 18 (16 requested) atoms. Cycle 40: After refmac, R = 0.2293 (Rfree = 0.000) for 5866 atoms. Found 16 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.02 Search for helices and strands: 0 residues in 0 chains, 6052 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6074 seeds are put forward Round 1: 378 peptides, 73 chains. Longest chain 13 peptides. Score 0.304 Round 2: 408 peptides, 67 chains. Longest chain 16 peptides. Score 0.384 Round 3: 383 peptides, 62 chains. Longest chain 16 peptides. Score 0.380 Round 4: 417 peptides, 66 chains. Longest chain 23 peptides. Score 0.402 Round 5: 429 peptides, 71 chains. Longest chain 15 peptides. Score 0.389 Taking the results from Round 4 Chains 66, Residues 351, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12049 reflections ( 99.74 % complete ) and 13972 restraints for refining 5992 atoms. 12634 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2499 (Rfree = 0.000) for 5992 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 42: After refmac, R = 0.2328 (Rfree = 0.000) for 5972 atoms. Found 24 (32 requested) and removed 30 (16 requested) atoms. Cycle 43: After refmac, R = 0.2183 (Rfree = 0.000) for 5943 atoms. Found 10 (32 requested) and removed 18 (16 requested) atoms. Cycle 44: After refmac, R = 0.1961 (Rfree = 0.000) for 5926 atoms. Found 4 (32 requested) and removed 31 (16 requested) atoms. Cycle 45: After refmac, R = 0.1995 (Rfree = 0.000) for 5893 atoms. Found 9 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.03 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: 346 peptides, 70 chains. Longest chain 11 peptides. Score 0.275 Round 2: 387 peptides, 69 chains. Longest chain 13 peptides. Score 0.343 Round 3: 405 peptides, 66 chains. Longest chain 14 peptides. Score 0.386 Round 4: 382 peptides, 63 chains. Longest chain 14 peptides. Score 0.373 Round 5: 383 peptides, 64 chains. Longest chain 14 peptides. Score 0.368 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 339, 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 13945 restraints for refining 5992 atoms. 12655 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2453 (Rfree = 0.000) for 5992 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2142 (Rfree = 0.000) for 5960 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2133 (Rfree = 0.000) for 5939 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2162 (Rfree = 0.000) for 5922 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 173.38