Tue 25 Dec 19:27:57 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 2go7-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2go7-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2go7-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-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/2go7-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-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 ============================================================ Tue 25 Dec 19:28:12 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/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-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 869 and 0 Target number of residues in the AU: 869 Target solvent content: 0.6166 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: 2go7-3.2-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: 2go7-3.2-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 3.200 Wilson plot Bfac: 59.74 20113 reflections ( 99.84 % complete ) and 0 restraints for refining 7423 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3491 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2870 (Rfree = 0.000) for 7423 atoms. Found 66 (66 requested) and removed 72 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.09 2.59 Search for helices and strands: 0 residues in 0 chains, 7570 seeds are put forward NCS extension: 0 residues added, 7570 seeds are put forward Round 1: 438 peptides, 75 chains. Longest chain 16 peptides. Score 0.377 Round 2: 538 peptides, 77 chains. Longest chain 24 peptides. Score 0.493 Round 3: 558 peptides, 71 chains. Longest chain 21 peptides. Score 0.546 Round 4: 579 peptides, 69 chains. Longest chain 29 peptides. Score 0.578 Round 5: 574 peptides, 71 chains. Longest chain 27 peptides. Score 0.563 Taking the results from Round 4 Chains 72, Residues 510, Estimated correctness of the model 35.0 % 3 chains (55 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20113 reflections ( 99.84 % complete ) and 12122 restraints for refining 6045 atoms. 9920 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2735 (Rfree = 0.000) for 6045 atoms. Found 54 (54 requested) and removed 54 (27 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2536 (Rfree = 0.000) for 5982 atoms. Found 31 (54 requested) and removed 38 (27 requested) atoms. Cycle 3: After refmac, R = 0.2414 (Rfree = 0.000) for 5934 atoms. Found 23 (53 requested) and removed 45 (26 requested) atoms. Cycle 4: After refmac, R = 0.2364 (Rfree = 0.000) for 5887 atoms. Found 16 (53 requested) and removed 29 (26 requested) atoms. Cycle 5: After refmac, R = 0.2348 (Rfree = 0.000) for 5855 atoms. Found 23 (52 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.08 2.58 Search for helices and strands: 0 residues in 0 chains, 6138 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 6157 seeds are put forward Round 1: 538 peptides, 71 chains. Longest chain 23 peptides. Score 0.524 Round 2: 597 peptides, 67 chains. Longest chain 28 peptides. Score 0.605 Round 3: 630 peptides, 66 chains. Longest chain 24 peptides. Score 0.641 Round 4: 627 peptides, 66 chains. Longest chain 46 peptides. Score 0.638 Round 5: 605 peptides, 63 chains. Longest chain 30 peptides. Score 0.631 Taking the results from Round 3 Chains 70, Residues 564, Estimated correctness of the model 51.6 % 6 chains (76 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 11759 restraints for refining 6047 atoms. 9271 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2533 (Rfree = 0.000) for 6047 atoms. Found 50 (54 requested) and removed 39 (27 requested) atoms. Cycle 7: After refmac, R = 0.2349 (Rfree = 0.000) for 6033 atoms. Found 16 (54 requested) and removed 32 (27 requested) atoms. Cycle 8: After refmac, R = 0.2283 (Rfree = 0.000) for 5997 atoms. Found 3 (54 requested) and removed 32 (27 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2223 (Rfree = 0.000) for 5961 atoms. Found 14 (53 requested) and removed 28 (26 requested) atoms. Cycle 10: After refmac, R = 0.2210 (Rfree = 0.000) for 5931 atoms. Found 14 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 2.58 Search for helices and strands: 0 residues in 0 chains, 6225 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 6241 seeds are put forward Round 1: 590 peptides, 67 chains. Longest chain 30 peptides. Score 0.598 Round 2: 614 peptides, 63 chains. Longest chain 37 peptides. Score 0.639 Round 3: 621 peptides, 63 chains. Longest chain 29 peptides. Score 0.645 Round 4: 631 peptides, 52 chains. Longest chain 51 peptides. Score 0.698 Round 5: 626 peptides, 55 chains. Longest chain 41 peptides. Score 0.683 Taking the results from Round 4 Chains 60, Residues 579, Estimated correctness of the model 64.8 % 9 chains (159 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 10990 restraints for refining 6047 atoms. 8080 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2607 (Rfree = 0.000) for 6047 atoms. Found 54 (54 requested) and removed 47 (27 requested) atoms. Cycle 12: After refmac, R = 0.2429 (Rfree = 0.000) for 6019 atoms. Found 36 (54 requested) and removed 41 (27 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2328 (Rfree = 0.000) for 5993 atoms. Found 18 (53 requested) and removed 32 (26 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2271 (Rfree = 0.000) for 5970 atoms. Found 13 (53 requested) and removed 26 (26 requested) atoms. Cycle 15: After refmac, R = 0.2230 (Rfree = 0.000) for 5954 atoms. Found 12 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 2.64 Search for helices and strands: 0 residues in 0 chains, 6186 seeds are put forward NCS extension: 29 residues added (16 deleted due to clashes), 6215 seeds are put forward Round 1: 598 peptides, 67 chains. Longest chain 37 peptides. Score 0.606 Round 2: 605 peptides, 56 chains. Longest chain 42 peptides. Score 0.661 Round 3: 618 peptides, 57 chains. Longest chain 46 peptides. Score 0.668 Round 4: 615 peptides, 59 chains. Longest chain 41 peptides. Score 0.657 Round 5: 597 peptides, 52 chains. Longest chain 35 peptides. Score 0.670 Taking the results from Round 5 Chains 57, Residues 545, Estimated correctness of the model 58.5 % 6 chains (87 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20113 reflections ( 99.84 % complete ) and 11860 restraints for refining 6046 atoms. 9380 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2535 (Rfree = 0.000) for 6046 atoms. Found 54 (54 requested) and removed 34 (27 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2351 (Rfree = 0.000) for 6044 atoms. Found 25 (54 requested) and removed 31 (27 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2276 (Rfree = 0.000) for 6014 atoms. Found 14 (54 requested) and removed 31 (27 requested) atoms. Cycle 19: After refmac, R = 0.2231 (Rfree = 0.000) for 5983 atoms. Found 15 (53 requested) and removed 27 (26 requested) atoms. Cycle 20: After refmac, R = 0.2208 (Rfree = 0.000) for 5966 atoms. Found 7 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 2.63 Search for helices and strands: 0 residues in 0 chains, 6181 seeds are put forward NCS extension: 35 residues added (4 deleted due to clashes), 6216 seeds are put forward Round 1: 582 peptides, 69 chains. Longest chain 29 peptides. Score 0.581 Round 2: 609 peptides, 54 chains. Longest chain 40 peptides. Score 0.672 Round 3: 602 peptides, 54 chains. Longest chain 32 peptides. Score 0.666 Round 4: 606 peptides, 61 chains. Longest chain 31 peptides. Score 0.640 Round 5: 623 peptides, 58 chains. Longest chain 31 peptides. Score 0.668 Taking the results from Round 2 Chains 61, Residues 555, Estimated correctness of the model 59.0 % 5 chains (87 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20113 reflections ( 99.84 % complete ) and 11549 restraints for refining 6046 atoms. 9024 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2440 (Rfree = 0.000) for 6046 atoms. Found 54 (54 requested) and removed 46 (27 requested) atoms. Cycle 22: After refmac, R = 0.2245 (Rfree = 0.000) for 6044 atoms. Found 24 (54 requested) and removed 30 (27 requested) atoms. Cycle 23: After refmac, R = 0.2176 (Rfree = 0.000) for 6031 atoms. Found 14 (54 requested) and removed 28 (27 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2133 (Rfree = 0.000) for 6012 atoms. Found 4 (54 requested) and removed 27 (27 requested) atoms. Cycle 25: After refmac, R = 0.2097 (Rfree = 0.000) for 5982 atoms. Found 8 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 2.63 Search for helices and strands: 0 residues in 0 chains, 6181 seeds are put forward NCS extension: 10 residues added (8 deleted due to clashes), 6191 seeds are put forward Round 1: 519 peptides, 62 chains. Longest chain 24 peptides. Score 0.548 Round 2: 571 peptides, 61 chains. Longest chain 30 peptides. Score 0.607 Round 3: 601 peptides, 60 chains. Longest chain 29 peptides. Score 0.640 Round 4: 578 peptides, 55 chains. Longest chain 26 peptides. Score 0.641 Round 5: 558 peptides, 53 chains. Longest chain 24 peptides. Score 0.631 Taking the results from Round 4 Chains 56, Residues 523, Estimated correctness of the model 51.6 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12409 restraints for refining 6045 atoms. 10216 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2425 (Rfree = 0.000) for 6045 atoms. Found 54 (54 requested) and removed 39 (27 requested) atoms. Cycle 27: After refmac, R = 0.2265 (Rfree = 0.000) for 6049 atoms. Found 21 (54 requested) and removed 32 (27 requested) atoms. Cycle 28: After refmac, R = 0.2211 (Rfree = 0.000) for 6030 atoms. Found 12 (54 requested) and removed 27 (27 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2181 (Rfree = 0.000) for 6010 atoms. Found 13 (53 requested) and removed 27 (26 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2168 (Rfree = 0.000) for 5994 atoms. Found 15 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 2.66 Search for helices and strands: 0 residues in 0 chains, 6189 seeds are put forward NCS extension: 11 residues added (12 deleted due to clashes), 6200 seeds are put forward Round 1: 545 peptides, 63 chains. Longest chain 27 peptides. Score 0.571 Round 2: 569 peptides, 59 chains. Longest chain 29 peptides. Score 0.614 Round 3: 593 peptides, 61 chains. Longest chain 24 peptides. Score 0.628 Round 4: 573 peptides, 60 chains. Longest chain 39 peptides. Score 0.614 Round 5: 580 peptides, 63 chains. Longest chain 30 peptides. Score 0.607 Taking the results from Round 3 Chains 62, Residues 532, Estimated correctness of the model 48.4 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12323 restraints for refining 6048 atoms. 10066 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2470 (Rfree = 0.000) for 6048 atoms. Found 52 (54 requested) and removed 35 (27 requested) atoms. Cycle 32: After refmac, R = 0.2295 (Rfree = 0.000) for 6060 atoms. Found 19 (54 requested) and removed 27 (27 requested) atoms. Cycle 33: After refmac, R = 0.2254 (Rfree = 0.000) for 6042 atoms. Found 15 (54 requested) and removed 27 (27 requested) atoms. Cycle 34: After refmac, R = 0.2229 (Rfree = 0.000) for 6020 atoms. Found 17 (54 requested) and removed 27 (27 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2229 (Rfree = 0.000) for 6000 atoms. Found 17 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 2.63 Search for helices and strands: 0 residues in 0 chains, 6225 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 6235 seeds are put forward Round 1: 529 peptides, 70 chains. Longest chain 26 peptides. Score 0.519 Round 2: 560 peptides, 59 chains. Longest chain 37 peptides. Score 0.606 Round 3: 582 peptides, 62 chains. Longest chain 27 peptides. Score 0.613 Round 4: 541 peptides, 63 chains. Longest chain 28 peptides. Score 0.567 Round 5: 563 peptides, 62 chains. Longest chain 30 peptides. Score 0.595 Taking the results from Round 3 Chains 64, Residues 520, Estimated correctness of the model 44.5 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20113 reflections ( 99.84 % complete ) and 12640 restraints for refining 6046 atoms. 10446 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2464 (Rfree = 0.000) for 6046 atoms. Found 42 (54 requested) and removed 32 (27 requested) atoms. Cycle 37: After refmac, R = 0.2334 (Rfree = 0.000) for 6043 atoms. Found 26 (54 requested) and removed 27 (27 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2270 (Rfree = 0.000) for 6038 atoms. Found 8 (54 requested) and removed 27 (27 requested) atoms. Cycle 39: After refmac, R = 0.2245 (Rfree = 0.000) for 6014 atoms. Found 11 (54 requested) and removed 28 (27 requested) atoms. Cycle 40: After refmac, R = 0.2221 (Rfree = 0.000) for 5992 atoms. Found 13 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.65 Search for helices and strands: 0 residues in 0 chains, 6214 seeds are put forward NCS extension: 25 residues added (7 deleted due to clashes), 6239 seeds are put forward Round 1: 479 peptides, 69 chains. Longest chain 20 peptides. Score 0.465 Round 2: 537 peptides, 64 chains. Longest chain 29 peptides. Score 0.558 Round 3: 547 peptides, 67 chains. Longest chain 21 peptides. Score 0.554 Round 4: 535 peptides, 60 chains. Longest chain 25 peptides. Score 0.576 Round 5: 554 peptides, 63 chains. Longest chain 20 peptides. Score 0.581 Taking the results from Round 5 Chains 63, Residues 491, Estimated correctness of the model 35.8 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12866 restraints for refining 6048 atoms. 10917 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2423 (Rfree = 0.000) for 6048 atoms. Found 45 (54 requested) and removed 29 (27 requested) atoms. Cycle 42: After refmac, R = 0.2285 (Rfree = 0.000) for 6054 atoms. Found 13 (54 requested) and removed 28 (27 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2237 (Rfree = 0.000) for 6031 atoms. Found 13 (54 requested) and removed 27 (27 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2192 (Rfree = 0.000) for 6011 atoms. Found 9 (54 requested) and removed 27 (27 requested) atoms. Cycle 45: After refmac, R = 0.2162 (Rfree = 0.000) for 5991 atoms. Found 13 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 2.63 Search for helices and strands: 0 residues in 0 chains, 6210 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 6222 seeds are put forward Round 1: 485 peptides, 62 chains. Longest chain 26 peptides. Score 0.510 Round 2: 537 peptides, 61 chains. Longest chain 32 peptides. Score 0.573 Round 3: 529 peptides, 59 chains. Longest chain 24 peptides. Score 0.574 Round 4: 525 peptides, 62 chains. Longest chain 23 peptides. Score 0.555 Round 5: 545 peptides, 58 chains. Longest chain 29 peptides. Score 0.595 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 487, Estimated correctness of the model 39.7 % 1 chains (16 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2go7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20113 reflections ( 99.84 % complete ) and 12704 restraints for refining 6047 atoms. 10748 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2292 (Rfree = 0.000) for 6047 atoms. Found 0 (54 requested) and removed 25 (27 requested) atoms. Cycle 47: After refmac, R = 0.2200 (Rfree = 0.000) for 6016 atoms. Found 0 (54 requested) and removed 11 (27 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2179 (Rfree = 0.000) for 6001 atoms. Found 0 (53 requested) and removed 15 (26 requested) atoms. Cycle 49: After refmac, R = 0.2157 (Rfree = 0.000) for 5981 atoms. Found 0 (53 requested) and removed 7 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:24:33 GMT 2018 Job finished. TimeTaking 116.59