null Sun 23 Dec 22:22:50 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 2go7-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2go7-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2go7-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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/2go7-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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 22:22:59 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/2go7-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.4-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 837 and 0 Target number of residues in the AU: 837 Target solvent content: 0.6307 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: 2go7-3.4-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: 2go7-3.4-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 3.400 Wilson plot Bfac: 66.73 16795 reflections ( 99.81 % complete ) and 0 restraints for refining 7353 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3530 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3104 (Rfree = 0.000) for 7353 atoms. Found 55 (55 requested) and removed 40 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 7532 seeds are put forward NCS extension: 0 residues added, 7532 seeds are put forward Round 1: 388 peptides, 69 chains. Longest chain 16 peptides. Score 0.344 Round 2: 516 peptides, 68 chains. Longest chain 18 peptides. Score 0.514 Round 3: 572 peptides, 71 chains. Longest chain 19 peptides. Score 0.561 Round 4: 557 peptides, 65 chains. Longest chain 21 peptides. Score 0.574 Round 5: 553 peptides, 66 chains. Longest chain 30 peptides. Score 0.565 Taking the results from Round 4 Chains 71, Residues 492, Estimated correctness of the model 20.0 % 9 chains (87 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12024 restraints for refining 6023 atoms. 9803 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2744 (Rfree = 0.000) for 6023 atoms. Found 45 (45 requested) and removed 95 (22 requested) atoms. Cycle 2: After refmac, R = 0.2480 (Rfree = 0.000) for 5855 atoms. Found 39 (45 requested) and removed 50 (22 requested) atoms. Cycle 3: After refmac, R = 0.2341 (Rfree = 0.000) for 5791 atoms. Found 26 (44 requested) and removed 26 (22 requested) atoms. Cycle 4: After refmac, R = 0.2225 (Rfree = 0.000) for 5780 atoms. Found 11 (43 requested) and removed 29 (21 requested) atoms. Cycle 5: After refmac, R = 0.2180 (Rfree = 0.000) for 5751 atoms. Found 12 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 2.71 Search for helices and strands: 0 residues in 0 chains, 5983 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 6001 seeds are put forward Round 1: 506 peptides, 72 chains. Longest chain 16 peptides. Score 0.481 Round 2: 540 peptides, 62 chains. Longest chain 26 peptides. Score 0.571 Round 3: 547 peptides, 63 chains. Longest chain 21 peptides. Score 0.574 Round 4: 547 peptides, 58 chains. Longest chain 23 peptides. Score 0.597 Round 5: 545 peptides, 62 chains. Longest chain 20 peptides. Score 0.576 Taking the results from Round 4 Chains 64, Residues 489, Estimated correctness of the model 27.7 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12328 restraints for refining 6022 atoms. 10214 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2499 (Rfree = 0.000) for 6022 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. Cycle 7: After refmac, R = 0.2299 (Rfree = 0.000) for 5963 atoms. Found 29 (45 requested) and removed 39 (22 requested) atoms. Cycle 8: After refmac, R = 0.2194 (Rfree = 0.000) for 5926 atoms. Found 16 (44 requested) and removed 32 (22 requested) atoms. Cycle 9: After refmac, R = 0.2137 (Rfree = 0.000) for 5897 atoms. Found 11 (44 requested) and removed 29 (22 requested) atoms. Cycle 10: After refmac, R = 0.2111 (Rfree = 0.000) for 5868 atoms. Found 10 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 2.74 Search for helices and strands: 0 residues in 0 chains, 6096 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 6112 seeds are put forward Round 1: 498 peptides, 74 chains. Longest chain 16 peptides. Score 0.461 Round 2: 545 peptides, 62 chains. Longest chain 24 peptides. Score 0.576 Round 3: 543 peptides, 64 chains. Longest chain 29 peptides. Score 0.564 Round 4: 551 peptides, 63 chains. Longest chain 25 peptides. Score 0.578 Round 5: 532 peptides, 62 chains. Longest chain 19 peptides. Score 0.563 Taking the results from Round 4 Chains 67, Residues 488, Estimated correctness of the model 21.3 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12500 restraints for refining 6019 atoms. 10470 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2409 (Rfree = 0.000) for 6019 atoms. Found 45 (45 requested) and removed 47 (22 requested) atoms. Cycle 12: After refmac, R = 0.2183 (Rfree = 0.000) for 5980 atoms. Found 31 (45 requested) and removed 38 (22 requested) atoms. Cycle 13: After refmac, R = 0.2111 (Rfree = 0.000) for 5959 atoms. Found 14 (45 requested) and removed 32 (22 requested) atoms. Cycle 14: After refmac, R = 0.2089 (Rfree = 0.000) for 5931 atoms. Found 14 (44 requested) and removed 28 (22 requested) atoms. Cycle 15: After refmac, R = 0.2071 (Rfree = 0.000) for 5917 atoms. Found 14 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 6162 seeds are put forward NCS extension: 22 residues added (12 deleted due to clashes), 6184 seeds are put forward Round 1: 492 peptides, 77 chains. Longest chain 15 peptides. Score 0.437 Round 2: 534 peptides, 62 chains. Longest chain 21 peptides. Score 0.565 Round 3: 547 peptides, 64 chains. Longest chain 21 peptides. Score 0.569 Round 4: 549 peptides, 67 chains. Longest chain 29 peptides. Score 0.556 Round 5: 538 peptides, 67 chains. Longest chain 22 peptides. Score 0.544 Taking the results from Round 3 Chains 66, Residues 483, Estimated correctness of the model 18.2 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12867 restraints for refining 6022 atoms. 10947 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2414 (Rfree = 0.000) for 6022 atoms. Found 45 (45 requested) and removed 53 (22 requested) atoms. Cycle 17: After refmac, R = 0.2179 (Rfree = 0.000) for 5998 atoms. Found 27 (45 requested) and removed 29 (22 requested) atoms. Cycle 18: After refmac, R = 0.2110 (Rfree = 0.000) for 5984 atoms. Found 13 (45 requested) and removed 31 (22 requested) atoms. Cycle 19: After refmac, R = 0.2079 (Rfree = 0.000) for 5959 atoms. Found 15 (45 requested) and removed 29 (22 requested) atoms. Cycle 20: After refmac, R = 0.2069 (Rfree = 0.000) for 5944 atoms. Found 19 (44 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 2.72 Search for helices and strands: 0 residues in 0 chains, 6163 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 6176 seeds are put forward Round 1: 510 peptides, 76 chains. Longest chain 18 peptides. Score 0.465 Round 2: 540 peptides, 62 chains. Longest chain 28 peptides. Score 0.571 Round 3: 558 peptides, 69 chains. Longest chain 21 peptides. Score 0.556 Round 4: 559 peptides, 65 chains. Longest chain 25 peptides. Score 0.576 Round 5: 536 peptides, 66 chains. Longest chain 23 peptides. Score 0.547 Taking the results from Round 4 Chains 66, Residues 494, Estimated correctness of the model 20.7 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12679 restraints for refining 6022 atoms. 10686 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2416 (Rfree = 0.000) for 6022 atoms. Found 45 (45 requested) and removed 37 (22 requested) atoms. Cycle 22: After refmac, R = 0.2229 (Rfree = 0.000) for 6006 atoms. Found 16 (45 requested) and removed 30 (22 requested) atoms. Cycle 23: After refmac, R = 0.2167 (Rfree = 0.000) for 5978 atoms. Found 18 (45 requested) and removed 31 (22 requested) atoms. Cycle 24: After refmac, R = 0.2109 (Rfree = 0.000) for 5952 atoms. Found 13 (45 requested) and removed 23 (22 requested) atoms. Cycle 25: After refmac, R = 0.2088 (Rfree = 0.000) for 5938 atoms. Found 12 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 6168 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6185 seeds are put forward Round 1: 481 peptides, 68 chains. Longest chain 25 peptides. Score 0.473 Round 2: 529 peptides, 69 chains. Longest chain 25 peptides. Score 0.524 Round 3: 514 peptides, 59 chains. Longest chain 30 peptides. Score 0.558 Round 4: 516 peptides, 65 chains. Longest chain 17 peptides. Score 0.530 Round 5: 538 peptides, 67 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 3 Chains 59, Residues 455, Estimated correctness of the model 14.4 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12455 restraints for refining 6022 atoms. 10439 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2402 (Rfree = 0.000) for 6022 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. Cycle 27: After refmac, R = 0.2209 (Rfree = 0.000) for 6011 atoms. Found 31 (45 requested) and removed 31 (22 requested) atoms. Cycle 28: After refmac, R = 0.2137 (Rfree = 0.000) for 5999 atoms. Found 14 (45 requested) and removed 26 (22 requested) atoms. Cycle 29: After refmac, R = 0.2101 (Rfree = 0.000) for 5980 atoms. Found 13 (45 requested) and removed 23 (22 requested) atoms. Cycle 30: After refmac, R = 0.2090 (Rfree = 0.000) for 5965 atoms. Found 11 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 2.75 Search for helices and strands: 0 residues in 0 chains, 6165 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 6180 seeds are put forward Round 1: 467 peptides, 68 chains. Longest chain 18 peptides. Score 0.456 Round 2: 513 peptides, 67 chains. Longest chain 20 peptides. Score 0.516 Round 3: 499 peptides, 59 chains. Longest chain 23 peptides. Score 0.542 Round 4: 516 peptides, 64 chains. Longest chain 23 peptides. Score 0.535 Round 5: 529 peptides, 60 chains. Longest chain 29 peptides. Score 0.569 Taking the results from Round 5 Chains 61, Residues 469, Estimated correctness of the model 18.2 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 12772 restraints for refining 6021 atoms. 10920 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2541 (Rfree = 0.000) for 6021 atoms. Found 45 (45 requested) and removed 33 (22 requested) atoms. Cycle 32: After refmac, R = 0.2297 (Rfree = 0.000) for 6021 atoms. Found 16 (45 requested) and removed 33 (22 requested) atoms. Cycle 33: After refmac, R = 0.2235 (Rfree = 0.000) for 6002 atoms. Found 17 (45 requested) and removed 30 (22 requested) atoms. Cycle 34: After refmac, R = 0.2184 (Rfree = 0.000) for 5985 atoms. Found 11 (45 requested) and removed 28 (22 requested) atoms. Cycle 35: After refmac, R = 0.2170 (Rfree = 0.000) for 5964 atoms. Found 17 (45 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 2.76 Search for helices and strands: 0 residues in 0 chains, 6211 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 6222 seeds are put forward Round 1: 463 peptides, 70 chains. Longest chain 21 peptides. Score 0.439 Round 2: 497 peptides, 64 chains. Longest chain 25 peptides. Score 0.514 Round 3: 491 peptides, 62 chains. Longest chain 26 peptides. Score 0.517 Round 4: 490 peptides, 61 chains. Longest chain 22 peptides. Score 0.521 Round 5: 474 peptides, 59 chains. Longest chain 20 peptides. Score 0.513 Taking the results from Round 4 Chains 61, Residues 429, Estimated correctness of the model 0.8 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 13279 restraints for refining 6022 atoms. 11599 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2313 (Rfree = 0.000) for 6022 atoms. Found 45 (45 requested) and removed 32 (22 requested) atoms. Cycle 37: After refmac, R = 0.2170 (Rfree = 0.000) for 6020 atoms. Found 23 (45 requested) and removed 29 (22 requested) atoms. Cycle 38: After refmac, R = 0.2111 (Rfree = 0.000) for 6010 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. Cycle 39: After refmac, R = 0.2076 (Rfree = 0.000) for 5992 atoms. Found 14 (45 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.2055 (Rfree = 0.000) for 5979 atoms. Found 11 (45 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 2.72 Search for helices and strands: 0 residues in 0 chains, 6194 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 6206 seeds are put forward Round 1: 443 peptides, 74 chains. Longest chain 16 peptides. Score 0.390 Round 2: 485 peptides, 65 chains. Longest chain 22 peptides. Score 0.494 Round 3: 476 peptides, 62 chains. Longest chain 21 peptides. Score 0.500 Round 4: 477 peptides, 62 chains. Longest chain 26 peptides. Score 0.501 Round 5: 481 peptides, 61 chains. Longest chain 26 peptides. Score 0.511 Taking the results from Round 5 Chains 61, Residues 420, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 16795 reflections ( 99.81 % complete ) and 13281 restraints for refining 6023 atoms. 11622 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2321 (Rfree = 0.000) for 6023 atoms. Found 44 (45 requested) and removed 29 (22 requested) atoms. Cycle 42: After refmac, R = 0.2177 (Rfree = 0.000) for 6018 atoms. Found 17 (45 requested) and removed 25 (22 requested) atoms. Cycle 43: After refmac, R = 0.2137 (Rfree = 0.000) for 6004 atoms. Found 10 (45 requested) and removed 25 (22 requested) atoms. Cycle 44: After refmac, R = 0.2134 (Rfree = 0.000) for 5982 atoms. Found 9 (45 requested) and removed 24 (22 requested) atoms. Cycle 45: After refmac, R = 0.2127 (Rfree = 0.000) for 5964 atoms. Found 10 (45 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 2.74 Search for helices and strands: 0 residues in 0 chains, 6180 seeds are put forward NCS extension: 22 residues added (8 deleted due to clashes), 6202 seeds are put forward Round 1: 410 peptides, 71 chains. Longest chain 14 peptides. Score 0.363 Round 2: 465 peptides, 66 chains. Longest chain 24 peptides. Score 0.464 Round 3: 472 peptides, 60 chains. Longest chain 26 peptides. Score 0.506 Round 4: 475 peptides, 61 chains. Longest chain 21 peptides. Score 0.504 Round 5: 465 peptides, 65 chains. Longest chain 21 peptides. Score 0.470 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 412, 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. 16795 reflections ( 99.81 % complete ) and 13436 restraints for refining 6023 atoms. 11848 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2340 (Rfree = 0.000) for 6023 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2232 (Rfree = 0.000) for 5992 atoms. Found 0 (45 requested) and removed 13 (22 requested) atoms. Cycle 48: After refmac, R = 0.2173 (Rfree = 0.000) for 5974 atoms. Found 0 (45 requested) and removed 10 (22 requested) atoms. Cycle 49: After refmac, R = 0.2181 (Rfree = 0.000) for 5961 atoms. Found 0 (45 requested) and removed 11 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:47:29 GMT 2018 Job finished. TimeTaking 84.66 Used memory is bytes: 4111936