Mon 24 Dec 07:48:09 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 2go7-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2go7-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2go7-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-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/2go7-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-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 07:48:13 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/2go7-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.2-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 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-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: 2go7-3.2-parrot-noncs.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 Failed to save intermediate PDB 20113 reflections ( 99.84 % complete ) and 0 restraints for refining 7441 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3572 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2979 (Rfree = 0.000) for 7441 atoms. Found 66 (66 requested) and removed 81 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.14 2.63 Search for helices and strands: 0 residues in 0 chains, 7596 seeds are put forward NCS extension: 0 residues added, 7596 seeds are put forward Round 1: 415 peptides, 72 chains. Longest chain 16 peptides. Score 0.364 Round 2: 514 peptides, 73 chains. Longest chain 21 peptides. Score 0.486 Round 3: 508 peptides, 68 chains. Longest chain 25 peptides. Score 0.505 Round 4: 538 peptides, 70 chains. Longest chain 22 peptides. Score 0.529 Round 5: 549 peptides, 65 chains. Longest chain 20 peptides. Score 0.566 Taking the results from Round 5 Chains 65, Residues 484, Estimated correctness of the model 31.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 13034 restraints for refining 6047 atoms. 11163 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2745 (Rfree = 0.000) for 6047 atoms. Found 54 (54 requested) and removed 41 (27 requested) atoms. Cycle 2: After refmac, R = 0.2521 (Rfree = 0.000) for 5976 atoms. Found 38 (54 requested) and removed 37 (27 requested) atoms. Cycle 3: After refmac, R = 0.2404 (Rfree = 0.000) for 5943 atoms. Found 26 (53 requested) and removed 34 (26 requested) atoms. Cycle 4: After refmac, R = 0.2318 (Rfree = 0.000) for 5919 atoms. Found 24 (53 requested) and removed 29 (26 requested) atoms. Cycle 5: After refmac, R = 0.2276 (Rfree = 0.000) for 5894 atoms. Found 22 (53 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 2.60 Search for helices and strands: 0 residues in 0 chains, 6200 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6213 seeds are put forward Round 1: 503 peptides, 77 chains. Longest chain 17 peptides. Score 0.451 Round 2: 535 peptides, 70 chains. Longest chain 21 peptides. Score 0.526 Round 3: 549 peptides, 62 chains. Longest chain 33 peptides. Score 0.580 Round 4: 563 peptides, 63 chains. Longest chain 25 peptides. Score 0.590 Round 5: 565 peptides, 68 chains. Longest chain 24 peptides. Score 0.568 Taking the results from Round 4 Chains 64, Residues 500, Estimated correctness of the model 38.3 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12597 restraints for refining 6048 atoms. 10565 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2646 (Rfree = 0.000) for 6048 atoms. Found 54 (54 requested) and removed 43 (27 requested) atoms. Cycle 7: After refmac, R = 0.2454 (Rfree = 0.000) for 6026 atoms. Found 31 (54 requested) and removed 36 (27 requested) atoms. Cycle 8: After refmac, R = 0.2382 (Rfree = 0.000) for 5994 atoms. Found 30 (54 requested) and removed 41 (27 requested) atoms. Cycle 9: After refmac, R = 0.2395 (Rfree = 0.000) for 5960 atoms. Found 39 (53 requested) and removed 30 (26 requested) atoms. Cycle 10: After refmac, R = 0.2310 (Rfree = 0.000) for 5954 atoms. Found 27 (53 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 2.63 Search for helices and strands: 0 residues in 0 chains, 6185 seeds are put forward NCS extension: 21 residues added (10 deleted due to clashes), 6206 seeds are put forward Round 1: 522 peptides, 80 chains. Longest chain 16 peptides. Score 0.458 Round 2: 544 peptides, 64 chains. Longest chain 22 peptides. Score 0.566 Round 3: 543 peptides, 68 chains. Longest chain 20 peptides. Score 0.545 Round 4: 546 peptides, 64 chains. Longest chain 18 peptides. Score 0.568 Round 5: 555 peptides, 67 chains. Longest chain 22 peptides. Score 0.563 Taking the results from Round 4 Chains 65, Residues 482, Estimated correctness of the model 32.1 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12817 restraints for refining 6048 atoms. 10871 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2586 (Rfree = 0.000) for 6048 atoms. Found 54 (54 requested) and removed 38 (27 requested) atoms. Cycle 12: After refmac, R = 0.2418 (Rfree = 0.000) for 6046 atoms. Found 27 (54 requested) and removed 33 (27 requested) atoms. Cycle 13: After refmac, R = 0.2377 (Rfree = 0.000) for 6026 atoms. Found 26 (54 requested) and removed 27 (27 requested) atoms. Cycle 14: After refmac, R = 0.2303 (Rfree = 0.000) for 6017 atoms. Found 18 (54 requested) and removed 29 (27 requested) atoms. Cycle 15: After refmac, R = 0.2188 (Rfree = 0.000) for 6003 atoms. Found 11 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.11 2.60 Search for helices and strands: 0 residues in 0 chains, 6240 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 6254 seeds are put forward Round 1: 510 peptides, 72 chains. Longest chain 25 peptides. Score 0.486 Round 2: 562 peptides, 66 chains. Longest chain 25 peptides. Score 0.575 Round 3: 557 peptides, 66 chains. Longest chain 25 peptides. Score 0.569 Round 4: 566 peptides, 64 chains. Longest chain 25 peptides. Score 0.588 Round 5: 567 peptides, 67 chains. Longest chain 22 peptides. Score 0.575 Taking the results from Round 4 Chains 67, Residues 502, Estimated correctness of the model 37.8 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12480 restraints for refining 6044 atoms. 10405 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2477 (Rfree = 0.000) for 6044 atoms. Found 53 (54 requested) and removed 28 (27 requested) atoms. Cycle 17: After refmac, R = 0.2324 (Rfree = 0.000) for 6050 atoms. Found 16 (54 requested) and removed 28 (27 requested) atoms. Cycle 18: After refmac, R = 0.2216 (Rfree = 0.000) for 6026 atoms. Found 22 (54 requested) and removed 27 (27 requested) atoms. Cycle 19: After refmac, R = 0.2159 (Rfree = 0.000) for 6013 atoms. Found 14 (54 requested) and removed 27 (27 requested) atoms. Cycle 20: After refmac, R = 0.2093 (Rfree = 0.000) for 5993 atoms. Found 12 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 2.64 Search for helices and strands: 0 residues in 0 chains, 6223 seeds are put forward NCS extension: 23 residues added (7 deleted due to clashes), 6246 seeds are put forward Round 1: 515 peptides, 73 chains. Longest chain 22 peptides. Score 0.487 Round 2: 536 peptides, 63 chains. Longest chain 21 peptides. Score 0.562 Round 3: 545 peptides, 67 chains. Longest chain 25 peptides. Score 0.552 Round 4: 567 peptides, 66 chains. Longest chain 36 peptides. Score 0.580 Round 5: 560 peptides, 64 chains. Longest chain 38 peptides. Score 0.582 Taking the results from Round 5 Chains 70, Residues 496, Estimated correctness of the model 36.1 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12386 restraints for refining 6048 atoms. 10339 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2469 (Rfree = 0.000) for 6048 atoms. Found 54 (54 requested) and removed 36 (27 requested) atoms. Cycle 22: After refmac, R = 0.2296 (Rfree = 0.000) for 6053 atoms. Found 23 (54 requested) and removed 27 (27 requested) atoms. Cycle 23: After refmac, R = 0.2236 (Rfree = 0.000) for 6034 atoms. Found 16 (54 requested) and removed 27 (27 requested) atoms. Cycle 24: After refmac, R = 0.2186 (Rfree = 0.000) for 6015 atoms. Found 7 (54 requested) and removed 27 (27 requested) atoms. Cycle 25: After refmac, R = 0.2163 (Rfree = 0.000) for 5994 atoms. Found 12 (53 requested) and removed 26 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.65 Search for helices and strands: 0 residues in 0 chains, 6236 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 6265 seeds are put forward Round 1: 518 peptides, 76 chains. Longest chain 15 peptides. Score 0.475 Round 2: 559 peptides, 70 chains. Longest chain 38 peptides. Score 0.552 Round 3: 554 peptides, 64 chains. Longest chain 21 peptides. Score 0.576 Round 4: 543 peptides, 62 chains. Longest chain 33 peptides. Score 0.574 Round 5: 551 peptides, 65 chains. Longest chain 34 peptides. Score 0.568 Taking the results from Round 3 Chains 65, Residues 490, Estimated correctness of the model 34.4 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12743 restraints for refining 6048 atoms. 10797 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2489 (Rfree = 0.000) for 6048 atoms. Found 54 (54 requested) and removed 42 (27 requested) atoms. Cycle 27: After refmac, R = 0.2311 (Rfree = 0.000) for 6044 atoms. Found 28 (54 requested) and removed 28 (27 requested) atoms. Cycle 28: After refmac, R = 0.2217 (Rfree = 0.000) for 6035 atoms. Found 18 (54 requested) and removed 27 (27 requested) atoms. Cycle 29: After refmac, R = 0.2169 (Rfree = 0.000) for 6018 atoms. Found 17 (54 requested) and removed 27 (27 requested) atoms. Cycle 30: After refmac, R = 0.2140 (Rfree = 0.000) for 6007 atoms. Found 4 (53 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 2.66 Search for helices and strands: 0 residues in 0 chains, 6211 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 6225 seeds are put forward Round 1: 519 peptides, 81 chains. Longest chain 21 peptides. Score 0.449 Round 2: 546 peptides, 69 chains. Longest chain 26 peptides. Score 0.543 Round 3: 553 peptides, 68 chains. Longest chain 23 peptides. Score 0.555 Round 4: 560 peptides, 71 chains. Longest chain 17 peptides. Score 0.548 Round 5: 568 peptides, 68 chains. Longest chain 26 peptides. Score 0.571 Taking the results from Round 5 Chains 72, Residues 500, Estimated correctness of the model 33.0 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12204 restraints for refining 6048 atoms. 10089 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2590 (Rfree = 0.000) for 6048 atoms. Found 54 (54 requested) and removed 31 (27 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2358 (Rfree = 0.000) for 6051 atoms. Found 34 (54 requested) and removed 29 (27 requested) atoms. Cycle 33: After refmac, R = 0.2244 (Rfree = 0.000) for 6039 atoms. Found 19 (54 requested) and removed 27 (27 requested) atoms. Cycle 34: After refmac, R = 0.2166 (Rfree = 0.000) for 6027 atoms. Found 17 (54 requested) and removed 27 (27 requested) atoms. Cycle 35: After refmac, R = 0.2139 (Rfree = 0.000) for 6013 atoms. Found 6 (54 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 2.64 Search for helices and strands: 0 residues in 0 chains, 6230 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 6242 seeds are put forward Round 1: 509 peptides, 73 chains. Longest chain 20 peptides. Score 0.480 Round 2: 529 peptides, 68 chains. Longest chain 20 peptides. Score 0.529 Round 3: 525 peptides, 65 chains. Longest chain 21 peptides. Score 0.540 Round 4: 546 peptides, 75 chains. Longest chain 26 peptides. Score 0.513 Round 5: 520 peptides, 68 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 3 Chains 65, Residues 460, Estimated correctness of the model 23.9 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12593 restraints for refining 6048 atoms. 10688 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2437 (Rfree = 0.000) for 6048 atoms. Found 44 (54 requested) and removed 31 (27 requested) atoms. Cycle 37: After refmac, R = 0.2274 (Rfree = 0.000) for 6052 atoms. Found 14 (54 requested) and removed 27 (27 requested) atoms. Cycle 38: After refmac, R = 0.2206 (Rfree = 0.000) for 6036 atoms. Found 8 (54 requested) and removed 27 (27 requested) atoms. Cycle 39: After refmac, R = 0.2157 (Rfree = 0.000) for 6012 atoms. Found 9 (54 requested) and removed 27 (27 requested) atoms. Cycle 40: After refmac, R = 0.2129 (Rfree = 0.000) for 5989 atoms. Found 11 (53 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 2.66 Search for helices and strands: 0 residues in 0 chains, 6213 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 6226 seeds are put forward Round 1: 462 peptides, 67 chains. Longest chain 20 peptides. Score 0.455 Round 2: 497 peptides, 64 chains. Longest chain 19 peptides. Score 0.514 Round 3: 513 peptides, 62 chains. Longest chain 18 peptides. Score 0.542 Round 4: 504 peptides, 63 chains. Longest chain 18 peptides. Score 0.527 Round 5: 496 peptides, 63 chains. Longest chain 18 peptides. Score 0.518 Taking the results from Round 3 Chains 63, Residues 451, Estimated correctness of the model 24.5 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 20113 reflections ( 99.84 % complete ) and 12879 restraints for refining 6048 atoms. 11050 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2381 (Rfree = 0.000) for 6048 atoms. Found 39 (54 requested) and removed 30 (27 requested) atoms. Cycle 42: After refmac, R = 0.2229 (Rfree = 0.000) for 6052 atoms. Found 16 (54 requested) and removed 27 (27 requested) atoms. Cycle 43: After refmac, R = 0.2171 (Rfree = 0.000) for 6038 atoms. Found 3 (54 requested) and removed 27 (27 requested) atoms. Cycle 44: After refmac, R = 0.2167 (Rfree = 0.000) for 6013 atoms. Found 9 (53 requested) and removed 26 (26 requested) atoms. Cycle 45: After refmac, R = 0.2164 (Rfree = 0.000) for 5993 atoms. Found 11 (53 requested) and removed 27 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.68 Search for helices and strands: 0 residues in 0 chains, 6187 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 6203 seeds are put forward Round 1: 432 peptides, 65 chains. Longest chain 22 peptides. Score 0.428 Round 2: 491 peptides, 62 chains. Longest chain 17 peptides. Score 0.517 Round 3: 491 peptides, 65 chains. Longest chain 25 peptides. Score 0.501 Round 4: 490 peptides, 61 chains. Longest chain 18 peptides. Score 0.521 Round 5: 481 peptides, 61 chains. Longest chain 24 peptides. Score 0.511 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 429, Estimated correctness of the model 18.0 % 2 chains (22 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2go7-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 94 A and 101 A 60 chains (431 residues) following loop building 1 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20113 reflections ( 99.84 % complete ) and 12914 restraints for refining 6048 atoms. 11186 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2494 (Rfree = 0.000) for 6048 atoms. Found 0 (54 requested) and removed 20 (27 requested) atoms. Cycle 47: After refmac, R = 0.2423 (Rfree = 0.000) for 6021 atoms. Found 0 (54 requested) and removed 9 (27 requested) atoms. Cycle 48: After refmac, R = 0.2380 (Rfree = 0.000) for 6007 atoms. Found 0 (53 requested) and removed 3 (26 requested) atoms. Cycle 49: After refmac, R = 0.2375 (Rfree = 0.000) for 6001 atoms. TimeTaking 66.68