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 1vp4-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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/1vp4-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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 ============================================================ Tue 25 Dec 19:28:07 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/1vp4-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.4-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 700 and 0 Target number of residues in the AU: 700 Target solvent content: 0.6481 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.4-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.80 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: 142.773 3.400 Wilson plot Bfac: 76.86 14842 reflections ( 99.78 % complete ) and 0 restraints for refining 7584 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3481 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3356 (Rfree = 0.000) for 7584 atoms. Found 57 (57 requested) and removed 208 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.03 Search for helices and strands: 0 residues in 0 chains, 7562 seeds are put forward NCS extension: 0 residues added, 7562 seeds are put forward Round 1: 328 peptides, 66 chains. Longest chain 12 peptides. Score 0.284 Round 2: 426 peptides, 72 chains. Longest chain 24 peptides. Score 0.400 Round 3: 466 peptides, 77 chains. Longest chain 16 peptides. Score 0.427 Round 4: 470 peptides, 72 chains. Longest chain 21 peptides. Score 0.463 Round 5: 473 peptides, 69 chains. Longest chain 21 peptides. Score 0.486 Taking the results from Round 5 Chains 73, Residues 404, Estimated correctness of the model 0.0 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13476 restraints for refining 6182 atoms. 11773 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2784 (Rfree = 0.000) for 6182 atoms. Found 32 (46 requested) and removed 67 (23 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2548 (Rfree = 0.000) for 6086 atoms. Found 24 (46 requested) and removed 40 (23 requested) atoms. Cycle 3: After refmac, R = 0.2472 (Rfree = 0.000) for 6054 atoms. Found 13 (45 requested) and removed 31 (22 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2440 (Rfree = 0.000) for 6026 atoms. Found 12 (45 requested) and removed 27 (22 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2404 (Rfree = 0.000) for 6008 atoms. Found 10 (45 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 6221 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6238 seeds are put forward Round 1: 477 peptides, 81 chains. Longest chain 15 peptides. Score 0.418 Round 2: 491 peptides, 67 chains. Longest chain 22 peptides. Score 0.521 Round 3: 507 peptides, 66 chains. Longest chain 20 peptides. Score 0.547 Round 4: 497 peptides, 61 chains. Longest chain 25 peptides. Score 0.562 Round 5: 471 peptides, 61 chains. Longest chain 19 peptides. Score 0.530 Taking the results from Round 4 Chains 63, Residues 436, Estimated correctness of the model 15.8 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14842 reflections ( 99.78 % complete ) and 13349 restraints for refining 6181 atoms. 11488 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2571 (Rfree = 0.000) for 6181 atoms. Found 42 (46 requested) and removed 38 (23 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2404 (Rfree = 0.000) for 6155 atoms. Found 26 (46 requested) and removed 34 (23 requested) atoms. Cycle 8: After refmac, R = 0.2372 (Rfree = 0.000) for 6137 atoms. Found 14 (46 requested) and removed 26 (23 requested) atoms. Cycle 9: After refmac, R = 0.2302 (Rfree = 0.000) for 6116 atoms. Found 13 (46 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2255 (Rfree = 0.000) for 6097 atoms. Found 7 (46 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 6300 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6318 seeds are put forward Round 1: 465 peptides, 75 chains. Longest chain 17 peptides. Score 0.438 Round 2: 511 peptides, 70 chains. Longest chain 22 peptides. Score 0.530 Round 3: 533 peptides, 72 chains. Longest chain 20 peptides. Score 0.546 Round 4: 510 peptides, 65 chains. Longest chain 22 peptides. Score 0.556 Round 5: 507 peptides, 62 chains. Longest chain 21 peptides. Score 0.569 Taking the results from Round 5 Chains 64, Residues 445, Estimated correctness of the model 18.2 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13735 restraints for refining 6181 atoms. 11981 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2434 (Rfree = 0.000) for 6181 atoms. Found 39 (46 requested) and removed 36 (23 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2275 (Rfree = 0.000) for 6162 atoms. Found 21 (46 requested) and removed 28 (23 requested) atoms. Cycle 13: After refmac, R = 0.2207 (Rfree = 0.000) for 6149 atoms. Found 10 (46 requested) and removed 25 (23 requested) atoms. Cycle 14: After refmac, R = 0.2197 (Rfree = 0.000) for 6129 atoms. Found 11 (46 requested) and removed 25 (23 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2170 (Rfree = 0.000) for 6107 atoms. Found 6 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.13 Search for helices and strands: 0 residues in 0 chains, 6359 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 6382 seeds are put forward Round 1: 471 peptides, 71 chains. Longest chain 19 peptides. Score 0.471 Round 2: 502 peptides, 68 chains. Longest chain 19 peptides. Score 0.529 Round 3: 490 peptides, 66 chains. Longest chain 33 peptides. Score 0.526 Round 4: 497 peptides, 62 chains. Longest chain 20 peptides. Score 0.557 Round 5: 513 peptides, 65 chains. Longest chain 21 peptides. Score 0.560 Taking the results from Round 5 Chains 66, Residues 448, Estimated correctness of the model 15.1 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13459 restraints for refining 6182 atoms. 11643 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2414 (Rfree = 0.000) for 6182 atoms. Found 37 (46 requested) and removed 29 (23 requested) atoms. Cycle 17: After refmac, R = 0.2307 (Rfree = 0.000) for 6167 atoms. Found 13 (46 requested) and removed 26 (23 requested) atoms. Cycle 18: After refmac, R = 0.2265 (Rfree = 0.000) for 6141 atoms. Found 9 (46 requested) and removed 26 (23 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2242 (Rfree = 0.000) for 6123 atoms. Found 13 (46 requested) and removed 23 (23 requested) atoms. Cycle 20: After refmac, R = 0.2217 (Rfree = 0.000) for 6108 atoms. Found 6 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 6315 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 6335 seeds are put forward Round 1: 457 peptides, 75 chains. Longest chain 17 peptides. Score 0.426 Round 2: 507 peptides, 71 chains. Longest chain 28 peptides. Score 0.519 Round 3: 509 peptides, 65 chains. Longest chain 24 peptides. Score 0.555 Round 4: 488 peptides, 71 chains. Longest chain 17 peptides. Score 0.494 Round 5: 488 peptides, 68 chains. Longest chain 19 peptides. Score 0.511 Taking the results from Round 3 Chains 71, Residues 444, Estimated correctness of the model 13.3 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14842 reflections ( 99.78 % complete ) and 13368 restraints for refining 6183 atoms. 11479 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2409 (Rfree = 0.000) for 6183 atoms. Found 39 (46 requested) and removed 34 (23 requested) atoms. Cycle 22: After refmac, R = 0.2303 (Rfree = 0.000) for 6158 atoms. Found 17 (46 requested) and removed 31 (23 requested) atoms. Cycle 23: After refmac, R = 0.2257 (Rfree = 0.000) for 6133 atoms. Found 16 (46 requested) and removed 26 (23 requested) atoms. Cycle 24: After refmac, R = 0.2205 (Rfree = 0.000) for 6117 atoms. Found 7 (46 requested) and removed 24 (23 requested) atoms. Cycle 25: After refmac, R = 0.2182 (Rfree = 0.000) for 6095 atoms. Found 7 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 6318 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 6343 seeds are put forward Round 1: 438 peptides, 78 chains. Longest chain 16 peptides. Score 0.379 Round 2: 473 peptides, 69 chains. Longest chain 20 peptides. Score 0.486 Round 3: 468 peptides, 64 chains. Longest chain 27 peptides. Score 0.509 Round 4: 483 peptides, 68 chains. Longest chain 20 peptides. Score 0.505 Round 5: 453 peptides, 65 chains. Longest chain 17 peptides. Score 0.483 Taking the results from Round 3 Chains 66, Residues 404, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13798 restraints for refining 6182 atoms. 12160 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2375 (Rfree = 0.000) for 6182 atoms. Found 40 (46 requested) and removed 35 (23 requested) atoms. Cycle 27: After refmac, R = 0.2246 (Rfree = 0.000) for 6177 atoms. Found 22 (46 requested) and removed 25 (23 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2199 (Rfree = 0.000) for 6168 atoms. Found 14 (46 requested) and removed 23 (23 requested) atoms. Cycle 29: After refmac, R = 0.2160 (Rfree = 0.000) for 6157 atoms. Found 7 (46 requested) and removed 23 (23 requested) atoms. Cycle 30: After refmac, R = 0.2132 (Rfree = 0.000) for 6136 atoms. Found 9 (46 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 6360 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6376 seeds are put forward Round 1: 406 peptides, 73 chains. Longest chain 14 peptides. Score 0.363 Round 2: 429 peptides, 69 chains. Longest chain 21 peptides. Score 0.424 Round 3: 462 peptides, 68 chains. Longest chain 24 peptides. Score 0.477 Round 4: 490 peptides, 69 chains. Longest chain 17 peptides. Score 0.508 Round 5: 463 peptides, 63 chains. Longest chain 19 peptides. Score 0.508 Taking the results from Round 5 Chains 65, Residues 400, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 13933 restraints for refining 6182 atoms. 12350 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2414 (Rfree = 0.000) for 6182 atoms. Found 29 (46 requested) and removed 30 (23 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2269 (Rfree = 0.000) for 6163 atoms. Found 20 (46 requested) and removed 24 (23 requested) atoms. Cycle 33: After refmac, R = 0.2229 (Rfree = 0.000) for 6153 atoms. Found 15 (46 requested) and removed 23 (23 requested) atoms. Cycle 34: After refmac, R = 0.2188 (Rfree = 0.000) for 6139 atoms. Found 7 (46 requested) and removed 23 (23 requested) atoms. Cycle 35: After refmac, R = 0.2151 (Rfree = 0.000) for 6120 atoms. Found 8 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.11 Search for helices and strands: 0 residues in 0 chains, 6338 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 6359 seeds are put forward Round 1: 410 peptides, 76 chains. Longest chain 12 peptides. Score 0.349 Round 2: 456 peptides, 67 chains. Longest chain 18 peptides. Score 0.475 Round 3: 442 peptides, 59 chains. Longest chain 19 peptides. Score 0.504 Round 4: 458 peptides, 69 chains. Longest chain 19 peptides. Score 0.465 Round 5: 462 peptides, 74 chains. Longest chain 19 peptides. Score 0.440 Taking the results from Round 3 Chains 61, Residues 383, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14842 reflections ( 99.78 % complete ) and 14003 restraints for refining 6182 atoms. 12465 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2314 (Rfree = 0.000) for 6182 atoms. Found 32 (46 requested) and removed 35 (23 requested) atoms. Cycle 37: After refmac, R = 0.2209 (Rfree = 0.000) for 6165 atoms. Found 15 (46 requested) and removed 25 (23 requested) atoms. Cycle 38: After refmac, R = 0.2173 (Rfree = 0.000) for 6150 atoms. Found 8 (46 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2155 (Rfree = 0.000) for 6131 atoms. Found 7 (46 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2110 (Rfree = 0.000) for 6110 atoms. Found 9 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 6326 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6345 seeds are put forward Round 1: 390 peptides, 73 chains. Longest chain 15 peptides. Score 0.337 Round 2: 420 peptides, 62 chains. Longest chain 17 peptides. Score 0.455 Round 3: 429 peptides, 65 chains. Longest chain 20 peptides. Score 0.449 Round 4: 431 peptides, 65 chains. Longest chain 20 peptides. Score 0.452 Round 5: 437 peptides, 62 chains. Longest chain 17 peptides. Score 0.479 Taking the results from Round 5 Chains 62, Residues 375, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14842 reflections ( 99.78 % complete ) and 14058 restraints for refining 6183 atoms. 12598 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2349 (Rfree = 0.000) for 6183 atoms. Found 34 (46 requested) and removed 33 (23 requested) atoms. Cycle 42: After refmac, R = 0.2174 (Rfree = 0.000) for 6166 atoms. Found 23 (46 requested) and removed 25 (23 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2150 (Rfree = 0.000) for 6153 atoms. Found 14 (46 requested) and removed 23 (23 requested) atoms. Cycle 44: After refmac, R = 0.2117 (Rfree = 0.000) for 6139 atoms. Found 6 (46 requested) and removed 23 (23 requested) atoms. Cycle 45: After refmac, R = 0.2117 (Rfree = 0.000) for 6119 atoms. Found 2 (46 requested) and removed 23 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 6338 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6357 seeds are put forward Round 1: 349 peptides, 65 chains. Longest chain 12 peptides. Score 0.326 Round 2: 420 peptides, 63 chains. Longest chain 16 peptides. Score 0.449 Round 3: 419 peptides, 59 chains. Longest chain 16 peptides. Score 0.473 Round 4: 429 peptides, 60 chains. Longest chain 19 peptides. Score 0.480 Round 5: 415 peptides, 62 chains. Longest chain 15 peptides. Score 0.448 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 369, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input Building loops using Loopy2018 63 chains (369 residues) following loop building 3 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14842 reflections ( 99.78 % complete ) and 13824 restraints for refining 6182 atoms. 12339 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2319 (Rfree = 0.000) for 6182 atoms. Found 0 (46 requested) and removed 22 (23 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2252 (Rfree = 0.000) for 6148 atoms. Found 0 (46 requested) and removed 11 (23 requested) atoms. Cycle 48: After refmac, R = 0.2241 (Rfree = 0.000) for 6133 atoms. Found 0 (46 requested) and removed 8 (23 requested) atoms. Cycle 49: After refmac, R = 0.2238 (Rfree = 0.000) for 6117 atoms. Found 0 (46 requested) and removed 7 (23 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 98.93