Sun 23 Dec 22:22:49 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 1vky-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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/1vky-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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/1vky-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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 727 and 0 Target number of residues in the AU: 727 Target solvent content: 0.5922 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 5552 target number of atoms Had to go as low as 0.75 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: 41.380 3.400 Wilson plot Bfac: 49.39 13613 reflections ( 99.72 % complete ) and 0 restraints for refining 6140 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3221 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2760 (Rfree = 0.000) for 6140 atoms. Found 46 (46 requested) and removed 89 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.01 2.59 Search for helices and strands: 0 residues in 0 chains, 6188 seeds are put forward NCS extension: 0 residues added, 6188 seeds are put forward Round 1: 342 peptides, 54 chains. Longest chain 15 peptides. Score 0.411 Round 2: 374 peptides, 51 chains. Longest chain 22 peptides. Score 0.484 Round 3: 394 peptides, 51 chains. Longest chain 24 peptides. Score 0.514 Round 4: 410 peptides, 50 chains. Longest chain 25 peptides. Score 0.543 Round 5: 411 peptides, 52 chains. Longest chain 25 peptides. Score 0.532 Taking the results from Round 4 Chains 52, Residues 360, Estimated correctness of the model 9.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 11011 restraints for refining 5047 atoms. 9538 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2533 (Rfree = 0.000) for 5047 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 2: After refmac, R = 0.2318 (Rfree = 0.000) for 5017 atoms. Found 25 (38 requested) and removed 29 (19 requested) atoms. Cycle 3: After refmac, R = 0.2250 (Rfree = 0.000) for 5000 atoms. Found 19 (37 requested) and removed 34 (18 requested) atoms. Cycle 4: After refmac, R = 0.2172 (Rfree = 0.000) for 4976 atoms. Found 12 (37 requested) and removed 30 (18 requested) atoms. Cycle 5: After refmac, R = 0.2154 (Rfree = 0.000) for 4948 atoms. Found 14 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.97 2.56 Search for helices and strands: 0 residues in 0 chains, 5090 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 5118 seeds are put forward Round 1: 377 peptides, 57 chains. Longest chain 22 peptides. Score 0.446 Round 2: 428 peptides, 54 chains. Longest chain 24 peptides. Score 0.543 Round 3: 412 peptides, 50 chains. Longest chain 25 peptides. Score 0.546 Round 4: 413 peptides, 52 chains. Longest chain 18 peptides. Score 0.535 Round 5: 415 peptides, 52 chains. Longest chain 30 peptides. Score 0.537 Taking the results from Round 3 Chains 53, Residues 362, Estimated correctness of the model 10.1 % 5 chains (68 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10327 restraints for refining 5048 atoms. 8656 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2528 (Rfree = 0.000) for 5048 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 7: After refmac, R = 0.2371 (Rfree = 0.000) for 5018 atoms. Found 31 (38 requested) and removed 37 (19 requested) atoms. Cycle 8: After refmac, R = 0.2206 (Rfree = 0.000) for 4987 atoms. Found 17 (37 requested) and removed 46 (18 requested) atoms. Cycle 9: After refmac, R = 0.2195 (Rfree = 0.000) for 4947 atoms. Found 21 (37 requested) and removed 30 (18 requested) atoms. Cycle 10: After refmac, R = 0.2090 (Rfree = 0.000) for 4932 atoms. Found 14 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 2.61 Search for helices and strands: 0 residues in 0 chains, 5027 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 5040 seeds are put forward Round 1: 360 peptides, 55 chains. Longest chain 35 peptides. Score 0.433 Round 2: 411 peptides, 57 chains. Longest chain 23 peptides. Score 0.499 Round 3: 386 peptides, 49 chains. Longest chain 24 peptides. Score 0.515 Round 4: 390 peptides, 48 chains. Longest chain 27 peptides. Score 0.528 Round 5: 416 peptides, 50 chains. Longest chain 26 peptides. Score 0.552 Taking the results from Round 5 Chains 54, Residues 366, Estimated correctness of the model 12.2 % 5 chains (72 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10072 restraints for refining 5048 atoms. 8339 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2592 (Rfree = 0.000) for 5048 atoms. Found 38 (38 requested) and removed 46 (19 requested) atoms. Cycle 12: After refmac, R = 0.2381 (Rfree = 0.000) for 5006 atoms. Found 38 (38 requested) and removed 34 (19 requested) atoms. Cycle 13: After refmac, R = 0.2309 (Rfree = 0.000) for 4997 atoms. Found 26 (37 requested) and removed 27 (18 requested) atoms. Cycle 14: After refmac, R = 0.2285 (Rfree = 0.000) for 4985 atoms. Found 23 (37 requested) and removed 30 (18 requested) atoms. Cycle 15: After refmac, R = 0.2255 (Rfree = 0.000) for 4970 atoms. Found 22 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.02 2.60 Search for helices and strands: 0 residues in 0 chains, 5092 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 5131 seeds are put forward Round 1: 386 peptides, 55 chains. Longest chain 22 peptides. Score 0.474 Round 2: 415 peptides, 49 chains. Longest chain 26 peptides. Score 0.557 Round 3: 417 peptides, 48 chains. Longest chain 33 peptides. Score 0.566 Round 4: 418 peptides, 53 chains. Longest chain 30 peptides. Score 0.535 Round 5: 421 peptides, 54 chains. Longest chain 32 peptides. Score 0.533 Taking the results from Round 3 Chains 49, Residues 369, Estimated correctness of the model 17.2 % 7 chains (81 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10020 restraints for refining 5049 atoms. 8290 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2499 (Rfree = 0.000) for 5049 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 17: After refmac, R = 0.2376 (Rfree = 0.000) for 5012 atoms. Found 25 (38 requested) and removed 38 (19 requested) atoms. Cycle 18: After refmac, R = 0.2267 (Rfree = 0.000) for 4985 atoms. Found 35 (37 requested) and removed 33 (18 requested) atoms. Cycle 19: After refmac, R = 0.2207 (Rfree = 0.000) for 4973 atoms. Found 24 (37 requested) and removed 28 (18 requested) atoms. Cycle 20: After refmac, R = 0.2038 (Rfree = 0.000) for 4952 atoms. Found 15 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 2.59 Search for helices and strands: 0 residues in 0 chains, 5094 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 5110 seeds are put forward Round 1: 400 peptides, 62 chains. Longest chain 28 peptides. Score 0.448 Round 2: 419 peptides, 49 chains. Longest chain 42 peptides. Score 0.562 Round 3: 422 peptides, 50 chains. Longest chain 39 peptides. Score 0.560 Round 4: 412 peptides, 49 chains. Longest chain 51 peptides. Score 0.552 Round 5: 397 peptides, 49 chains. Longest chain 51 peptides. Score 0.531 Taking the results from Round 2 Failed to save intermediate PDB Chains 55, Residues 370, Estimated correctness of the model 15.8 % 5 chains (68 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13613 reflections ( 99.72 % complete ) and 10241 restraints for refining 5048 atoms. 8525 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2455 (Rfree = 0.000) for 5048 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2323 (Rfree = 0.000) for 5004 atoms. Found 37 (38 requested) and removed 30 (19 requested) atoms. Cycle 23: After refmac, R = 0.2248 (Rfree = 0.000) for 5000 atoms. Found 31 (37 requested) and removed 25 (18 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2194 (Rfree = 0.000) for 5000 atoms. Found 13 (37 requested) and removed 32 (18 requested) atoms. Cycle 25: After refmac, R = 0.2148 (Rfree = 0.000) for 4976 atoms. Found 16 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.98 2.57 Search for helices and strands: 0 residues in 0 chains, 5093 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5111 seeds are put forward Round 1: 362 peptides, 51 chains. Longest chain 24 peptides. Score 0.465 Round 2: 390 peptides, 50 chains. Longest chain 35 peptides. Score 0.515 Round 3: 392 peptides, 50 chains. Longest chain 23 peptides. Score 0.517 Round 4: 363 peptides, 45 chains. Longest chain 28 peptides. Score 0.509 Round 5: 387 peptides, 52 chains. Longest chain 23 peptides. Score 0.497 Taking the results from Round 3 Chains 51, Residues 342, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10727 restraints for refining 5049 atoms. 9273 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2364 (Rfree = 0.000) for 5049 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 27: After refmac, R = 0.2161 (Rfree = 0.000) for 5037 atoms. Found 20 (38 requested) and removed 31 (19 requested) atoms. Cycle 28: After refmac, R = 0.2075 (Rfree = 0.000) for 5017 atoms. Found 13 (37 requested) and removed 21 (18 requested) atoms. Cycle 29: After refmac, R = 0.2036 (Rfree = 0.000) for 5005 atoms. Found 6 (37 requested) and removed 21 (18 requested) atoms. Cycle 30: After refmac, R = 0.2019 (Rfree = 0.000) for 4987 atoms. Found 13 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.04 2.62 Search for helices and strands: 0 residues in 0 chains, 5089 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5106 seeds are put forward Round 1: 349 peptides, 52 chains. Longest chain 23 peptides. Score 0.437 Round 2: 389 peptides, 49 chains. Longest chain 24 peptides. Score 0.520 Round 3: 403 peptides, 51 chains. Longest chain 36 peptides. Score 0.527 Round 4: 395 peptides, 51 chains. Longest chain 20 peptides. Score 0.515 Round 5: 370 peptides, 48 chains. Longest chain 21 peptides. Score 0.498 Taking the results from Round 3 Chains 52, Residues 352, Estimated correctness of the model 3.1 % 1 chains (33 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10665 restraints for refining 5048 atoms. 9177 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2329 (Rfree = 0.000) for 5048 atoms. Found 34 (38 requested) and removed 39 (19 requested) atoms. Cycle 32: After refmac, R = 0.2132 (Rfree = 0.000) for 5029 atoms. Found 14 (38 requested) and removed 29 (19 requested) atoms. Cycle 33: After refmac, R = 0.2066 (Rfree = 0.000) for 5003 atoms. Found 17 (37 requested) and removed 27 (18 requested) atoms. Cycle 34: After refmac, R = 0.2043 (Rfree = 0.000) for 4989 atoms. Found 12 (37 requested) and removed 18 (18 requested) atoms. Cycle 35: After refmac, R = 0.2019 (Rfree = 0.000) for 4976 atoms. Found 9 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 2.61 Search for helices and strands: 0 residues in 0 chains, 5078 seeds are put forward NCS extension: 39 residues added (3 deleted due to clashes), 5117 seeds are put forward Round 1: 360 peptides, 56 chains. Longest chain 39 peptides. Score 0.426 Round 2: 407 peptides, 55 chains. Longest chain 25 peptides. Score 0.506 Round 3: 416 peptides, 57 chains. Longest chain 25 peptides. Score 0.506 Round 4: 396 peptides, 54 chains. Longest chain 20 peptides. Score 0.496 Round 5: 392 peptides, 55 chains. Longest chain 23 peptides. Score 0.484 Taking the results from Round 3 Chains 59, Residues 359, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 10722 restraints for refining 5048 atoms. 9258 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2318 (Rfree = 0.000) for 5048 atoms. Found 38 (38 requested) and removed 32 (19 requested) atoms. Cycle 37: After refmac, R = 0.2115 (Rfree = 0.000) for 5035 atoms. Found 31 (38 requested) and removed 24 (19 requested) atoms. Cycle 38: After refmac, R = 0.2083 (Rfree = 0.000) for 5032 atoms. Found 22 (38 requested) and removed 21 (19 requested) atoms. Cycle 39: After refmac, R = 0.2020 (Rfree = 0.000) for 5021 atoms. Found 17 (38 requested) and removed 22 (19 requested) atoms. Cycle 40: After refmac, R = 0.2006 (Rfree = 0.000) for 5007 atoms. Found 20 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 2.64 Search for helices and strands: 0 residues in 0 chains, 5121 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 5142 seeds are put forward Round 1: 357 peptides, 61 chains. Longest chain 20 peptides. Score 0.384 Round 2: 384 peptides, 53 chains. Longest chain 24 peptides. Score 0.485 Round 3: 402 peptides, 57 chains. Longest chain 21 peptides. Score 0.485 Round 4: 393 peptides, 54 chains. Longest chain 20 peptides. Score 0.492 Round 5: 414 peptides, 49 chains. Longest chain 35 peptides. Score 0.555 Taking the results from Round 5 Chains 54, Residues 365, Estimated correctness of the model 13.3 % 6 chains (93 residues) have been docked in sequence ------------------------------------------------------ 13613 reflections ( 99.72 % complete ) and 9911 restraints for refining 5049 atoms. 8163 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2473 (Rfree = 0.000) for 5049 atoms. Found 38 (38 requested) and removed 40 (19 requested) atoms. Cycle 42: After refmac, R = 0.2331 (Rfree = 0.000) for 5025 atoms. Found 22 (38 requested) and removed 23 (19 requested) atoms. Cycle 43: After refmac, R = 0.2290 (Rfree = 0.000) for 5021 atoms. Found 8 (37 requested) and removed 20 (18 requested) atoms. Cycle 44: After refmac, R = 0.2260 (Rfree = 0.000) for 5002 atoms. Found 5 (37 requested) and removed 20 (18 requested) atoms. Cycle 45: After refmac, R = 0.2251 (Rfree = 0.000) for 4983 atoms. Found 8 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 2.64 Search for helices and strands: 0 residues in 0 chains, 5059 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5084 seeds are put forward Round 1: 355 peptides, 62 chains. Longest chain 24 peptides. Score 0.373 Round 2: 415 peptides, 62 chains. Longest chain 20 peptides. Score 0.471 Round 3: 403 peptides, 59 chains. Longest chain 19 peptides. Score 0.473 Round 4: 413 peptides, 56 chains. Longest chain 24 peptides. Score 0.508 Round 5: 403 peptides, 57 chains. Longest chain 29 peptides. Score 0.487 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 357, Estimated correctness of the model 0.0 % 5 chains (62 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 59 chains (357 residues) following loop building 5 chains (62 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13613 reflections ( 99.72 % complete ) and 10525 restraints for refining 5049 atoms. 8927 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2486 (Rfree = 0.000) for 5049 atoms. Found 0 (38 requested) and removed 15 (19 requested) atoms. Cycle 47: After refmac, R = 0.2427 (Rfree = 0.000) for 5014 atoms. Found 0 (38 requested) and removed 4 (19 requested) atoms. Cycle 48: After refmac, R = 0.2359 (Rfree = 0.000) for 5006 atoms. Found 0 (37 requested) and removed 6 (18 requested) atoms. Cycle 49: After refmac, R = 0.2313 (Rfree = 0.000) for 4995 atoms. TimeTaking 74.65