null Sun 23 Dec 22:22:56 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vky-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vky-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-4.0-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 22:23:05 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-4.0-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 666 and 0 Target number of residues in the AU: 666 Target solvent content: 0.6264 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5552 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: 41.380 4.000 Wilson plot Bfac: 64.68 8439 reflections ( 99.70 % complete ) and 0 restraints for refining 6120 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3325 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3295 (Rfree = 0.000) for 6120 atoms. Found 29 (29 requested) and removed 51 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 6209 seeds are put forward NCS extension: 0 residues added, 6209 seeds are put forward Round 1: 290 peptides, 47 chains. Longest chain 15 peptides. Score 0.374 Round 2: 351 peptides, 48 chains. Longest chain 29 peptides. Score 0.469 Round 3: 379 peptides, 52 chains. Longest chain 22 peptides. Score 0.484 Round 4: 364 peptides, 48 chains. Longest chain 21 peptides. Score 0.489 Round 5: 368 peptides, 44 chains. Longest chain 25 peptides. Score 0.523 Taking the results from Round 5 Chains 44, Residues 324, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11573 restraints for refining 5011 atoms. 10308 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2641 (Rfree = 0.000) for 5011 atoms. Found 23 (23 requested) and removed 50 (11 requested) atoms. Cycle 2: After refmac, R = 0.2549 (Rfree = 0.000) for 4880 atoms. Found 23 (23 requested) and removed 49 (11 requested) atoms. Cycle 3: After refmac, R = 0.2361 (Rfree = 0.000) for 4788 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 4: After refmac, R = 0.2198 (Rfree = 0.000) for 4753 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 5: After refmac, R = 0.2299 (Rfree = 0.000) for 4711 atoms. Found 22 (22 requested) and removed 46 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 2.93 Search for helices and strands: 0 residues in 0 chains, 4810 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 4833 seeds are put forward Round 1: 341 peptides, 56 chains. Longest chain 20 peptides. Score 0.394 Round 2: 380 peptides, 48 chains. Longest chain 25 peptides. Score 0.513 Round 3: 373 peptides, 46 chains. Longest chain 25 peptides. Score 0.517 Round 4: 364 peptides, 42 chains. Longest chain 25 peptides. Score 0.531 Round 5: 370 peptides, 41 chains. Longest chain 25 peptides. Score 0.546 Taking the results from Round 5 Chains 45, Residues 329, Estimated correctness of the model 0.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 10882 restraints for refining 5012 atoms. 9442 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2424 (Rfree = 0.000) for 5012 atoms. Found 23 (23 requested) and removed 70 (11 requested) atoms. Cycle 7: After refmac, R = 0.2282 (Rfree = 0.000) for 4915 atoms. Found 23 (23 requested) and removed 48 (11 requested) atoms. Cycle 8: After refmac, R = 0.2246 (Rfree = 0.000) for 4861 atoms. Found 23 (23 requested) and removed 51 (11 requested) atoms. Cycle 9: After refmac, R = 0.2172 (Rfree = 0.000) for 4806 atoms. Found 22 (22 requested) and removed 46 (11 requested) atoms. Cycle 10: After refmac, R = 0.2147 (Rfree = 0.000) for 4764 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 2.95 Search for helices and strands: 0 residues in 0 chains, 4878 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 4908 seeds are put forward Round 1: 338 peptides, 48 chains. Longest chain 18 peptides. Score 0.448 Round 2: 357 peptides, 50 chains. Longest chain 15 peptides. Score 0.464 Round 3: 361 peptides, 45 chains. Longest chain 17 peptides. Score 0.506 Round 4: 369 peptides, 45 chains. Longest chain 18 peptides. Score 0.517 Round 5: 368 peptides, 46 chains. Longest chain 21 peptides. Score 0.509 Taking the results from Round 4 Chains 45, Residues 324, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11370 restraints for refining 5012 atoms. 10087 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2307 (Rfree = 0.000) for 5012 atoms. Found 23 (23 requested) and removed 50 (11 requested) atoms. Cycle 12: After refmac, R = 0.2335 (Rfree = 0.000) for 4922 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 13: After refmac, R = 0.2148 (Rfree = 0.000) for 4862 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 14: After refmac, R = 0.2210 (Rfree = 0.000) for 4828 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Cycle 15: After refmac, R = 0.1883 (Rfree = 0.000) for 4803 atoms. Found 10 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.00 Search for helices and strands: 0 residues in 0 chains, 4911 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4935 seeds are put forward Round 1: 325 peptides, 52 chains. Longest chain 15 peptides. Score 0.397 Round 2: 372 peptides, 51 chains. Longest chain 20 peptides. Score 0.481 Round 3: 358 peptides, 46 chains. Longest chain 26 peptides. Score 0.494 Round 4: 377 peptides, 55 chains. Longest chain 19 peptides. Score 0.460 Round 5: 349 peptides, 46 chains. Longest chain 21 peptides. Score 0.480 Taking the results from Round 3 Chains 47, Residues 312, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11409 restraints for refining 5011 atoms. 10172 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2335 (Rfree = 0.000) for 5011 atoms. Found 23 (23 requested) and removed 44 (11 requested) atoms. Cycle 17: After refmac, R = 0.2251 (Rfree = 0.000) for 4950 atoms. Found 23 (23 requested) and removed 44 (11 requested) atoms. Cycle 18: After refmac, R = 0.2176 (Rfree = 0.000) for 4911 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 19: After refmac, R = 0.2128 (Rfree = 0.000) for 4880 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 20: After refmac, R = 0.2086 (Rfree = 0.000) for 4861 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 2.98 Search for helices and strands: 0 residues in 0 chains, 4988 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 5003 seeds are put forward Round 1: 309 peptides, 54 chains. Longest chain 12 peptides. Score 0.353 Round 2: 350 peptides, 49 chains. Longest chain 25 peptides. Score 0.460 Round 3: 352 peptides, 52 chains. Longest chain 16 peptides. Score 0.442 Round 4: 367 peptides, 49 chains. Longest chain 18 peptides. Score 0.487 Round 5: 374 peptides, 51 chains. Longest chain 26 peptides. Score 0.484 Taking the results from Round 4 Chains 49, Residues 318, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11551 restraints for refining 5013 atoms. 10328 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2321 (Rfree = 0.000) for 5013 atoms. Found 23 (23 requested) and removed 45 (11 requested) atoms. Cycle 22: After refmac, R = 0.2243 (Rfree = 0.000) for 4945 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 23: After refmac, R = 0.2277 (Rfree = 0.000) for 4910 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 24: After refmac, R = 0.2071 (Rfree = 0.000) for 4871 atoms. Found 17 (23 requested) and removed 23 (11 requested) atoms. Cycle 25: After refmac, R = 0.1871 (Rfree = 0.000) for 4847 atoms. Found 5 (23 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 2.98 Search for helices and strands: 0 residues in 0 chains, 4991 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5007 seeds are put forward Round 1: 321 peptides, 58 chains. Longest chain 12 peptides. Score 0.343 Round 2: 346 peptides, 47 chains. Longest chain 19 peptides. Score 0.468 Round 3: 354 peptides, 52 chains. Longest chain 15 peptides. Score 0.445 Round 4: 354 peptides, 50 chains. Longest chain 18 peptides. Score 0.460 Round 5: 358 peptides, 51 chains. Longest chain 15 peptides. Score 0.459 Taking the results from Round 2 Chains 47, Residues 299, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11011 restraints for refining 4964 atoms. 9849 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2143 (Rfree = 0.000) for 4964 atoms. Found 23 (23 requested) and removed 55 (11 requested) atoms. Cycle 27: After refmac, R = 0.2067 (Rfree = 0.000) for 4895 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 28: After refmac, R = 0.1957 (Rfree = 0.000) for 4856 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 29: After refmac, R = 0.1977 (Rfree = 0.000) for 4827 atoms. Found 23 (23 requested) and removed 23 (11 requested) atoms. Cycle 30: After refmac, R = 0.1660 (Rfree = 0.000) for 4814 atoms. Found 7 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 2.96 Search for helices and strands: 0 residues in 0 chains, 4954 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 4982 seeds are put forward Round 1: 303 peptides, 55 chains. Longest chain 15 peptides. Score 0.334 Round 2: 340 peptides, 48 chains. Longest chain 20 peptides. Score 0.452 Round 3: 348 peptides, 51 chains. Longest chain 15 peptides. Score 0.443 Round 4: 367 peptides, 50 chains. Longest chain 36 peptides. Score 0.480 Round 5: 380 peptides, 49 chains. Longest chain 21 peptides. Score 0.506 Taking the results from Round 5 Chains 51, Residues 331, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 10707 restraints for refining 5013 atoms. 9346 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2358 (Rfree = 0.000) for 5013 atoms. Found 23 (23 requested) and removed 50 (11 requested) atoms. Cycle 32: After refmac, R = 0.2075 (Rfree = 0.000) for 4926 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 33: After refmac, R = 0.2046 (Rfree = 0.000) for 4876 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 34: After refmac, R = 0.1966 (Rfree = 0.000) for 4855 atoms. Found 17 (23 requested) and removed 35 (11 requested) atoms. Cycle 35: After refmac, R = 0.1993 (Rfree = 0.000) for 4819 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 2.90 Search for helices and strands: 0 residues in 0 chains, 4940 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 4959 seeds are put forward Round 1: 320 peptides, 56 chains. Longest chain 13 peptides. Score 0.357 Round 2: 342 peptides, 47 chains. Longest chain 17 peptides. Score 0.462 Round 3: 340 peptides, 52 chains. Longest chain 15 peptides. Score 0.422 Round 4: 355 peptides, 51 chains. Longest chain 18 peptides. Score 0.454 Round 5: 347 peptides, 47 chains. Longest chain 20 peptides. Score 0.470 Taking the results from Round 5 Chains 47, Residues 300, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11363 restraints for refining 5012 atoms. 10210 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2465 (Rfree = 0.000) for 5012 atoms. Found 23 (23 requested) and removed 49 (11 requested) atoms. Cycle 37: After refmac, R = 0.2284 (Rfree = 0.000) for 4937 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 38: After refmac, R = 0.2220 (Rfree = 0.000) for 4901 atoms. Found 23 (23 requested) and removed 45 (11 requested) atoms. Cycle 39: After refmac, R = 0.2228 (Rfree = 0.000) for 4867 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Cycle 40: After refmac, R = 0.2092 (Rfree = 0.000) for 4841 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.04 Search for helices and strands: 0 residues in 0 chains, 4976 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4996 seeds are put forward Round 1: 292 peptides, 58 chains. Longest chain 11 peptides. Score 0.290 Round 2: 329 peptides, 53 chains. Longest chain 18 peptides. Score 0.396 Round 3: 325 peptides, 51 chains. Longest chain 15 peptides. Score 0.404 Round 4: 336 peptides, 46 chains. Longest chain 15 peptides. Score 0.460 Round 5: 331 peptides, 46 chains. Longest chain 21 peptides. Score 0.452 Taking the results from Round 4 Chains 47, Residues 290, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8439 reflections ( 99.70 % complete ) and 11153 restraints for refining 5013 atoms. 10007 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2350 (Rfree = 0.000) for 5013 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 42: After refmac, R = 0.2232 (Rfree = 0.000) for 4962 atoms. Found 23 (23 requested) and removed 34 (11 requested) atoms. Cycle 43: After refmac, R = 0.2169 (Rfree = 0.000) for 4919 atoms. Found 23 (23 requested) and removed 33 (11 requested) atoms. Cycle 44: After refmac, R = 0.2097 (Rfree = 0.000) for 4890 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 45: After refmac, R = 0.2073 (Rfree = 0.000) for 4862 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 2.96 Search for helices and strands: 0 residues in 0 chains, 4970 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4985 seeds are put forward Round 1: 274 peptides, 51 chains. Longest chain 11 peptides. Score 0.312 Round 2: 311 peptides, 48 chains. Longest chain 16 peptides. Score 0.403 Round 3: 321 peptides, 49 chains. Longest chain 14 peptides. Score 0.413 Round 4: 310 peptides, 48 chains. Longest chain 14 peptides. Score 0.402 Round 5: 306 peptides, 47 chains. Longest chain 18 peptides. Score 0.402 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 272, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vky-4_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (272 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8439 reflections ( 99.70 % complete ) and 11225 restraints for refining 5012 atoms. 10133 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2257 (Rfree = 0.000) for 5012 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2165 (Rfree = 0.000) for 4962 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2159 (Rfree = 0.000) for 4929 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2159 (Rfree = 0.000) for 4899 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:35:34 GMT 2018 Job finished. TimeTaking 72.64 Used memory is bytes: 7640312