null Mon 24 Dec 07:27:23 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 1vll-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vll-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vll-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-4.0-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/1vll-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-4.0-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 07:27:28 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/1vll-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-4.0-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6989 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-4.0-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: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5344 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: 76.441 4.000 Wilson plot Bfac: 121.02 6431 reflections ( 99.95 % complete ) and 0 restraints for refining 5945 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3844 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3601 (Rfree = 0.000) for 5945 atoms. Found 28 (28 requested) and removed 41 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.18 4.24 Search for helices and strands: 0 residues in 0 chains, 6052 seeds are put forward NCS extension: 0 residues added, 6052 seeds are put forward Round 1: 208 peptides, 44 chains. Longest chain 8 peptides. Score 0.257 Round 2: 268 peptides, 48 chains. Longest chain 10 peptides. Score 0.364 Round 3: 282 peptides, 50 chains. Longest chain 13 peptides. Score 0.377 Round 4: 294 peptides, 47 chains. Longest chain 12 peptides. Score 0.433 Round 5: 301 peptides, 44 chains. Longest chain 19 peptides. Score 0.476 Taking the results from Round 5 Chains 44, Residues 257, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11919 restraints for refining 4823 atoms. 10892 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2966 (Rfree = 0.000) for 4823 atoms. Found 8 (22 requested) and removed 28 (11 requested) atoms. Cycle 2: After refmac, R = 0.2732 (Rfree = 0.000) for 4731 atoms. Found 10 (22 requested) and removed 30 (11 requested) atoms. Cycle 3: After refmac, R = 0.2581 (Rfree = 0.000) for 4654 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 4: After refmac, R = 0.2465 (Rfree = 0.000) for 4613 atoms. Found 14 (22 requested) and removed 31 (11 requested) atoms. Cycle 5: After refmac, R = 0.2591 (Rfree = 0.000) for 4574 atoms. Found 16 (21 requested) and removed 39 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.09 4.14 Search for helices and strands: 0 residues in 0 chains, 4775 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4790 seeds are put forward Round 1: 230 peptides, 44 chains. Longest chain 14 peptides. Score 0.314 Round 2: 266 peptides, 45 chains. Longest chain 13 peptides. Score 0.390 Round 3: 270 peptides, 45 chains. Longest chain 15 peptides. Score 0.399 Round 4: 294 peptides, 45 chains. Longest chain 20 peptides. Score 0.452 Round 5: 274 peptides, 37 chains. Longest chain 20 peptides. Score 0.486 Taking the results from Round 5 Chains 37, Residues 237, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11304 restraints for refining 4826 atoms. 10266 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2393 (Rfree = 0.000) for 4826 atoms. Found 10 (22 requested) and removed 50 (11 requested) atoms. Cycle 7: After refmac, R = 0.2393 (Rfree = 0.000) for 4740 atoms. Found 9 (22 requested) and removed 42 (11 requested) atoms. Cycle 8: After refmac, R = 0.1960 (Rfree = 0.000) for 4676 atoms. Found 2 (22 requested) and removed 24 (11 requested) atoms. Cycle 9: After refmac, R = 0.1790 (Rfree = 0.000) for 4633 atoms. Found 1 (22 requested) and removed 18 (11 requested) atoms. Cycle 10: After refmac, R = 0.1813 (Rfree = 0.000) for 4606 atoms. Found 0 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.11 4.17 Search for helices and strands: 0 residues in 0 chains, 4742 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4764 seeds are put forward Round 1: 252 peptides, 47 chains. Longest chain 14 peptides. Score 0.336 Round 2: 277 peptides, 43 chains. Longest chain 18 peptides. Score 0.435 Round 3: 264 peptides, 41 chains. Longest chain 14 peptides. Score 0.425 Round 4: 288 peptides, 40 chains. Longest chain 22 peptides. Score 0.486 Round 5: 269 peptides, 40 chains. Longest chain 19 peptides. Score 0.446 Taking the results from Round 4 Chains 42, Residues 248, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10864 restraints for refining 4746 atoms. 9815 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2581 (Rfree = 0.000) for 4746 atoms. Found 6 (22 requested) and removed 44 (11 requested) atoms. Cycle 12: After refmac, R = 0.2430 (Rfree = 0.000) for 4671 atoms. Found 5 (22 requested) and removed 34 (11 requested) atoms. Cycle 13: After refmac, R = 0.2365 (Rfree = 0.000) for 4607 atoms. Found 5 (22 requested) and removed 29 (11 requested) atoms. Cycle 14: After refmac, R = 0.2355 (Rfree = 0.000) for 4562 atoms. Found 5 (21 requested) and removed 22 (10 requested) atoms. Cycle 15: After refmac, R = 0.2320 (Rfree = 0.000) for 4525 atoms. Found 2 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.12 4.18 Search for helices and strands: 0 residues in 0 chains, 4680 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 4711 seeds are put forward Round 1: 234 peptides, 48 chains. Longest chain 10 peptides. Score 0.281 Round 2: 293 peptides, 49 chains. Longest chain 13 peptides. Score 0.412 Round 3: 295 peptides, 44 chains. Longest chain 19 peptides. Score 0.464 Round 4: 291 peptides, 42 chains. Longest chain 21 peptides. Score 0.474 Round 5: 282 peptides, 42 chains. Longest chain 20 peptides. Score 0.455 Taking the results from Round 4 Chains 43, Residues 249, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10732 restraints for refining 4633 atoms. 9761 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2507 (Rfree = 0.000) for 4633 atoms. Found 8 (22 requested) and removed 54 (11 requested) atoms. Cycle 17: After refmac, R = 0.2507 (Rfree = 0.000) for 4560 atoms. Found 16 (21 requested) and removed 41 (10 requested) atoms. Cycle 18: After refmac, R = 0.2411 (Rfree = 0.000) for 4514 atoms. Found 9 (21 requested) and removed 38 (10 requested) atoms. Cycle 19: After refmac, R = 0.2408 (Rfree = 0.000) for 4470 atoms. Found 13 (21 requested) and removed 25 (10 requested) atoms. Cycle 20: After refmac, R = 0.2339 (Rfree = 0.000) for 4445 atoms. Found 9 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.15 4.21 Search for helices and strands: 0 residues in 0 chains, 4617 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 4645 seeds are put forward Round 1: 227 peptides, 48 chains. Longest chain 8 peptides. Score 0.263 Round 2: 266 peptides, 40 chains. Longest chain 16 peptides. Score 0.440 Round 3: 269 peptides, 43 chains. Longest chain 16 peptides. Score 0.417 Round 4: 263 peptides, 39 chains. Longest chain 23 peptides. Score 0.443 Round 5: 268 peptides, 38 chains. Longest chain 22 peptides. Score 0.463 Taking the results from Round 5 Chains 38, Residues 230, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11133 restraints for refining 4784 atoms. 10174 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2455 (Rfree = 0.000) for 4784 atoms. Found 9 (22 requested) and removed 68 (11 requested) atoms. Cycle 22: After refmac, R = 0.2342 (Rfree = 0.000) for 4699 atoms. Found 10 (22 requested) and removed 40 (11 requested) atoms. Cycle 23: After refmac, R = 0.2159 (Rfree = 0.000) for 4660 atoms. Found 3 (22 requested) and removed 32 (11 requested) atoms. Cycle 24: After refmac, R = 0.1833 (Rfree = 0.000) for 4614 atoms. Found 2 (22 requested) and removed 19 (11 requested) atoms. Cycle 25: After refmac, R = 0.1842 (Rfree = 0.000) for 4588 atoms. Found 0 (21 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.09 4.14 Search for helices and strands: 0 residues in 0 chains, 4706 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 4739 seeds are put forward Round 1: 237 peptides, 45 chains. Longest chain 17 peptides. Score 0.320 Round 2: 278 peptides, 47 chains. Longest chain 21 peptides. Score 0.398 Round 3: 290 peptides, 50 chains. Longest chain 17 peptides. Score 0.395 Round 4: 296 peptides, 44 chains. Longest chain 18 peptides. Score 0.466 Round 5: 303 peptides, 45 chains. Longest chain 15 peptides. Score 0.471 Taking the results from Round 5 Chains 45, Residues 258, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11047 restraints for refining 4806 atoms. 10060 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2729 (Rfree = 0.000) for 4806 atoms. Found 13 (22 requested) and removed 62 (11 requested) atoms. Cycle 27: After refmac, R = 0.2382 (Rfree = 0.000) for 4729 atoms. Found 10 (22 requested) and removed 43 (11 requested) atoms. Cycle 28: After refmac, R = 0.2452 (Rfree = 0.000) for 4678 atoms. Found 14 (22 requested) and removed 40 (11 requested) atoms. Cycle 29: After refmac, R = 0.2472 (Rfree = 0.000) for 4640 atoms. Found 12 (22 requested) and removed 36 (11 requested) atoms. Cycle 30: After refmac, R = 0.2461 (Rfree = 0.000) for 4600 atoms. Found 7 (21 requested) and removed 24 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.11 4.17 Search for helices and strands: 0 residues in 0 chains, 4744 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4757 seeds are put forward Round 1: 194 peptides, 41 chains. Longest chain 8 peptides. Score 0.253 Round 2: 242 peptides, 39 chains. Longest chain 15 peptides. Score 0.395 Round 3: 258 peptides, 40 chains. Longest chain 20 peptides. Score 0.422 Round 4: 252 peptides, 37 chains. Longest chain 18 peptides. Score 0.438 Round 5: 257 peptides, 37 chains. Longest chain 17 peptides. Score 0.449 Taking the results from Round 5 Chains 37, Residues 220, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11107 restraints for refining 4740 atoms. 10264 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2610 (Rfree = 0.000) for 4740 atoms. Found 13 (22 requested) and removed 47 (11 requested) atoms. Cycle 32: After refmac, R = 0.2605 (Rfree = 0.000) for 4688 atoms. Found 18 (22 requested) and removed 35 (11 requested) atoms. Cycle 33: After refmac, R = 0.2442 (Rfree = 0.000) for 4650 atoms. Found 18 (22 requested) and removed 32 (11 requested) atoms. Cycle 34: After refmac, R = 0.2437 (Rfree = 0.000) for 4618 atoms. Found 18 (22 requested) and removed 15 (11 requested) atoms. Cycle 35: After refmac, R = 0.2514 (Rfree = 0.000) for 4609 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.11 4.17 Search for helices and strands: 0 residues in 0 chains, 4716 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4732 seeds are put forward Round 1: 182 peptides, 39 chains. Longest chain 10 peptides. Score 0.243 Round 2: 221 peptides, 41 chains. Longest chain 14 peptides. Score 0.323 Round 3: 233 peptides, 39 chains. Longest chain 16 peptides. Score 0.374 Round 4: 243 peptides, 45 chains. Longest chain 15 peptides. Score 0.335 Round 5: 244 peptides, 40 chains. Longest chain 15 peptides. Score 0.390 Taking the results from Round 5 Chains 42, Residues 204, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11044 restraints for refining 4732 atoms. 10222 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2458 (Rfree = 0.000) for 4732 atoms. Found 6 (22 requested) and removed 44 (11 requested) atoms. Cycle 37: After refmac, R = 0.2450 (Rfree = 0.000) for 4664 atoms. Found 8 (22 requested) and removed 33 (11 requested) atoms. Cycle 38: After refmac, R = 0.2457 (Rfree = 0.000) for 4615 atoms. Found 9 (22 requested) and removed 21 (11 requested) atoms. Cycle 39: After refmac, R = 0.2308 (Rfree = 0.000) for 4587 atoms. Found 12 (21 requested) and removed 21 (10 requested) atoms. Cycle 40: After refmac, R = 0.2234 (Rfree = 0.000) for 4564 atoms. Found 5 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.11 4.17 Search for helices and strands: 0 residues in 0 chains, 4692 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 4710 seeds are put forward Round 1: 172 peptides, 37 chains. Longest chain 10 peptides. Score 0.238 Round 2: 192 peptides, 39 chains. Longest chain 10 peptides. Score 0.270 Round 3: 192 peptides, 36 chains. Longest chain 10 peptides. Score 0.304 Round 4: 204 peptides, 35 chains. Longest chain 12 peptides. Score 0.346 Round 5: 204 peptides, 34 chains. Longest chain 9 peptides. Score 0.357 Taking the results from Round 5 Chains 34, Residues 170, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11079 restraints for refining 4640 atoms. 10393 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2256 (Rfree = 0.000) for 4640 atoms. Found 19 (22 requested) and removed 36 (11 requested) atoms. Cycle 42: After refmac, R = 0.2268 (Rfree = 0.000) for 4610 atoms. Found 10 (21 requested) and removed 31 (10 requested) atoms. Cycle 43: After refmac, R = 0.2180 (Rfree = 0.000) for 4574 atoms. Found 14 (21 requested) and removed 26 (10 requested) atoms. Cycle 44: After refmac, R = 0.2226 (Rfree = 0.000) for 4548 atoms. Found 13 (21 requested) and removed 19 (10 requested) atoms. Cycle 45: After refmac, R = 0.2255 (Rfree = 0.000) for 4529 atoms. Found 12 (21 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.12 4.18 Search for helices and strands: 0 residues in 0 chains, 4654 seeds are put forward NCS extension: 0 residues added, 4654 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 9 peptides. Score 0.241 Round 2: 176 peptides, 34 chains. Longest chain 11 peptides. Score 0.285 Round 3: 181 peptides, 34 chains. Longest chain 8 peptides. Score 0.298 Round 4: 183 peptides, 31 chains. Longest chain 13 peptides. Score 0.338 Round 5: 171 peptides, 31 chains. Longest chain 13 peptides. Score 0.306 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 152, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vll-4_warpNtrace.pdb as input Building loops using Loopy2018 31 chains (152 residues) following loop building 2 chains (11 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6431 reflections ( 99.95 % complete ) and 10786 restraints for refining 4569 atoms. 10174 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2411 (Rfree = 0.000) for 4569 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2233 (Rfree = 0.000) for 4541 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1903 (Rfree = 0.000) for 4512 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1800 (Rfree = 0.000) for 4490 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:16:43 GMT 2018 Job finished. TimeTaking 49.33 Used memory is bytes: 2465664