Sun 23 Dec 23:42:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqs-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.4-parrot-mrncs ############### 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 23:42:34 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.4-parrot-mrncs/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 495 and 0 Target number of residues in the AU: 495 Target solvent content: 0.6064 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-3.4-parrot-mrncs.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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4640 target number of atoms Had to go as low as 0.85 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: 29.971 3.400 Wilson plot Bfac: 55.24 9962 reflections ( 99.63 % complete ) and 0 restraints for refining 5153 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3218 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3040 (Rfree = 0.000) for 5153 atoms. Found 38 (38 requested) and removed 45 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 5257 seeds are put forward NCS extension: 0 residues added, 5257 seeds are put forward Round 1: 291 peptides, 50 chains. Longest chain 11 peptides. Score 0.405 Round 2: 344 peptides, 47 chains. Longest chain 17 peptides. Score 0.547 Round 3: 360 peptides, 39 chains. Longest chain 24 peptides. Score 0.640 Round 4: 380 peptides, 44 chains. Longest chain 48 peptides. Score 0.635 Round 5: 383 peptides, 39 chains. Longest chain 25 peptides. Score 0.676 Taking the results from Round 5 Chains 42, Residues 344, Estimated correctness of the model 51.5 % 4 chains (77 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 7979 restraints for refining 4218 atoms. 6294 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2756 (Rfree = 0.000) for 4218 atoms. Found 31 (31 requested) and removed 31 (15 requested) atoms. Cycle 2: After refmac, R = 0.2663 (Rfree = 0.000) for 4153 atoms. Found 25 (31 requested) and removed 24 (15 requested) atoms. Cycle 3: After refmac, R = 0.2509 (Rfree = 0.000) for 4126 atoms. Found 15 (31 requested) and removed 23 (15 requested) atoms. Cycle 4: After refmac, R = 0.2497 (Rfree = 0.000) for 4097 atoms. Found 23 (31 requested) and removed 17 (15 requested) atoms. Cycle 5: After refmac, R = 0.2405 (Rfree = 0.000) for 4092 atoms. Found 12 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 4226 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4249 seeds are put forward Round 1: 347 peptides, 48 chains. Longest chain 19 peptides. Score 0.544 Round 2: 382 peptides, 41 chains. Longest chain 24 peptides. Score 0.660 Round 3: 375 peptides, 44 chains. Longest chain 26 peptides. Score 0.627 Round 4: 382 peptides, 39 chains. Longest chain 26 peptides. Score 0.674 Round 5: 371 peptides, 37 chains. Longest chain 36 peptides. Score 0.672 Taking the results from Round 4 Chains 44, Residues 343, Estimated correctness of the model 50.9 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8739 restraints for refining 4217 atoms. 7235 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2651 (Rfree = 0.000) for 4217 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 7: After refmac, R = 0.2565 (Rfree = 0.000) for 4206 atoms. Found 21 (31 requested) and removed 19 (15 requested) atoms. Cycle 8: After refmac, R = 0.2441 (Rfree = 0.000) for 4193 atoms. Found 27 (31 requested) and removed 20 (15 requested) atoms. Cycle 9: After refmac, R = 0.2328 (Rfree = 0.000) for 4184 atoms. Found 15 (31 requested) and removed 21 (15 requested) atoms. Cycle 10: After refmac, R = 0.2331 (Rfree = 0.000) for 4166 atoms. Found 16 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 4303 seeds are put forward NCS extension: 10 residues added (9 deleted due to clashes), 4313 seeds are put forward Round 1: 369 peptides, 51 chains. Longest chain 22 peptides. Score 0.560 Round 2: 385 peptides, 44 chains. Longest chain 31 peptides. Score 0.643 Round 3: 390 peptides, 45 chains. Longest chain 30 peptides. Score 0.644 Round 4: 371 peptides, 39 chains. Longest chain 25 peptides. Score 0.657 Round 5: 371 peptides, 43 chains. Longest chain 27 peptides. Score 0.628 Taking the results from Round 4 Chains 40, Residues 332, Estimated correctness of the model 46.2 % 3 chains (48 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8648 restraints for refining 4218 atoms. 7128 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2598 (Rfree = 0.000) for 4218 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 12: After refmac, R = 0.2501 (Rfree = 0.000) for 4203 atoms. Found 23 (31 requested) and removed 23 (15 requested) atoms. Cycle 13: After refmac, R = 0.2428 (Rfree = 0.000) for 4196 atoms. Found 19 (31 requested) and removed 23 (15 requested) atoms. Cycle 14: After refmac, R = 0.2243 (Rfree = 0.000) for 4182 atoms. Found 9 (31 requested) and removed 18 (15 requested) atoms. Cycle 15: After refmac, R = 0.2367 (Rfree = 0.000) for 4166 atoms. Found 12 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 4316 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 4331 seeds are put forward Round 1: 337 peptides, 43 chains. Longest chain 22 peptides. Score 0.567 Round 2: 381 peptides, 44 chains. Longest chain 27 peptides. Score 0.636 Round 3: 369 peptides, 39 chains. Longest chain 20 peptides. Score 0.654 Round 4: 371 peptides, 41 chains. Longest chain 22 peptides. Score 0.643 Round 5: 380 peptides, 40 chains. Longest chain 25 peptides. Score 0.664 Taking the results from Round 5 Chains 43, Residues 340, Estimated correctness of the model 48.2 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8777 restraints for refining 4219 atoms. 7314 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2604 (Rfree = 0.000) for 4219 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 17: After refmac, R = 0.2462 (Rfree = 0.000) for 4208 atoms. Found 27 (31 requested) and removed 19 (15 requested) atoms. Cycle 18: After refmac, R = 0.2401 (Rfree = 0.000) for 4202 atoms. Found 16 (31 requested) and removed 17 (15 requested) atoms. Cycle 19: After refmac, R = 0.2357 (Rfree = 0.000) for 4190 atoms. Found 25 (31 requested) and removed 17 (15 requested) atoms. Cycle 20: After refmac, R = 0.2328 (Rfree = 0.000) for 4191 atoms. Found 11 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 4310 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 4320 seeds are put forward Round 1: 337 peptides, 49 chains. Longest chain 23 peptides. Score 0.515 Round 2: 360 peptides, 41 chains. Longest chain 23 peptides. Score 0.624 Round 3: 352 peptides, 42 chains. Longest chain 24 peptides. Score 0.603 Round 4: 356 peptides, 41 chains. Longest chain 23 peptides. Score 0.618 Round 5: 354 peptides, 43 chains. Longest chain 20 peptides. Score 0.598 Taking the results from Round 2 Chains 41, Residues 319, Estimated correctness of the model 36.3 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9018 restraints for refining 4219 atoms. 7709 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2480 (Rfree = 0.000) for 4219 atoms. Found 19 (31 requested) and removed 22 (15 requested) atoms. Cycle 22: After refmac, R = 0.2487 (Rfree = 0.000) for 4202 atoms. Found 29 (31 requested) and removed 23 (15 requested) atoms. Cycle 23: After refmac, R = 0.2306 (Rfree = 0.000) for 4199 atoms. Found 22 (31 requested) and removed 17 (15 requested) atoms. Cycle 24: After refmac, R = 0.2276 (Rfree = 0.000) for 4195 atoms. Found 19 (31 requested) and removed 18 (15 requested) atoms. Cycle 25: After refmac, R = 0.2256 (Rfree = 0.000) for 4188 atoms. Found 23 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 4301 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 4321 seeds are put forward Round 1: 316 peptides, 49 chains. Longest chain 20 peptides. Score 0.471 Round 2: 332 peptides, 40 chains. Longest chain 23 peptides. Score 0.583 Round 3: 347 peptides, 42 chains. Longest chain 24 peptides. Score 0.594 Round 4: 346 peptides, 42 chains. Longest chain 26 peptides. Score 0.592 Round 5: 350 peptides, 45 chains. Longest chain 20 peptides. Score 0.575 Taking the results from Round 3 Chains 43, Residues 305, Estimated correctness of the model 26.7 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8770 restraints for refining 4219 atoms. 7432 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2476 (Rfree = 0.000) for 4219 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. Cycle 27: After refmac, R = 0.2370 (Rfree = 0.000) for 4214 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 28: After refmac, R = 0.2391 (Rfree = 0.000) for 4218 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. Cycle 29: After refmac, R = 0.2267 (Rfree = 0.000) for 4216 atoms. Found 22 (31 requested) and removed 17 (15 requested) atoms. Cycle 30: After refmac, R = 0.2306 (Rfree = 0.000) for 4211 atoms. Found 23 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 4336 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 4360 seeds are put forward Round 1: 282 peptides, 45 chains. Longest chain 23 peptides. Score 0.435 Round 2: 327 peptides, 46 chains. Longest chain 16 peptides. Score 0.522 Round 3: 335 peptides, 42 chains. Longest chain 23 peptides. Score 0.572 Round 4: 312 peptides, 42 chains. Longest chain 18 peptides. Score 0.528 Round 5: 330 peptides, 44 chains. Longest chain 24 peptides. Score 0.545 Taking the results from Round 3 Chains 42, Residues 293, Estimated correctness of the model 19.3 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9065 restraints for refining 4217 atoms. 7870 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2388 (Rfree = 0.000) for 4217 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 32: After refmac, R = 0.2310 (Rfree = 0.000) for 4205 atoms. Found 27 (31 requested) and removed 16 (15 requested) atoms. Cycle 33: After refmac, R = 0.2217 (Rfree = 0.000) for 4206 atoms. Found 27 (31 requested) and removed 20 (15 requested) atoms. Cycle 34: After refmac, R = 0.2171 (Rfree = 0.000) for 4208 atoms. Found 25 (31 requested) and removed 16 (15 requested) atoms. Cycle 35: After refmac, R = 0.2110 (Rfree = 0.000) for 4210 atoms. Found 20 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 4328 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 4353 seeds are put forward Round 1: 256 peptides, 44 chains. Longest chain 17 peptides. Score 0.384 Round 2: 285 peptides, 43 chains. Longest chain 17 peptides. Score 0.461 Round 3: 277 peptides, 42 chains. Longest chain 15 peptides. Score 0.453 Round 4: 283 peptides, 41 chains. Longest chain 17 peptides. Score 0.476 Round 5: 287 peptides, 43 chains. Longest chain 16 peptides. Score 0.466 Taking the results from Round 4 Chains 41, Residues 242, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9691 restraints for refining 4219 atoms. 8764 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2257 (Rfree = 0.000) for 4219 atoms. Found 31 (31 requested) and removed 18 (15 requested) atoms. Cycle 37: After refmac, R = 0.2177 (Rfree = 0.000) for 4223 atoms. Found 31 (31 requested) and removed 17 (15 requested) atoms. Cycle 38: After refmac, R = 0.2174 (Rfree = 0.000) for 4231 atoms. Found 30 (31 requested) and removed 17 (15 requested) atoms. Cycle 39: After refmac, R = 0.2112 (Rfree = 0.000) for 4239 atoms. Found 20 (32 requested) and removed 19 (16 requested) atoms. Cycle 40: After refmac, R = 0.2053 (Rfree = 0.000) for 4234 atoms. Found 23 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 4363 seeds are put forward NCS extension: 18 residues added (7 deleted due to clashes), 4381 seeds are put forward Round 1: 258 peptides, 47 chains. Longest chain 15 peptides. Score 0.357 Round 2: 296 peptides, 43 chains. Longest chain 19 peptides. Score 0.485 Round 3: 300 peptides, 45 chains. Longest chain 17 peptides. Score 0.475 Round 4: 307 peptides, 45 chains. Longest chain 17 peptides. Score 0.490 Round 5: 296 peptides, 42 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 5 Chains 42, Residues 254, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9543 restraints for refining 4219 atoms. 8569 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2296 (Rfree = 0.000) for 4219 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 42: After refmac, R = 0.2151 (Rfree = 0.000) for 4211 atoms. Found 25 (31 requested) and removed 16 (15 requested) atoms. Cycle 43: After refmac, R = 0.2149 (Rfree = 0.000) for 4216 atoms. Found 20 (31 requested) and removed 21 (15 requested) atoms. Cycle 44: After refmac, R = 0.2138 (Rfree = 0.000) for 4211 atoms. Found 25 (31 requested) and removed 18 (15 requested) atoms. Cycle 45: After refmac, R = 0.2150 (Rfree = 0.000) for 4208 atoms. Found 24 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 4304 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4319 seeds are put forward Round 1: 267 peptides, 54 chains. Longest chain 11 peptides. Score 0.305 Round 2: 302 peptides, 50 chains. Longest chain 24 peptides. Score 0.431 Round 3: 309 peptides, 52 chains. Longest chain 22 peptides. Score 0.427 Round 4: 297 peptides, 45 chains. Longest chain 16 peptides. Score 0.468 Round 5: 302 peptides, 50 chains. Longest chain 13 peptides. Score 0.431 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 45, Residues 252, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9962 reflections ( 99.63 % complete ) and 9485 restraints for refining 4219 atoms. 8522 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2437 (Rfree = 0.000) for 4219 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2339 (Rfree = 0.000) for 4190 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2145 (Rfree = 0.000) for 4167 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2179 (Rfree = 0.000) for 4147 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... TimeTaking 56.97