Sun 23 Dec 22:23:10 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 1vll-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vll-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vll-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-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/1vll-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-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 22:23:20 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/1vll-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-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 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-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: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-4.0-parrot-hancs.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 = 0.3762 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3503 (Rfree = 0.000) for 5945 atoms. Found 28 (28 requested) and removed 36 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.16 4.22 Search for helices and strands: 0 residues in 0 chains, 6074 seeds are put forward NCS extension: 0 residues added, 6074 seeds are put forward Round 1: 204 peptides, 41 chains. Longest chain 11 peptides. Score 0.280 Round 2: 271 peptides, 46 chains. Longest chain 12 peptides. Score 0.391 Round 3: 287 peptides, 41 chains. Longest chain 20 peptides. Score 0.475 Round 4: 304 peptides, 44 chains. Longest chain 18 peptides. Score 0.482 Round 5: 318 peptides, 48 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 4 Chains 46, Residues 260, Estimated correctness of the model 0.0 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 11521 restraints for refining 4822 atoms. 10415 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3099 (Rfree = 0.000) for 4822 atoms. Found 9 (22 requested) and removed 28 (11 requested) atoms. Cycle 2: After refmac, R = 0.2927 (Rfree = 0.000) for 4718 atoms. Found 13 (22 requested) and removed 36 (11 requested) atoms. Cycle 3: After refmac, R = 0.2698 (Rfree = 0.000) for 4662 atoms. Found 12 (22 requested) and removed 28 (11 requested) atoms. Cycle 4: After refmac, R = 0.2342 (Rfree = 0.000) for 4605 atoms. Found 2 (22 requested) and removed 23 (11 requested) atoms. Cycle 5: After refmac, R = 0.2620 (Rfree = 0.000) for 4565 atoms. Found 11 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.15 4.21 Search for helices and strands: 0 residues in 0 chains, 4735 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4758 seeds are put forward Round 1: 260 peptides, 45 chains. Longest chain 12 peptides. Score 0.376 Round 2: 299 peptides, 45 chains. Longest chain 15 peptides. Score 0.463 Round 3: 327 peptides, 48 chains. Longest chain 19 peptides. Score 0.493 Round 4: 305 peptides, 42 chains. Longest chain 18 peptides. Score 0.503 Round 5: 311 peptides, 46 chains. Longest chain 14 peptides. Score 0.479 Taking the results from Round 4 Chains 44, Residues 263, Estimated correctness of the model 0.0 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10900 restraints for refining 4703 atoms. 9761 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2667 (Rfree = 0.000) for 4703 atoms. Found 10 (22 requested) and removed 50 (11 requested) atoms. Cycle 7: After refmac, R = 0.2452 (Rfree = 0.000) for 4627 atoms. Found 8 (22 requested) and removed 28 (11 requested) atoms. Cycle 8: After refmac, R = 0.2528 (Rfree = 0.000) for 4573 atoms. Found 12 (21 requested) and removed 24 (10 requested) atoms. Cycle 9: After refmac, R = 0.2410 (Rfree = 0.000) for 4531 atoms. Found 13 (21 requested) and removed 21 (10 requested) atoms. Cycle 10: After refmac, R = 0.2072 (Rfree = 0.000) for 4496 atoms. Found 5 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.15 4.21 Search for helices and strands: 0 residues in 0 chains, 4633 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 4652 seeds are put forward Round 1: 221 peptides, 41 chains. Longest chain 9 peptides. Score 0.323 Round 2: 282 peptides, 45 chains. Longest chain 12 peptides. Score 0.426 Round 3: 281 peptides, 43 chains. Longest chain 11 peptides. Score 0.443 Round 4: 282 peptides, 44 chains. Longest chain 13 peptides. Score 0.436 Round 5: 289 peptides, 42 chains. Longest chain 15 peptides. Score 0.470 Taking the results from Round 5 Chains 42, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10949 restraints for refining 4629 atoms. 10003 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2792 (Rfree = 0.000) for 4629 atoms. Found 16 (21 requested) and removed 41 (10 requested) atoms. Cycle 12: After refmac, R = 0.2481 (Rfree = 0.000) for 4568 atoms. Found 16 (21 requested) and removed 32 (10 requested) atoms. Cycle 13: After refmac, R = 0.2268 (Rfree = 0.000) for 4517 atoms. Found 9 (21 requested) and removed 26 (10 requested) atoms. Cycle 14: After refmac, R = 0.2377 (Rfree = 0.000) for 4470 atoms. Found 15 (21 requested) and removed 22 (10 requested) atoms. Cycle 15: After refmac, R = 0.2493 (Rfree = 0.000) for 4439 atoms. Found 18 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.09 4.14 Search for helices and strands: 0 residues in 0 chains, 4679 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 4702 seeds are put forward Round 1: 224 peptides, 46 chains. Longest chain 8 peptides. Score 0.277 Round 2: 269 peptides, 47 chains. Longest chain 15 peptides. Score 0.377 Round 3: 260 peptides, 44 chains. Longest chain 18 peptides. Score 0.386 Round 4: 257 peptides, 44 chains. Longest chain 16 peptides. Score 0.379 Round 5: 269 peptides, 41 chains. Longest chain 15 peptides. Score 0.436 Taking the results from Round 5 Chains 41, Residues 228, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10958 restraints for refining 4609 atoms. 10072 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2960 (Rfree = 0.000) for 4609 atoms. Found 21 (21 requested) and removed 47 (10 requested) atoms. Cycle 17: After refmac, R = 0.2620 (Rfree = 0.000) for 4544 atoms. Found 17 (21 requested) and removed 30 (10 requested) atoms. Cycle 18: After refmac, R = 0.2706 (Rfree = 0.000) for 4493 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 19: After refmac, R = 0.2443 (Rfree = 0.000) for 4461 atoms. Found 15 (21 requested) and removed 25 (10 requested) atoms. Cycle 20: After refmac, R = 0.2403 (Rfree = 0.000) for 4426 atoms. Found 16 (21 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.12 4.18 Search for helices and strands: 0 residues in 0 chains, 4624 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4645 seeds are put forward Round 1: 201 peptides, 43 chains. Longest chain 9 peptides. Score 0.249 Round 2: 262 peptides, 47 chains. Longest chain 18 peptides. Score 0.360 Round 3: 245 peptides, 45 chains. Longest chain 11 peptides. Score 0.340 Round 4: 254 peptides, 44 chains. Longest chain 12 peptides. Score 0.372 Round 5: 261 peptides, 44 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Chains 44, Residues 217, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10315 restraints for refining 4442 atoms. 9467 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2650 (Rfree = 0.000) for 4442 atoms. Found 10 (21 requested) and removed 42 (10 requested) atoms. Cycle 22: After refmac, R = 0.2498 (Rfree = 0.000) for 4384 atoms. Found 20 (20 requested) and removed 28 (10 requested) atoms. Cycle 23: After refmac, R = 0.1995 (Rfree = 0.000) for 4361 atoms. Found 0 (20 requested) and removed 23 (10 requested) atoms. Cycle 24: After refmac, R = 0.1867 (Rfree = 0.000) for 4329 atoms. Found 0 (20 requested) and removed 16 (10 requested) atoms. Cycle 25: After refmac, R = 0.1854 (Rfree = 0.000) for 4303 atoms. Found 0 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.08 4.13 Search for helices and strands: 0 residues in 0 chains, 4424 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 4432 seeds are put forward Round 1: 231 peptides, 47 chains. Longest chain 10 peptides. Score 0.284 Round 2: 260 peptides, 48 chains. Longest chain 13 peptides. Score 0.345 Round 3: 274 peptides, 45 chains. Longest chain 15 peptides. Score 0.408 Round 4: 263 peptides, 41 chains. Longest chain 14 peptides. Score 0.423 Round 5: 293 peptides, 48 chains. Longest chain 18 peptides. Score 0.421 Taking the results from Round 4 Chains 42, Residues 222, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10133 restraints for refining 4494 atoms. 9213 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2363 (Rfree = 0.000) for 4494 atoms. Found 10 (21 requested) and removed 43 (10 requested) atoms. Cycle 27: After refmac, R = 0.2331 (Rfree = 0.000) for 4435 atoms. Found 19 (21 requested) and removed 26 (10 requested) atoms. Cycle 28: After refmac, R = 0.2225 (Rfree = 0.000) for 4409 atoms. Found 10 (21 requested) and removed 23 (10 requested) atoms. Cycle 29: After refmac, R = 0.1812 (Rfree = 0.000) for 4381 atoms. Found 0 (20 requested) and removed 21 (10 requested) atoms. Cycle 30: After refmac, R = 0.1715 (Rfree = 0.000) for 4340 atoms. Found 1 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.12 4.18 Search for helices and strands: 0 residues in 0 chains, 4448 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 4461 seeds are put forward Round 1: 197 peptides, 40 chains. Longest chain 8 peptides. Score 0.272 Round 2: 235 peptides, 39 chains. Longest chain 12 peptides. Score 0.379 Round 3: 242 peptides, 37 chains. Longest chain 13 peptides. Score 0.416 Round 4: 233 peptides, 39 chains. Longest chain 13 peptides. Score 0.374 Round 5: 225 peptides, 34 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 3 Chains 37, Residues 205, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10173 restraints for refining 4431 atoms. 9374 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2210 (Rfree = 0.000) for 4431 atoms. Found 14 (21 requested) and removed 32 (10 requested) atoms. Cycle 32: After refmac, R = 0.2335 (Rfree = 0.000) for 4390 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. Cycle 33: After refmac, R = 0.2195 (Rfree = 0.000) for 4366 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 34: After refmac, R = 0.1717 (Rfree = 0.000) for 4345 atoms. Found 7 (20 requested) and removed 16 (10 requested) atoms. Cycle 35: After refmac, R = 0.1583 (Rfree = 0.000) for 4325 atoms. Found 0 (20 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.09 4.14 Search for helices and strands: 0 residues in 0 chains, 4437 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4453 seeds are put forward Round 1: 198 peptides, 43 chains. Longest chain 8 peptides. Score 0.241 Round 2: 225 peptides, 43 chains. Longest chain 9 peptides. Score 0.312 Round 3: 225 peptides, 38 chains. Longest chain 13 peptides. Score 0.365 Round 4: 231 peptides, 41 chains. Longest chain 10 peptides. Score 0.348 Round 5: 248 peptides, 44 chains. Longest chain 16 peptides. Score 0.358 Taking the results from Round 3 Chains 38, Residues 187, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10165 restraints for refining 4414 atoms. 9432 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2338 (Rfree = 0.000) for 4414 atoms. Found 20 (20 requested) and removed 37 (10 requested) atoms. Cycle 37: After refmac, R = 0.2419 (Rfree = 0.000) for 4389 atoms. Found 20 (20 requested) and removed 29 (10 requested) atoms. Cycle 38: After refmac, R = 0.2187 (Rfree = 0.000) for 4364 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 39: After refmac, R = 0.2340 (Rfree = 0.000) for 4344 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 40: After refmac, R = 0.2309 (Rfree = 0.000) for 4330 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.08 4.13 Search for helices and strands: 0 residues in 0 chains, 4492 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4506 seeds are put forward Round 1: 150 peptides, 34 chains. Longest chain 9 peptides. Score 0.210 Round 2: 191 peptides, 38 chains. Longest chain 10 peptides. Score 0.279 Round 3: 202 peptides, 37 chains. Longest chain 13 peptides. Score 0.319 Round 4: 180 peptides, 32 chains. Longest chain 12 peptides. Score 0.319 Round 5: 180 peptides, 34 chains. Longest chain 8 peptides. Score 0.296 Taking the results from Round 4 Chains 32, Residues 148, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6431 reflections ( 99.95 % complete ) and 10475 restraints for refining 4451 atoms. 9887 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2547 (Rfree = 0.000) for 4451 atoms. Found 19 (21 requested) and removed 65 (10 requested) atoms. Cycle 42: After refmac, R = 0.2647 (Rfree = 0.000) for 4376 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 43: After refmac, R = 0.2574 (Rfree = 0.000) for 4353 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 44: After refmac, R = 0.2489 (Rfree = 0.000) for 4330 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 45: After refmac, R = 0.2477 (Rfree = 0.000) for 4322 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.09 4.14 Search for helices and strands: 0 residues in 0 chains, 4487 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4504 seeds are put forward Round 1: 121 peptides, 28 chains. Longest chain 6 peptides. Score 0.197 Round 2: 161 peptides, 35 chains. Longest chain 8 peptides. Score 0.231 Round 3: 158 peptides, 31 chains. Longest chain 12 peptides. Score 0.271 Round 4: 150 peptides, 26 chains. Longest chain 12 peptides. Score 0.310 Round 5: 157 peptides, 29 chains. Longest chain 12 peptides. Score 0.292 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 124, Estimated correctness of the model 0.0 % 2 chains (9 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 26 chains (124 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6431 reflections ( 99.95 % complete ) and 9389 restraints for refining 4104 atoms. 8906 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2528 (Rfree = 0.000) for 4104 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2426 (Rfree = 0.000) for 4080 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2581 (Rfree = 0.000) for 4055 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2372 (Rfree = 0.000) for 4040 atoms. TimeTaking 64.45