Tue 25 Dec 19:27:57 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 1vqs-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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/1vqs-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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 ============================================================ Tue 25 Dec 19:28:06 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/1vqs-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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 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-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.4-parrot-hancs.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 5103 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.3215 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2937 (Rfree = 0.000) for 5103 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.04 Search for helices and strands: 0 residues in 0 chains, 5213 seeds are put forward NCS extension: 0 residues added, 5213 seeds are put forward Round 1: 308 peptides, 51 chains. Longest chain 14 peptides. Score 0.434 Round 2: 365 peptides, 52 chains. Longest chain 20 peptides. Score 0.544 Round 3: 391 peptides, 44 chains. Longest chain 29 peptides. Score 0.652 Round 4: 394 peptides, 40 chains. Longest chain 25 peptides. Score 0.685 Round 5: 397 peptides, 38 chains. Longest chain 31 peptides. Score 0.702 Taking the results from Round 5 Chains 43, Residues 359, Estimated correctness of the model 58.4 % 5 chains (84 residues) have been docked in sequence Building loops using Loopy2018 43 chains (359 residues) following loop building 5 chains (84 residues) in sequence following loop building ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 7842 restraints for refining 4219 atoms. 6050 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2740 (Rfree = 0.000) for 4219 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Cycle 2: After refmac, R = 0.2606 (Rfree = 0.000) for 4159 atoms. Found 21 (30 requested) and removed 21 (15 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2528 (Rfree = 0.000) for 4133 atoms. Found 15 (30 requested) and removed 23 (15 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2456 (Rfree = 0.000) for 4113 atoms. Found 18 (29 requested) and removed 21 (15 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2415 (Rfree = 0.000) for 4092 atoms. Found 18 (28 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 4202 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 4226 seeds are put forward Round 1: 368 peptides, 40 chains. Longest chain 28 peptides. Score 0.645 Round 2: 401 peptides, 40 chains. Longest chain 28 peptides. Score 0.695 Round 3: 380 peptides, 39 chains. Longest chain 26 peptides. Score 0.671 Round 4: 395 peptides, 38 chains. Longest chain 30 peptides. Score 0.700 Round 5: 385 peptides, 35 chains. Longest chain 36 peptides. Score 0.706 Taking the results from Round 5 Chains 37, Residues 350, Estimated correctness of the model 59.4 % 3 chains (40 residues) have been docked in sequence Building loops using Loopy2018 37 chains (350 residues) following loop building 3 chains (40 residues) in sequence following loop building ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8724 restraints for refining 4219 atoms. 7187 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2687 (Rfree = 0.000) for 4219 atoms. Found 28 (28 requested) and removed 28 (15 requested) atoms. Cycle 7: After refmac, R = 0.2555 (Rfree = 0.000) for 4203 atoms. Found 27 (27 requested) and removed 25 (15 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2487 (Rfree = 0.000) for 4192 atoms. Found 17 (27 requested) and removed 25 (15 requested) atoms. Cycle 9: After refmac, R = 0.2415 (Rfree = 0.000) for 4175 atoms. Found 26 (26 requested) and removed 19 (15 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2439 (Rfree = 0.000) for 4172 atoms. Found 25 (25 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 4303 seeds are put forward NCS extension: 33 residues added (15 deleted due to clashes), 4336 seeds are put forward Round 1: 357 peptides, 46 chains. Longest chain 22 peptides. Score 0.579 Round 2: 391 peptides, 45 chains. Longest chain 25 peptides. Score 0.645 Round 3: 398 peptides, 42 chains. Longest chain 28 peptides. Score 0.677 Round 4: 395 peptides, 43 chains. Longest chain 24 peptides. Score 0.666 Round 5: 400 peptides, 46 chains. Longest chain 22 peptides. Score 0.652 Taking the results from Round 3 Chains 43, Residues 356, Estimated correctness of the model 51.8 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9962 reflections ( 99.63 % complete ) and 9038 restraints for refining 4218 atoms. 7591 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2628 (Rfree = 0.000) for 4218 atoms. Found 25 (25 requested) and removed 22 (15 requested) atoms. Cycle 12: After refmac, R = 0.2534 (Rfree = 0.000) for 4208 atoms. Found 21 (25 requested) and removed 20 (15 requested) atoms. Cycle 13: After refmac, R = 0.2493 (Rfree = 0.000) for 4195 atoms. Found 24 (25 requested) and removed 25 (15 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 14: After refmac, R = 0.2481 (Rfree = 0.000) for 4189 atoms. Found 20 (25 requested) and removed 18 (15 requested) atoms. Cycle 15: After refmac, R = 0.2511 (Rfree = 0.000) for 4187 atoms. Found 25 (25 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 4293 seeds are put forward NCS extension: 21 residues added (21 deleted due to clashes), 4314 seeds are put forward Round 1: 352 peptides, 43 chains. Longest chain 24 peptides. Score 0.595 Round 2: 392 peptides, 41 chains. Longest chain 23 peptides. Score 0.675 Round 3: 393 peptides, 39 chains. Longest chain 29 peptides. Score 0.690 Round 4: 387 peptides, 41 chains. Longest chain 27 peptides. Score 0.668 Round 5: 382 peptides, 39 chains. Longest chain 28 peptides. Score 0.674 Taking the results from Round 3 Chains 43, Residues 354, Estimated correctness of the model 55.3 % 4 chains (69 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9962 reflections ( 99.63 % complete ) and 8206 restraints for refining 4219 atoms. 6507 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2701 (Rfree = 0.000) for 4219 atoms. Found 25 (25 requested) and removed 24 (15 requested) atoms. Cycle 17: After refmac, R = 0.2615 (Rfree = 0.000) for 4195 atoms. Found 25 (25 requested) and removed 20 (15 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 18: After refmac, R = 0.2613 (Rfree = 0.000) for 4190 atoms. Found 24 (25 requested) and removed 23 (15 requested) atoms. Cycle 19: After refmac, R = 0.2398 (Rfree = 0.000) for 4181 atoms. Found 8 (25 requested) and removed 15 (15 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2376 (Rfree = 0.000) for 4166 atoms. Found 10 (25 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 4273 seeds are put forward NCS extension: 10 residues added (9 deleted due to clashes), 4283 seeds are put forward Round 1: 346 peptides, 45 chains. Longest chain 22 peptides. Score 0.567 Round 2: 360 peptides, 44 chains. Longest chain 22 peptides. Score 0.601 Round 3: 376 peptides, 40 chains. Longest chain 23 peptides. Score 0.658 Round 4: 363 peptides, 40 chains. Longest chain 25 peptides. Score 0.637 Round 5: 374 peptides, 41 chains. Longest chain 25 peptides. Score 0.647 Taking the results from Round 3 Chains 44, Residues 336, Estimated correctness of the model 46.5 % 4 chains (79 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8362 restraints for refining 4218 atoms. 6708 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2624 (Rfree = 0.000) for 4218 atoms. Found 25 (25 requested) and removed 20 (15 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2633 (Rfree = 0.000) for 4201 atoms. Found 25 (25 requested) and removed 22 (15 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2565 (Rfree = 0.000) for 4187 atoms. Found 25 (25 requested) and removed 19 (15 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2562 (Rfree = 0.000) for 4188 atoms. Found 25 (25 requested) and removed 18 (15 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2507 (Rfree = 0.000) for 4186 atoms. Found 24 (25 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 4282 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 4301 seeds are put forward Round 1: 331 peptides, 47 chains. Longest chain 22 peptides. Score 0.521 Round 2: 366 peptides, 52 chains. Longest chain 18 peptides. Score 0.546 Round 3: 378 peptides, 48 chains. Longest chain 18 peptides. Score 0.601 Round 4: 371 peptides, 51 chains. Longest chain 22 peptides. Score 0.564 Round 5: 374 peptides, 48 chains. Longest chain 22 peptides. Score 0.594 Taking the results from Round 3 Chains 48, Residues 330, Estimated correctness of the model 29.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 8930 restraints for refining 4219 atoms. 7581 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2565 (Rfree = 0.000) for 4219 atoms. Found 25 (25 requested) and removed 18 (15 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2592 (Rfree = 0.000) for 4212 atoms. Found 25 (25 requested) and removed 22 (15 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2255 (Rfree = 0.000) for 4209 atoms. Found 14 (25 requested) and removed 18 (15 requested) atoms. Cycle 29: After refmac, R = 0.2443 (Rfree = 0.000) for 4193 atoms. Found 25 (25 requested) and removed 18 (15 requested) atoms. Cycle 30: After refmac, R = 0.2232 (Rfree = 0.000) for 4194 atoms. Found 11 (25 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 4299 seeds are put forward NCS extension: 5 residues added (7 deleted due to clashes), 4304 seeds are put forward Round 1: 298 peptides, 46 chains. Longest chain 24 peptides. Score 0.461 Round 2: 317 peptides, 44 chains. Longest chain 23 peptides. Score 0.520 Round 3: 333 peptides, 44 chains. Longest chain 22 peptides. Score 0.551 Round 4: 334 peptides, 43 chains. Longest chain 22 peptides. Score 0.562 Round 5: 333 peptides, 43 chains. Longest chain 22 peptides. Score 0.560 Taking the results from Round 4 Chains 43, Residues 291, Estimated correctness of the model 15.8 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9140 restraints for refining 4219 atoms. 7929 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2527 (Rfree = 0.000) for 4219 atoms. Found 25 (25 requested) and removed 21 (15 requested) atoms. Cycle 32: After refmac, R = 0.2564 (Rfree = 0.000) for 4208 atoms. Found 25 (25 requested) and removed 19 (15 requested) atoms. Cycle 33: After refmac, R = 0.2523 (Rfree = 0.000) for 4202 atoms. Found 25 (25 requested) and removed 23 (15 requested) atoms. Cycle 34: After refmac, R = 0.2458 (Rfree = 0.000) for 4195 atoms. Found 25 (25 requested) and removed 19 (15 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2153 (Rfree = 0.000) for 4191 atoms. Found 13 (25 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 2.99 Search for helices and strands: 0 residues in 0 chains, 4281 seeds are put forward NCS extension: 12 residues added (7 deleted due to clashes), 4293 seeds are put forward Round 1: 284 peptides, 42 chains. Longest chain 23 peptides. Score 0.469 Round 2: 303 peptides, 42 chains. Longest chain 23 peptides. Score 0.509 Round 3: 313 peptides, 43 chains. Longest chain 18 peptides. Score 0.521 Round 4: 313 peptides, 37 chains. Longest chain 23 peptides. Score 0.574 Round 5: 314 peptides, 45 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 4 Chains 37, Residues 276, Estimated correctness of the model 20.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9343 restraints for refining 4215 atoms. 8276 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2490 (Rfree = 0.000) for 4215 atoms. Found 25 (25 requested) and removed 26 (15 requested) atoms. Cycle 37: After refmac, R = 0.2256 (Rfree = 0.000) for 4212 atoms. Found 22 (25 requested) and removed 18 (15 requested) atoms. Cycle 38: After refmac, R = 0.2491 (Rfree = 0.000) for 4209 atoms. Found 25 (25 requested) and removed 19 (15 requested) atoms. Cycle 39: After refmac, R = 0.2462 (Rfree = 0.000) for 4209 atoms. Found 25 (25 requested) and removed 19 (15 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2176 (Rfree = 0.000) for 4207 atoms. Found 12 (25 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.14 2.98 Search for helices and strands: 0 residues in 0 chains, 4325 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 4334 seeds are put forward Round 1: 280 peptides, 49 chains. Longest chain 15 peptides. Score 0.390 Round 2: 317 peptides, 45 chains. Longest chain 17 peptides. Score 0.510 Round 3: 335 peptides, 47 chains. Longest chain 18 peptides. Score 0.529 Round 4: 332 peptides, 47 chains. Longest chain 22 peptides. Score 0.523 Round 5: 325 peptides, 43 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 5 Chains 43, Residues 282, Estimated correctness of the model 9.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9962 reflections ( 99.63 % complete ) and 9526 restraints for refining 4219 atoms. 8441 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2626 (Rfree = 0.000) for 4219 atoms. Found 25 (25 requested) and removed 18 (15 requested) atoms. Cycle 42: After refmac, R = 0.2674 (Rfree = 0.000) for 4220 atoms. Found 25 (25 requested) and removed 19 (15 requested) atoms. Cycle 43: After refmac, R = 0.2621 (Rfree = 0.000) for 4216 atoms. Found 25 (25 requested) and removed 24 (15 requested) atoms. Cycle 44: After refmac, R = 0.2253 (Rfree = 0.000) for 4211 atoms. Found 13 (25 requested) and removed 17 (15 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2352 (Rfree = 0.000) for 4202 atoms. Found 22 (25 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, 4316 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 4336 seeds are put forward Round 1: 251 peptides, 44 chains. Longest chain 14 peptides. Score 0.372 Round 2: 297 peptides, 43 chains. Longest chain 18 peptides. Score 0.487 Round 3: 300 peptides, 44 chains. Longest chain 18 peptides. Score 0.484 Round 4: 274 peptides, 42 chains. Longest chain 18 peptides. Score 0.446 Round 5: 279 peptides, 39 chains. Longest chain 19 peptides. Score 0.487 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 240, 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 9525 restraints for refining 4219 atoms. 8604 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2589 (Rfree = 0.000) for 4219 atoms. Found 0 (25 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2576 (Rfree = 0.000) for 4196 atoms. Found 0 (25 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2571 (Rfree = 0.000) for 4174 atoms. Found 0 (25 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2239 (Rfree = 0.000) for 4150 atoms. Found 0 (25 requested) and removed 15 (15 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 81.13