Mon 24 Dec 00:10:57 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 2fg0-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fg0-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-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/2fg0-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-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 ============================================================ Mon 24 Dec 00:11:01 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/2fg0-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fg0-3.6-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 511 and 0 Target number of residues in the AU: 511 Target solvent content: 0.6364 Checking the provided sequence file Detected sequence length: 246 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 492 Adjusted target solvent content: 0.65 Input MTZ file: 2fg0-3.6-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: 92 Cell parameters: 124.890 124.890 97.540 90.000 90.000 90.000 Input sequence file: 2fg0-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3936 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: 88.311 3.600 Wilson plot Bfac: 69.79 9346 reflections ( 99.70 % complete ) and 0 restraints for refining 4331 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.2987 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3050 (Rfree = 0.000) for 4331 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 2.81 Search for helices and strands: 0 residues in 0 chains, 4412 seeds are put forward NCS extension: 0 residues added, 4412 seeds are put forward Round 1: 274 peptides, 37 chains. Longest chain 16 peptides. Score 0.471 Round 2: 306 peptides, 32 chains. Longest chain 23 peptides. Score 0.574 Round 3: 312 peptides, 33 chains. Longest chain 24 peptides. Score 0.576 Round 4: 322 peptides, 32 chains. Longest chain 30 peptides. Score 0.600 Round 5: 324 peptides, 32 chains. Longest chain 23 peptides. Score 0.603 Taking the results from Round 5 Chains 32, Residues 292, Estimated correctness of the model 15.8 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7378 restraints for refining 3568 atoms. 6082 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2853 (Rfree = 0.000) for 3568 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 2: After refmac, R = 0.2668 (Rfree = 0.000) for 3493 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 3: After refmac, R = 0.2538 (Rfree = 0.000) for 3450 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 4: After refmac, R = 0.2282 (Rfree = 0.000) for 3420 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 5: After refmac, R = 0.2148 (Rfree = 0.000) for 3401 atoms. Found 20 (21 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 2.78 Search for helices and strands: 0 residues in 0 chains, 3542 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3562 seeds are put forward Round 1: 309 peptides, 36 chains. Longest chain 25 peptides. Score 0.546 Round 2: 322 peptides, 30 chains. Longest chain 36 peptides. Score 0.615 Round 3: 324 peptides, 33 chains. Longest chain 26 peptides. Score 0.596 Round 4: 330 peptides, 29 chains. Longest chain 36 peptides. Score 0.635 Round 5: 335 peptides, 32 chains. Longest chain 31 peptides. Score 0.621 Taking the results from Round 4 Chains 33, Residues 301, Estimated correctness of the model 27.8 % 5 chains (92 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6819 restraints for refining 3567 atoms. 5274 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3217 (Rfree = 0.000) for 3567 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. Cycle 7: After refmac, R = 0.2838 (Rfree = 0.000) for 3475 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 8: After refmac, R = 0.2756 (Rfree = 0.000) for 3427 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 9: After refmac, R = 0.2584 (Rfree = 0.000) for 3405 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 10: After refmac, R = 0.2490 (Rfree = 0.000) for 3377 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.79 Search for helices and strands: 0 residues in 0 chains, 3488 seeds are put forward NCS extension: 31 residues added (12 deleted due to clashes), 3519 seeds are put forward Round 1: 302 peptides, 36 chains. Longest chain 25 peptides. Score 0.533 Round 2: 335 peptides, 32 chains. Longest chain 34 peptides. Score 0.621 Round 3: 338 peptides, 33 chains. Longest chain 32 peptides. Score 0.618 Round 4: 327 peptides, 32 chains. Longest chain 29 peptides. Score 0.608 Round 5: 332 peptides, 33 chains. Longest chain 42 peptides. Score 0.609 Taking the results from Round 2 Chains 33, Residues 303, Estimated correctness of the model 22.7 % 3 chains (69 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6984 restraints for refining 3563 atoms. 5530 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2604 (Rfree = 0.000) for 3563 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 12: After refmac, R = 0.2475 (Rfree = 0.000) for 3538 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 13: After refmac, R = 0.2423 (Rfree = 0.000) for 3524 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 14: After refmac, R = 0.2402 (Rfree = 0.000) for 3509 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 15: After refmac, R = 0.2415 (Rfree = 0.000) for 3500 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 2.78 Search for helices and strands: 0 residues in 0 chains, 3601 seeds are put forward NCS extension: 25 residues added (20 deleted due to clashes), 3626 seeds are put forward Round 1: 301 peptides, 35 chains. Longest chain 29 peptides. Score 0.540 Round 2: 334 peptides, 29 chains. Longest chain 41 peptides. Score 0.641 Round 3: 334 peptides, 27 chains. Longest chain 44 peptides. Score 0.656 Round 4: 331 peptides, 31 chains. Longest chain 38 peptides. Score 0.622 Round 5: 315 peptides, 28 chains. Longest chain 26 peptides. Score 0.620 Taking the results from Round 3 Chains 32, Residues 307, Estimated correctness of the model 35.2 % 5 chains (95 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6822 restraints for refining 3568 atoms. 5266 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2498 (Rfree = 0.000) for 3568 atoms. Found 20 (22 requested) and removed 26 (11 requested) atoms. Cycle 17: After refmac, R = 0.2450 (Rfree = 0.000) for 3531 atoms. Found 20 (22 requested) and removed 26 (11 requested) atoms. Cycle 18: After refmac, R = 0.2341 (Rfree = 0.000) for 3509 atoms. Found 14 (22 requested) and removed 21 (11 requested) atoms. Cycle 19: After refmac, R = 0.2390 (Rfree = 0.000) for 3495 atoms. Found 11 (22 requested) and removed 17 (11 requested) atoms. Cycle 20: After refmac, R = 0.2346 (Rfree = 0.000) for 3486 atoms. Found 5 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 2.81 Search for helices and strands: 0 residues in 0 chains, 3605 seeds are put forward NCS extension: 48 residues added (6 deleted due to clashes), 3653 seeds are put forward Round 1: 299 peptides, 34 chains. Longest chain 22 peptides. Score 0.545 Round 2: 330 peptides, 32 chains. Longest chain 42 peptides. Score 0.613 Round 3: 317 peptides, 34 chains. Longest chain 29 peptides. Score 0.576 Round 4: 323 peptides, 31 chains. Longest chain 51 peptides. Score 0.609 Round 5: 329 peptides, 32 chains. Longest chain 42 peptides. Score 0.611 Taking the results from Round 2 Chains 32, Residues 298, Estimated correctness of the model 19.7 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7702 restraints for refining 3567 atoms. 6475 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2525 (Rfree = 0.000) for 3567 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 22: After refmac, R = 0.2444 (Rfree = 0.000) for 3552 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 23: After refmac, R = 0.2511 (Rfree = 0.000) for 3539 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 24: After refmac, R = 0.2249 (Rfree = 0.000) for 3533 atoms. Found 11 (22 requested) and removed 17 (11 requested) atoms. Cycle 25: After refmac, R = 0.2274 (Rfree = 0.000) for 3520 atoms. Found 21 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 2.75 Search for helices and strands: 0 residues in 0 chains, 3633 seeds are put forward NCS extension: 59 residues added (30 deleted due to clashes), 3692 seeds are put forward Round 1: 291 peptides, 40 chains. Longest chain 19 peptides. Score 0.478 Round 2: 309 peptides, 34 chains. Longest chain 29 peptides. Score 0.562 Round 3: 308 peptides, 31 chains. Longest chain 36 peptides. Score 0.585 Round 4: 315 peptides, 30 chains. Longest chain 44 peptides. Score 0.604 Round 5: 304 peptides, 33 chains. Longest chain 22 peptides. Score 0.562 Taking the results from Round 4 Chains 32, Residues 285, Estimated correctness of the model 16.2 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7371 restraints for refining 3568 atoms. 6069 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2585 (Rfree = 0.000) for 3568 atoms. Found 21 (22 requested) and removed 23 (11 requested) atoms. Cycle 27: After refmac, R = 0.2454 (Rfree = 0.000) for 3530 atoms. Found 21 (22 requested) and removed 16 (11 requested) atoms. Cycle 28: After refmac, R = 0.2243 (Rfree = 0.000) for 3509 atoms. Found 17 (22 requested) and removed 14 (11 requested) atoms. Cycle 29: After refmac, R = 0.2171 (Rfree = 0.000) for 3500 atoms. Found 9 (22 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.2141 (Rfree = 0.000) for 3486 atoms. Found 11 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 2.77 Search for helices and strands: 0 residues in 0 chains, 3610 seeds are put forward NCS extension: 31 residues added (12 deleted due to clashes), 3641 seeds are put forward Round 1: 280 peptides, 37 chains. Longest chain 25 peptides. Score 0.483 Round 2: 316 peptides, 30 chains. Longest chain 34 peptides. Score 0.606 Round 3: 323 peptides, 33 chains. Longest chain 30 peptides. Score 0.594 Round 4: 322 peptides, 35 chains. Longest chain 44 peptides. Score 0.577 Round 5: 305 peptides, 32 chains. Longest chain 31 peptides. Score 0.572 Taking the results from Round 2 Chains 35, Residues 286, Estimated correctness of the model 17.0 % 7 chains (110 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 6759 restraints for refining 3567 atoms. 5238 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2430 (Rfree = 0.000) for 3567 atoms. Found 20 (22 requested) and removed 28 (11 requested) atoms. Cycle 32: After refmac, R = 0.2296 (Rfree = 0.000) for 3535 atoms. Found 11 (22 requested) and removed 18 (11 requested) atoms. Cycle 33: After refmac, R = 0.2253 (Rfree = 0.000) for 3517 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.2231 (Rfree = 0.000) for 3503 atoms. Found 12 (22 requested) and removed 16 (11 requested) atoms. Cycle 35: After refmac, R = 0.2225 (Rfree = 0.000) for 3489 atoms. Found 17 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 2.76 Search for helices and strands: 0 residues in 0 chains, 3591 seeds are put forward NCS extension: 22 residues added (19 deleted due to clashes), 3613 seeds are put forward Round 1: 298 peptides, 36 chains. Longest chain 29 peptides. Score 0.526 Round 2: 295 peptides, 35 chains. Longest chain 21 peptides. Score 0.529 Round 3: 301 peptides, 33 chains. Longest chain 26 peptides. Score 0.557 Round 4: 313 peptides, 33 chains. Longest chain 32 peptides. Score 0.577 Round 5: 309 peptides, 36 chains. Longest chain 47 peptides. Score 0.546 Taking the results from Round 4 Chains 33, Residues 280, Estimated correctness of the model 5.5 % 5 chains (58 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7568 restraints for refining 3567 atoms. 6271 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2547 (Rfree = 0.000) for 3567 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 37: After refmac, R = 0.2458 (Rfree = 0.000) for 3538 atoms. Found 22 (22 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2335 (Rfree = 0.000) for 3533 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 39: After refmac, R = 0.2288 (Rfree = 0.000) for 3528 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 40: After refmac, R = 0.2258 (Rfree = 0.000) for 3522 atoms. Found 21 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 2.77 Search for helices and strands: 0 residues in 0 chains, 3631 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 3668 seeds are put forward Round 1: 287 peptides, 43 chains. Longest chain 17 peptides. Score 0.443 Round 2: 305 peptides, 41 chains. Longest chain 24 peptides. Score 0.496 Round 3: 291 peptides, 33 chains. Longest chain 29 peptides. Score 0.539 Round 4: 284 peptides, 36 chains. Longest chain 18 peptides. Score 0.500 Round 5: 313 peptides, 39 chains. Longest chain 19 peptides. Score 0.528 Taking the results from Round 3 Chains 35, Residues 258, Estimated correctness of the model 0.0 % 5 chains (69 residues) have been docked in sequence ------------------------------------------------------ 9346 reflections ( 99.70 % complete ) and 7333 restraints for refining 3567 atoms. 6070 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2525 (Rfree = 0.000) for 3567 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 42: After refmac, R = 0.2504 (Rfree = 0.000) for 3542 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 43: After refmac, R = 0.2460 (Rfree = 0.000) for 3535 atoms. Found 22 (22 requested) and removed 18 (11 requested) atoms. Cycle 44: After refmac, R = 0.2360 (Rfree = 0.000) for 3530 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 45: After refmac, R = 0.2335 (Rfree = 0.000) for 3525 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 2.82 Search for helices and strands: 0 residues in 0 chains, 3636 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 3658 seeds are put forward Round 1: 265 peptides, 42 chains. Longest chain 17 peptides. Score 0.406 Round 2: 281 peptides, 36 chains. Longest chain 21 peptides. Score 0.494 Round 3: 294 peptides, 36 chains. Longest chain 19 peptides. Score 0.519 Round 4: 300 peptides, 34 chains. Longest chain 28 peptides. Score 0.547 Round 5: 314 peptides, 41 chains. Longest chain 22 peptides. Score 0.513 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 266, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2fg0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9346 reflections ( 99.70 % complete ) and 7831 restraints for refining 3567 atoms. 6713 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2491 (Rfree = 0.000) for 3567 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2501 (Rfree = 0.000) for 3536 atoms. Found 0 (22 requested) and removed 9 (11 requested) atoms. Cycle 48: After refmac, R = 0.2449 (Rfree = 0.000) for 3513 atoms. Found 0 (22 requested) and removed 8 (11 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2395 (Rfree = 0.000) for 3503 atoms. TimeTaking 46.92