Mon 24 Dec 00:12:00 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 2fno-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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/2fno-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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 ============================================================ Mon 24 Dec 00:12:04 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/2fno-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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 403 and 0 Target number of residues in the AU: 403 Target solvent content: 0.6285 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3968 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: 106.006 3.400 Wilson plot Bfac: 65.36 8176 reflections ( 99.32 % complete ) and 0 restraints for refining 4386 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3164 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3159 (Rfree = 0.000) for 4386 atoms. Found 33 (33 requested) and removed 56 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 4464 seeds are put forward NCS extension: 0 residues added, 4464 seeds are put forward Round 1: 220 peptides, 44 chains. Longest chain 8 peptides. Score 0.307 Round 2: 270 peptides, 42 chains. Longest chain 14 peptides. Score 0.468 Round 3: 269 peptides, 41 chains. Longest chain 19 peptides. Score 0.476 Round 4: 283 peptides, 43 chains. Longest chain 16 peptides. Score 0.489 Round 5: 292 peptides, 41 chains. Longest chain 16 peptides. Score 0.531 Taking the results from Round 5 Chains 41, Residues 251, Estimated correctness of the model 4.6 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 7864 restraints for refining 3605 atoms. 6831 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2677 (Rfree = 0.000) for 3605 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. Cycle 2: After refmac, R = 0.2656 (Rfree = 0.000) for 3555 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 3: After refmac, R = 0.2599 (Rfree = 0.000) for 3543 atoms. Found 26 (26 requested) and removed 35 (13 requested) atoms. Cycle 4: After refmac, R = 0.2508 (Rfree = 0.000) for 3520 atoms. Found 26 (26 requested) and removed 32 (13 requested) atoms. Cycle 5: After refmac, R = 0.2477 (Rfree = 0.000) for 3499 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3649 seeds are put forward NCS extension: 27 residues added (2 deleted due to clashes), 3676 seeds are put forward Round 1: 278 peptides, 46 chains. Longest chain 15 peptides. Score 0.444 Round 2: 298 peptides, 38 chains. Longest chain 21 peptides. Score 0.574 Round 3: 298 peptides, 36 chains. Longest chain 17 peptides. Score 0.593 Round 4: 307 peptides, 39 chains. Longest chain 25 peptides. Score 0.584 Round 5: 294 peptides, 37 chains. Longest chain 19 peptides. Score 0.575 Taking the results from Round 3 Chains 39, Residues 262, Estimated correctness of the model 26.4 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 7606 restraints for refining 3606 atoms. 6402 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2524 (Rfree = 0.000) for 3606 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 7: After refmac, R = 0.2446 (Rfree = 0.000) for 3594 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 8: After refmac, R = 0.2728 (Rfree = 0.000) for 3587 atoms. Found 21 (27 requested) and removed 28 (13 requested) atoms. Cycle 9: After refmac, R = 0.2459 (Rfree = 0.000) for 3551 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 10: After refmac, R = 0.2350 (Rfree = 0.000) for 3553 atoms. Found 16 (26 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 3691 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3710 seeds are put forward Round 1: 256 peptides, 41 chains. Longest chain 13 peptides. Score 0.443 Round 2: 293 peptides, 38 chains. Longest chain 20 peptides. Score 0.564 Round 3: 287 peptides, 40 chains. Longest chain 22 peptides. Score 0.530 Round 4: 285 peptides, 34 chains. Longest chain 21 peptides. Score 0.585 Round 5: 282 peptides, 38 chains. Longest chain 20 peptides. Score 0.539 Taking the results from Round 4 Chains 37, Residues 251, Estimated correctness of the model 23.7 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 7916 restraints for refining 3608 atoms. 6801 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2713 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 12: After refmac, R = 0.2577 (Rfree = 0.000) for 3589 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 13: After refmac, R = 0.2542 (Rfree = 0.000) for 3582 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 14: After refmac, R = 0.2440 (Rfree = 0.000) for 3576 atoms. Found 27 (27 requested) and removed 22 (13 requested) atoms. Cycle 15: After refmac, R = 0.2415 (Rfree = 0.000) for 3575 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3731 seeds are put forward Round 1: 254 peptides, 45 chains. Longest chain 14 peptides. Score 0.392 Round 2: 282 peptides, 41 chains. Longest chain 18 peptides. Score 0.508 Round 3: 266 peptides, 38 chains. Longest chain 14 peptides. Score 0.501 Round 4: 272 peptides, 37 chains. Longest chain 18 peptides. Score 0.526 Round 5: 264 peptides, 32 chains. Longest chain 25 peptides. Score 0.560 Taking the results from Round 5 Chains 34, Residues 232, Estimated correctness of the model 15.1 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8117 restraints for refining 3608 atoms. 7173 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2456 (Rfree = 0.000) for 3608 atoms. Found 23 (27 requested) and removed 20 (13 requested) atoms. Cycle 17: After refmac, R = 0.2455 (Rfree = 0.000) for 3596 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. Cycle 18: After refmac, R = 0.2562 (Rfree = 0.000) for 3595 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 19: After refmac, R = 0.2548 (Rfree = 0.000) for 3589 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 20: After refmac, R = 0.2572 (Rfree = 0.000) for 3581 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.19 Search for helices and strands: 0 residues in 0 chains, 3730 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 3756 seeds are put forward Round 1: 229 peptides, 43 chains. Longest chain 11 peptides. Score 0.345 Round 2: 255 peptides, 37 chains. Longest chain 16 peptides. Score 0.485 Round 3: 273 peptides, 33 chains. Longest chain 22 peptides. Score 0.569 Round 4: 277 peptides, 35 chains. Longest chain 26 peptides. Score 0.558 Round 5: 289 peptides, 37 chains. Longest chain 17 peptides. Score 0.565 Taking the results from Round 3 Chains 33, Residues 240, Estimated correctness of the model 18.2 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 7747 restraints for refining 3607 atoms. 6658 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2480 (Rfree = 0.000) for 3607 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Cycle 22: After refmac, R = 0.2682 (Rfree = 0.000) for 3588 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 23: After refmac, R = 0.2643 (Rfree = 0.000) for 3581 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 24: After refmac, R = 0.2581 (Rfree = 0.000) for 3572 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 25: After refmac, R = 0.2475 (Rfree = 0.000) for 3570 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 3.18 Search for helices and strands: 0 residues in 0 chains, 3712 seeds are put forward NCS extension: 50 residues added (1 deleted due to clashes), 3762 seeds are put forward Round 1: 215 peptides, 34 chains. Longest chain 16 peptides. Score 0.416 Round 2: 260 peptides, 37 chains. Longest chain 17 peptides. Score 0.498 Round 3: 257 peptides, 37 chains. Longest chain 18 peptides. Score 0.490 Round 4: 263 peptides, 37 chains. Longest chain 19 peptides. Score 0.505 Round 5: 251 peptides, 35 chains. Longest chain 18 peptides. Score 0.497 Taking the results from Round 4 Chains 38, Residues 226, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8290 restraints for refining 3607 atoms. 7397 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2545 (Rfree = 0.000) for 3607 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 27: After refmac, R = 0.2322 (Rfree = 0.000) for 3598 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. Cycle 28: After refmac, R = 0.2358 (Rfree = 0.000) for 3602 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 29: After refmac, R = 0.2220 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 30: After refmac, R = 0.2256 (Rfree = 0.000) for 3604 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3771 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3790 seeds are put forward Round 1: 205 peptides, 35 chains. Longest chain 15 peptides. Score 0.375 Round 2: 249 peptides, 37 chains. Longest chain 12 peptides. Score 0.470 Round 3: 260 peptides, 37 chains. Longest chain 18 peptides. Score 0.498 Round 4: 258 peptides, 39 chains. Longest chain 21 peptides. Score 0.471 Round 5: 256 peptides, 37 chains. Longest chain 13 peptides. Score 0.488 Taking the results from Round 3 Chains 37, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8364 restraints for refining 3608 atoms. 7509 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2476 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 14 (13 requested) atoms. Cycle 32: After refmac, R = 0.2262 (Rfree = 0.000) for 3614 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.2245 (Rfree = 0.000) for 3615 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 34: After refmac, R = 0.2196 (Rfree = 0.000) for 3619 atoms. Found 26 (27 requested) and removed 42 (13 requested) atoms. Cycle 35: After refmac, R = 0.1975 (Rfree = 0.000) for 3593 atoms. Found 15 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3750 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3765 seeds are put forward Round 1: 228 peptides, 45 chains. Longest chain 11 peptides. Score 0.318 Round 2: 270 peptides, 40 chains. Longest chain 18 peptides. Score 0.490 Round 3: 260 peptides, 40 chains. Longest chain 16 peptides. Score 0.465 Round 4: 262 peptides, 37 chains. Longest chain 17 peptides. Score 0.502 Round 5: 266 peptides, 37 chains. Longest chain 19 peptides. Score 0.512 Taking the results from Round 5 Chains 39, Residues 229, Estimated correctness of the model 0.0 % 4 chains (36 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 7861 restraints for refining 3608 atoms. 6876 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2512 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 24 (13 requested) atoms. Cycle 37: After refmac, R = 0.2301 (Rfree = 0.000) for 3586 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 38: After refmac, R = 0.2389 (Rfree = 0.000) for 3579 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 39: After refmac, R = 0.2092 (Rfree = 0.000) for 3577 atoms. Found 23 (27 requested) and removed 17 (13 requested) atoms. Cycle 40: After refmac, R = 0.2023 (Rfree = 0.000) for 3576 atoms. Found 17 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 3713 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3730 seeds are put forward Round 1: 209 peptides, 41 chains. Longest chain 11 peptides. Score 0.311 Round 2: 219 peptides, 38 chains. Longest chain 12 peptides. Score 0.378 Round 3: 240 peptides, 38 chains. Longest chain 13 peptides. Score 0.435 Round 4: 234 peptides, 35 chains. Longest chain 19 peptides. Score 0.454 Round 5: 226 peptides, 35 chains. Longest chain 14 peptides. Score 0.433 Taking the results from Round 4 Chains 35, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8176 reflections ( 99.32 % complete ) and 8481 restraints for refining 3608 atoms. 7720 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2539 (Rfree = 0.000) for 3608 atoms. Found 27 (27 requested) and removed 54 (13 requested) atoms. Cycle 42: After refmac, R = 0.2338 (Rfree = 0.000) for 3569 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. Cycle 43: After refmac, R = 0.2022 (Rfree = 0.000) for 3569 atoms. Found 17 (27 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1945 (Rfree = 0.000) for 3563 atoms. Found 14 (26 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1897 (Rfree = 0.000) for 3559 atoms. Found 9 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3690 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3709 seeds are put forward Round 1: 169 peptides, 36 chains. Longest chain 10 peptides. Score 0.252 Round 2: 188 peptides, 34 chains. Longest chain 12 peptides. Score 0.338 Round 3: 196 peptides, 33 chains. Longest chain 13 peptides. Score 0.375 Round 4: 190 peptides, 29 chains. Longest chain 18 peptides. Score 0.408 Round 5: 193 peptides, 33 chains. Longest chain 12 peptides. Score 0.366 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 161, 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 2fno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8176 reflections ( 99.32 % complete ) and 8757 restraints for refining 3607 atoms. 8142 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2360 (Rfree = 0.000) for 3607 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1886 (Rfree = 0.000) for 3585 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1912 (Rfree = 0.000) for 3566 atoms. Found 0 (26 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1768 (Rfree = 0.000) for 3551 atoms. TimeTaking 42.08