Mon 24 Dec 00:30:58 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 2it9-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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/2it9-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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 00:31:08 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/2it9-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-3.8-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 383 and 0 Target number of residues in the AU: 383 Target solvent content: 0.6555 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.8-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4064 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: 67.879 3.800 Wilson plot Bfac: 81.37 6215 reflections ( 98.15 % complete ) and 0 restraints for refining 4532 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3618 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3324 (Rfree = 0.000) for 4532 atoms. Found 24 (24 requested) and removed 66 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 4605 seeds are put forward NCS extension: 0 residues added, 4605 seeds are put forward Round 1: 229 peptides, 44 chains. Longest chain 10 peptides. Score 0.330 Round 2: 259 peptides, 39 chains. Longest chain 14 peptides. Score 0.468 Round 3: 260 peptides, 37 chains. Longest chain 20 peptides. Score 0.492 Round 4: 280 peptides, 38 chains. Longest chain 22 peptides. Score 0.528 Round 5: 279 peptides, 36 chains. Longest chain 20 peptides. Score 0.546 Taking the results from Round 5 Chains 36, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8370 restraints for refining 3674 atoms. 7434 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2519 (Rfree = 0.000) for 3674 atoms. Found 20 (20 requested) and removed 38 (10 requested) atoms. Cycle 2: After refmac, R = 0.2328 (Rfree = 0.000) for 3613 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 3: After refmac, R = 0.2172 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 4: After refmac, R = 0.2073 (Rfree = 0.000) for 3570 atoms. Found 17 (19 requested) and removed 16 (9 requested) atoms. Cycle 5: After refmac, R = 0.1724 (Rfree = 0.000) for 3560 atoms. Found 7 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3706 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 3719 seeds are put forward Round 1: 266 peptides, 45 chains. Longest chain 26 peptides. Score 0.419 Round 2: 299 peptides, 45 chains. Longest chain 17 peptides. Score 0.500 Round 3: 276 peptides, 40 chains. Longest chain 26 peptides. Score 0.498 Round 4: 275 peptides, 43 chains. Longest chain 30 peptides. Score 0.464 Round 5: 297 peptides, 40 chains. Longest chain 26 peptides. Score 0.546 Taking the results from Round 5 Chains 40, Residues 257, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8214 restraints for refining 3676 atoms. 7226 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2239 (Rfree = 0.000) for 3676 atoms. Found 15 (20 requested) and removed 36 (10 requested) atoms. Cycle 7: After refmac, R = 0.1979 (Rfree = 0.000) for 3621 atoms. Found 5 (20 requested) and removed 21 (10 requested) atoms. Cycle 8: After refmac, R = 0.1998 (Rfree = 0.000) for 3581 atoms. Found 11 (19 requested) and removed 18 (9 requested) atoms. Cycle 9: After refmac, R = 0.1946 (Rfree = 0.000) for 3555 atoms. Found 6 (19 requested) and removed 16 (9 requested) atoms. Cycle 10: After refmac, R = 0.1849 (Rfree = 0.000) for 3539 atoms. Found 13 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 3680 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3708 seeds are put forward Round 1: 232 peptides, 39 chains. Longest chain 19 peptides. Score 0.398 Round 2: 275 peptides, 41 chains. Longest chain 24 peptides. Score 0.485 Round 3: 287 peptides, 42 chains. Longest chain 25 peptides. Score 0.503 Round 4: 285 peptides, 42 chains. Longest chain 14 peptides. Score 0.498 Round 5: 277 peptides, 39 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 5 Chains 39, Residues 238, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8211 restraints for refining 3675 atoms. 7247 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2238 (Rfree = 0.000) for 3675 atoms. Found 15 (20 requested) and removed 29 (10 requested) atoms. Cycle 12: After refmac, R = 0.2207 (Rfree = 0.000) for 3641 atoms. Found 17 (20 requested) and removed 22 (10 requested) atoms. Cycle 13: After refmac, R = 0.2220 (Rfree = 0.000) for 3626 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 14: After refmac, R = 0.1822 (Rfree = 0.000) for 3609 atoms. Found 6 (19 requested) and removed 16 (9 requested) atoms. Cycle 15: After refmac, R = 0.1771 (Rfree = 0.000) for 3591 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 3707 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3726 seeds are put forward Round 1: 251 peptides, 44 chains. Longest chain 13 peptides. Score 0.391 Round 2: 274 peptides, 43 chains. Longest chain 14 peptides. Score 0.461 Round 3: 280 peptides, 40 chains. Longest chain 21 peptides. Score 0.507 Round 4: 275 peptides, 38 chains. Longest chain 17 peptides. Score 0.517 Round 5: 274 peptides, 39 chains. Longest chain 19 peptides. Score 0.504 Taking the results from Round 4 Chains 41, Residues 237, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8152 restraints for refining 3675 atoms. 7170 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2348 (Rfree = 0.000) for 3675 atoms. Found 7 (20 requested) and removed 20 (10 requested) atoms. Cycle 17: After refmac, R = 0.2228 (Rfree = 0.000) for 3639 atoms. Found 7 (20 requested) and removed 15 (10 requested) atoms. Cycle 18: After refmac, R = 0.2258 (Rfree = 0.000) for 3626 atoms. Found 7 (19 requested) and removed 15 (9 requested) atoms. Cycle 19: After refmac, R = 0.1925 (Rfree = 0.000) for 3612 atoms. Found 4 (19 requested) and removed 16 (9 requested) atoms. Cycle 20: After refmac, R = 0.1971 (Rfree = 0.000) for 3590 atoms. Found 6 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 3668 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3685 seeds are put forward Round 1: 220 peptides, 40 chains. Longest chain 13 peptides. Score 0.353 Round 2: 268 peptides, 43 chains. Longest chain 14 peptides. Score 0.446 Round 3: 270 peptides, 42 chains. Longest chain 14 peptides. Score 0.462 Round 4: 260 peptides, 39 chains. Longest chain 14 peptides. Score 0.470 Round 5: 284 peptides, 41 chains. Longest chain 19 peptides. Score 0.507 Taking the results from Round 5 Chains 41, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8259 restraints for refining 3676 atoms. 7328 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2315 (Rfree = 0.000) for 3676 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 22: After refmac, R = 0.2220 (Rfree = 0.000) for 3664 atoms. Found 18 (20 requested) and removed 20 (10 requested) atoms. Cycle 23: After refmac, R = 0.1877 (Rfree = 0.000) for 3648 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. Cycle 24: After refmac, R = 0.1802 (Rfree = 0.000) for 3624 atoms. Found 4 (20 requested) and removed 11 (10 requested) atoms. Cycle 25: After refmac, R = 0.1816 (Rfree = 0.000) for 3613 atoms. Found 6 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 3726 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3739 seeds are put forward Round 1: 210 peptides, 40 chains. Longest chain 11 peptides. Score 0.324 Round 2: 244 peptides, 40 chains. Longest chain 16 peptides. Score 0.418 Round 3: 255 peptides, 42 chains. Longest chain 15 peptides. Score 0.424 Round 4: 259 peptides, 40 chains. Longest chain 12 peptides. Score 0.457 Round 5: 250 peptides, 41 chains. Longest chain 12 peptides. Score 0.423 Taking the results from Round 4 Chains 40, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8470 restraints for refining 3675 atoms. 7634 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2384 (Rfree = 0.000) for 3675 atoms. Found 17 (20 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2336 (Rfree = 0.000) for 3644 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 28: After refmac, R = 0.2364 (Rfree = 0.000) for 3633 atoms. Found 19 (20 requested) and removed 17 (10 requested) atoms. Cycle 29: After refmac, R = 0.2243 (Rfree = 0.000) for 3615 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 30: After refmac, R = 0.2150 (Rfree = 0.000) for 3604 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 3725 seeds are put forward NCS extension: 0 residues added, 3725 seeds are put forward Round 1: 213 peptides, 42 chains. Longest chain 8 peptides. Score 0.308 Round 2: 221 peptides, 36 chains. Longest chain 13 peptides. Score 0.404 Round 3: 220 peptides, 35 chains. Longest chain 11 peptides. Score 0.413 Round 4: 227 peptides, 34 chains. Longest chain 21 peptides. Score 0.443 Round 5: 235 peptides, 35 chains. Longest chain 14 peptides. Score 0.452 Taking the results from Round 5 Chains 35, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8493 restraints for refining 3676 atoms. 7728 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2150 (Rfree = 0.000) for 3676 atoms. Found 16 (20 requested) and removed 25 (10 requested) atoms. Cycle 32: After refmac, R = 0.1919 (Rfree = 0.000) for 3647 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. Cycle 33: After refmac, R = 0.1983 (Rfree = 0.000) for 3633 atoms. Found 4 (20 requested) and removed 16 (10 requested) atoms. Cycle 34: After refmac, R = 0.1785 (Rfree = 0.000) for 3615 atoms. Found 1 (19 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.1777 (Rfree = 0.000) for 3596 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 3708 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3727 seeds are put forward Round 1: 205 peptides, 42 chains. Longest chain 11 peptides. Score 0.284 Round 2: 213 peptides, 37 chains. Longest chain 11 peptides. Score 0.370 Round 3: 217 peptides, 39 chains. Longest chain 16 peptides. Score 0.357 Round 4: 223 peptides, 38 chains. Longest chain 15 peptides. Score 0.385 Round 5: 216 peptides, 37 chains. Longest chain 13 peptides. Score 0.378 Taking the results from Round 4 Chains 38, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8462 restraints for refining 3676 atoms. 7760 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2198 (Rfree = 0.000) for 3676 atoms. Found 10 (20 requested) and removed 24 (10 requested) atoms. Cycle 37: After refmac, R = 0.2073 (Rfree = 0.000) for 3651 atoms. Found 9 (20 requested) and removed 23 (10 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2012 (Rfree = 0.000) for 3632 atoms. Found 8 (20 requested) and removed 15 (10 requested) atoms. Cycle 39: After refmac, R = 0.1825 (Rfree = 0.000) for 3624 atoms. Found 5 (19 requested) and removed 17 (9 requested) atoms. Cycle 40: After refmac, R = 0.1890 (Rfree = 0.000) for 3610 atoms. Found 2 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 3701 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3727 seeds are put forward Round 1: 190 peptides, 40 chains. Longest chain 7 peptides. Score 0.264 Round 2: 205 peptides, 38 chains. Longest chain 9 peptides. Score 0.334 Round 3: 213 peptides, 38 chains. Longest chain 11 peptides. Score 0.357 Round 4: 223 peptides, 35 chains. Longest chain 13 peptides. Score 0.421 Round 5: 201 peptides, 35 chains. Longest chain 15 peptides. Score 0.360 Taking the results from Round 4 Chains 36, Residues 188, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6215 reflections ( 98.15 % complete ) and 8284 restraints for refining 3675 atoms. 7529 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2117 (Rfree = 0.000) for 3675 atoms. Found 7 (20 requested) and removed 20 (10 requested) atoms. Cycle 42: After refmac, R = 0.1995 (Rfree = 0.000) for 3645 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. Cycle 43: After refmac, R = 0.1881 (Rfree = 0.000) for 3626 atoms. Found 5 (19 requested) and removed 16 (9 requested) atoms. Cycle 44: After refmac, R = 0.1894 (Rfree = 0.000) for 3602 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. Cycle 45: After refmac, R = 0.1704 (Rfree = 0.000) for 3593 atoms. Found 0 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 3690 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3702 seeds are put forward Round 1: 163 peptides, 35 chains. Longest chain 8 peptides. Score 0.245 Round 2: 184 peptides, 35 chains. Longest chain 9 peptides. Score 0.310 Round 3: 185 peptides, 33 chains. Longest chain 10 peptides. Score 0.339 Round 4: 198 peptides, 34 chains. Longest chain 10 peptides. Score 0.364 Round 5: 185 peptides, 32 chains. Longest chain 9 peptides. Score 0.352 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 164, 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 2it9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6215 reflections ( 98.15 % complete ) and 8568 restraints for refining 3676 atoms. 7946 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2113 (Rfree = 0.000) for 3676 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2205 (Rfree = 0.000) for 3644 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1849 (Rfree = 0.000) for 3622 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2472 (Rfree = 0.000) for 3604 atoms. TimeTaking 50.47