Mon 24 Dec 00:04:03 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 1vpm-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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/1vpm-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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 00:04:07 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/1vpm-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-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 329 and 0 Target number of residues in the AU: 329 Target solvent content: 0.6645 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4056 target number of atoms Had to go as low as 0.60 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: 79.699 3.801 Wilson plot Bfac: 87.91 Failed to save intermediate PDB 5369 reflections ( 97.71 % complete ) and 0 restraints for refining 4506 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3203 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3319 (Rfree = 0.000) for 4506 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 4574 seeds are put forward NCS extension: 0 residues added, 4574 seeds are put forward Round 1: 207 peptides, 40 chains. Longest chain 9 peptides. Score 0.330 Round 2: 265 peptides, 34 chains. Longest chain 23 peptides. Score 0.567 Round 3: 260 peptides, 34 chains. Longest chain 17 peptides. Score 0.555 Round 4: 281 peptides, 34 chains. Longest chain 25 peptides. Score 0.605 Round 5: 290 peptides, 36 chains. Longest chain 21 peptides. Score 0.604 Taking the results from Round 4 Chains 37, Residues 247, Estimated correctness of the model 1.1 % 4 chains (56 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7981 restraints for refining 3667 atoms. 6844 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2653 (Rfree = 0.000) for 3667 atoms. Found 10 (20 requested) and removed 35 (10 requested) atoms. Cycle 2: After refmac, R = 0.2668 (Rfree = 0.000) for 3532 atoms. Found 20 (20 requested) and removed 62 (10 requested) atoms. Cycle 3: After refmac, R = 0.2469 (Rfree = 0.000) for 3441 atoms. Found 11 (19 requested) and removed 26 (9 requested) atoms. Cycle 4: After refmac, R = 0.2078 (Rfree = 0.000) for 3389 atoms. Found 10 (18 requested) and removed 15 (9 requested) atoms. Cycle 5: After refmac, R = 0.2296 (Rfree = 0.000) for 3365 atoms. Found 5 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 3475 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 3500 seeds are put forward Round 1: 253 peptides, 42 chains. Longest chain 19 peptides. Score 0.443 Round 2: 284 peptides, 38 chains. Longest chain 25 peptides. Score 0.570 Round 3: 286 peptides, 31 chains. Longest chain 22 peptides. Score 0.645 Round 4: 289 peptides, 38 chains. Longest chain 18 peptides. Score 0.582 Round 5: 303 peptides, 35 chains. Longest chain 21 peptides. Score 0.642 Taking the results from Round 3 Chains 32, Residues 255, Estimated correctness of the model 18.7 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 7472 restraints for refining 3467 atoms. 6403 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2681 (Rfree = 0.000) for 3467 atoms. Found 13 (19 requested) and removed 34 (9 requested) atoms. Cycle 7: After refmac, R = 0.2169 (Rfree = 0.000) for 3389 atoms. Found 8 (18 requested) and removed 22 (9 requested) atoms. Cycle 8: After refmac, R = 0.2054 (Rfree = 0.000) for 3354 atoms. Found 10 (18 requested) and removed 18 (9 requested) atoms. Cycle 9: After refmac, R = 0.1981 (Rfree = 0.000) for 3330 atoms. Found 7 (18 requested) and removed 14 (9 requested) atoms. Cycle 10: After refmac, R = 0.2063 (Rfree = 0.000) for 3314 atoms. Found 9 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 3440 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3452 seeds are put forward Round 1: 227 peptides, 43 chains. Longest chain 14 peptides. Score 0.353 Round 2: 273 peptides, 41 chains. Longest chain 17 peptides. Score 0.510 Round 3: 275 peptides, 36 chains. Longest chain 18 peptides. Score 0.570 Round 4: 271 peptides, 35 chains. Longest chain 17 peptides. Score 0.571 Round 5: 271 peptides, 31 chains. Longest chain 26 peptides. Score 0.613 Taking the results from Round 5 Chains 32, Residues 240, Estimated correctness of the model 4.7 % 3 chains (59 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5369 reflections ( 97.71 % complete ) and 7703 restraints for refining 3669 atoms. 6540 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2318 (Rfree = 0.000) for 3669 atoms. Found 20 (20 requested) and removed 63 (10 requested) atoms. Cycle 12: After refmac, R = 0.2152 (Rfree = 0.000) for 3583 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 13: After refmac, R = 0.2053 (Rfree = 0.000) for 3544 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 14: After refmac, R = 0.2022 (Rfree = 0.000) for 3527 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 15: After refmac, R = 0.1902 (Rfree = 0.000) for 3507 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.72 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 3654 seeds are put forward Round 1: 220 peptides, 40 chains. Longest chain 10 peptides. Score 0.371 Round 2: 249 peptides, 37 chains. Longest chain 16 peptides. Score 0.493 Round 3: 251 peptides, 38 chains. Longest chain 16 peptides. Score 0.486 Round 4: 274 peptides, 36 chains. Longest chain 21 peptides. Score 0.567 Round 5: 257 peptides, 36 chains. Longest chain 17 peptides. Score 0.525 Taking the results from Round 4 Chains 38, Residues 238, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8199 restraints for refining 3668 atoms. 7225 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2320 (Rfree = 0.000) for 3668 atoms. Found 20 (20 requested) and removed 44 (10 requested) atoms. Cycle 17: After refmac, R = 0.2108 (Rfree = 0.000) for 3619 atoms. Found 20 (20 requested) and removed 70 (10 requested) atoms. Cycle 18: After refmac, R = 0.2102 (Rfree = 0.000) for 3546 atoms. Found 19 (19 requested) and removed 42 (9 requested) atoms. Cycle 19: After refmac, R = 0.2098 (Rfree = 0.000) for 3508 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 20: After refmac, R = 0.2062 (Rfree = 0.000) for 3487 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 3.78 Search for helices and strands: 0 residues in 0 chains, 3604 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3617 seeds are put forward Round 1: 188 peptides, 39 chains. Longest chain 9 peptides. Score 0.281 Round 2: 225 peptides, 36 chains. Longest chain 17 peptides. Score 0.438 Round 3: 219 peptides, 35 chains. Longest chain 17 peptides. Score 0.433 Round 4: 236 peptides, 35 chains. Longest chain 17 peptides. Score 0.481 Round 5: 227 peptides, 32 chains. Longest chain 18 peptides. Score 0.493 Taking the results from Round 5 Chains 32, Residues 195, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8218 restraints for refining 3582 atoms. 7429 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2363 (Rfree = 0.000) for 3582 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 22: After refmac, R = 0.2126 (Rfree = 0.000) for 3530 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 23: After refmac, R = 0.2175 (Rfree = 0.000) for 3506 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 24: After refmac, R = 0.1992 (Rfree = 0.000) for 3504 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 25: After refmac, R = 0.1921 (Rfree = 0.000) for 3501 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3653 seeds are put forward Round 1: 194 peptides, 38 chains. Longest chain 10 peptides. Score 0.315 Round 2: 232 peptides, 36 chains. Longest chain 12 peptides. Score 0.458 Round 3: 241 peptides, 37 chains. Longest chain 13 peptides. Score 0.471 Round 4: 240 peptides, 35 chains. Longest chain 14 peptides. Score 0.492 Round 5: 243 peptides, 36 chains. Longest chain 23 peptides. Score 0.488 Taking the results from Round 4 Chains 38, Residues 205, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8067 restraints for refining 3535 atoms. 7228 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2559 (Rfree = 0.000) for 3535 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 27: After refmac, R = 0.2275 (Rfree = 0.000) for 3509 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 28: After refmac, R = 0.2205 (Rfree = 0.000) for 3488 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.2127 (Rfree = 0.000) for 3477 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 30: After refmac, R = 0.1944 (Rfree = 0.000) for 3469 atoms. Found 18 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3609 seeds are put forward Round 1: 170 peptides, 35 chains. Longest chain 10 peptides. Score 0.277 Round 2: 198 peptides, 33 chains. Longest chain 12 peptides. Score 0.396 Round 3: 212 peptides, 36 chains. Longest chain 15 peptides. Score 0.399 Round 4: 207 peptides, 34 chains. Longest chain 13 peptides. Score 0.410 Round 5: 228 peptides, 35 chains. Longest chain 16 peptides. Score 0.459 Taking the results from Round 5 Chains 35, Residues 193, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8172 restraints for refining 3533 atoms. 7435 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2421 (Rfree = 0.000) for 3533 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 32: After refmac, R = 0.2087 (Rfree = 0.000) for 3499 atoms. Found 16 (19 requested) and removed 19 (9 requested) atoms. Cycle 33: After refmac, R = 0.2018 (Rfree = 0.000) for 3481 atoms. Found 18 (19 requested) and removed 17 (9 requested) atoms. Cycle 34: After refmac, R = 0.1972 (Rfree = 0.000) for 3471 atoms. Found 17 (19 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.2141 (Rfree = 0.000) for 3466 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.81 Search for helices and strands: 0 residues in 0 chains, 3592 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3608 seeds are put forward Round 1: 179 peptides, 38 chains. Longest chain 9 peptides. Score 0.264 Round 2: 186 peptides, 36 chains. Longest chain 10 peptides. Score 0.317 Round 3: 191 peptides, 32 chains. Longest chain 15 peptides. Score 0.388 Round 4: 204 peptides, 33 chains. Longest chain 14 peptides. Score 0.415 Round 5: 205 peptides, 33 chains. Longest chain 14 peptides. Score 0.417 Taking the results from Round 5 Chains 33, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8567 restraints for refining 3606 atoms. 7912 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2284 (Rfree = 0.000) for 3606 atoms. Found 18 (19 requested) and removed 31 (9 requested) atoms. Cycle 37: After refmac, R = 0.2224 (Rfree = 0.000) for 3575 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 38: After refmac, R = 0.2238 (Rfree = 0.000) for 3557 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. Cycle 39: After refmac, R = 0.2327 (Rfree = 0.000) for 3537 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.2149 (Rfree = 0.000) for 3529 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3644 seeds are put forward Round 1: 152 peptides, 32 chains. Longest chain 12 peptides. Score 0.258 Round 2: 196 peptides, 39 chains. Longest chain 14 peptides. Score 0.308 Round 3: 214 peptides, 40 chains. Longest chain 12 peptides. Score 0.352 Round 4: 216 peptides, 40 chains. Longest chain 12 peptides. Score 0.358 Round 5: 205 peptides, 36 chains. Longest chain 12 peptides. Score 0.378 Taking the results from Round 5 Chains 36, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5369 reflections ( 97.71 % complete ) and 8211 restraints for refining 3497 atoms. 7571 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1949 (Rfree = 0.000) for 3497 atoms. Found 13 (19 requested) and removed 18 (9 requested) atoms. Cycle 42: After refmac, R = 0.1928 (Rfree = 0.000) for 3477 atoms. Found 13 (19 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.1998 (Rfree = 0.000) for 3471 atoms. Found 9 (19 requested) and removed 21 (9 requested) atoms. Cycle 44: After refmac, R = 0.1840 (Rfree = 0.000) for 3450 atoms. Found 15 (19 requested) and removed 20 (9 requested) atoms. Cycle 45: After refmac, R = 0.1765 (Rfree = 0.000) for 3441 atoms. Found 15 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.73 Search for helices and strands: 0 residues in 0 chains, 3540 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3558 seeds are put forward Round 1: 166 peptides, 34 chains. Longest chain 12 peptides. Score 0.277 Round 2: 190 peptides, 33 chains. Longest chain 13 peptides. Score 0.371 Round 3: 188 peptides, 33 chains. Longest chain 15 peptides. Score 0.365 Round 4: 190 peptides, 32 chains. Longest chain 14 peptides. Score 0.385 Round 5: 191 peptides, 32 chains. Longest chain 16 peptides. Score 0.388 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 159, 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 1vpm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5369 reflections ( 97.71 % complete ) and 8571 restraints for refining 3577 atoms. 7967 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1929 (Rfree = 0.000) for 3577 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1895 (Rfree = 0.000) for 3553 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1873 (Rfree = 0.000) for 3536 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2024 (Rfree = 0.000) for 3521 atoms. TimeTaking 40.85