Mon 24 Dec 08:08:17 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fg0-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fg0-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fg0-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-parrot-noncs ############### 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 08:08:21 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/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fg0-4.0-parrot-noncs/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 479 and 0 Target number of residues in the AU: 479 Target solvent content: 0.6592 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: 2fg0-4.0-parrot-noncs.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: 2fg0-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3936 target number of atoms Had to go as low as 0.80 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 4.000 Wilson plot Bfac: 84.34 6886 reflections ( 99.59 % complete ) and 0 restraints for refining 4347 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3135 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3217 (Rfree = 0.000) for 4347 atoms. Found 20 (20 requested) and removed 30 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.09 Search for helices and strands: 0 residues in 0 chains, 4419 seeds are put forward NCS extension: 0 residues added, 4419 seeds are put forward Round 1: 231 peptides, 38 chains. Longest chain 12 peptides. Score 0.370 Round 2: 283 peptides, 32 chains. Longest chain 34 peptides. Score 0.533 Round 3: 294 peptides, 34 chains. Longest chain 17 peptides. Score 0.536 Round 4: 303 peptides, 32 chains. Longest chain 23 peptides. Score 0.568 Round 5: 304 peptides, 29 chains. Longest chain 24 peptides. Score 0.594 Taking the results from Round 5 Chains 33, Residues 275, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7561 restraints for refining 3554 atoms. 6344 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2741 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 2: After refmac, R = 0.2823 (Rfree = 0.000) for 3464 atoms. Found 13 (16 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.2863 (Rfree = 0.000) for 3443 atoms. Found 12 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2868 (Rfree = 0.000) for 3429 atoms. Found 2 (16 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2725 (Rfree = 0.000) for 3408 atoms. Found 11 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 3.07 Search for helices and strands: 0 residues in 0 chains, 3515 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3535 seeds are put forward Round 1: 285 peptides, 34 chains. Longest chain 21 peptides. Score 0.519 Round 2: 299 peptides, 33 chains. Longest chain 33 peptides. Score 0.553 Round 3: 291 peptides, 28 chains. Longest chain 23 peptides. Score 0.581 Round 4: 298 peptides, 31 chains. Longest chain 24 peptides. Score 0.568 Round 5: 294 peptides, 29 chains. Longest chain 36 peptides. Score 0.578 Taking the results from Round 3 Chains 29, Residues 263, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7635 restraints for refining 3444 atoms. 6584 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2908 (Rfree = 0.000) for 3444 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 7: After refmac, R = 0.2992 (Rfree = 0.000) for 3403 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 8: After refmac, R = 0.3006 (Rfree = 0.000) for 3385 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 9: After refmac, R = 0.2405 (Rfree = 0.000) for 3358 atoms. Found 14 (16 requested) and removed 17 (8 requested) atoms. Cycle 10: After refmac, R = 0.2298 (Rfree = 0.000) for 3343 atoms. Found 7 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.08 Search for helices and strands: 0 residues in 0 chains, 3456 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3478 seeds are put forward Round 1: 260 peptides, 37 chains. Longest chain 16 peptides. Score 0.443 Round 2: 288 peptides, 32 chains. Longest chain 22 peptides. Score 0.542 Round 3: 297 peptides, 34 chains. Longest chain 21 peptides. Score 0.541 Round 4: 305 peptides, 31 chains. Longest chain 28 peptides. Score 0.580 Round 5: 294 peptides, 33 chains. Longest chain 24 peptides. Score 0.544 Taking the results from Round 4 Chains 33, Residues 274, Estimated correctness of the model 0.0 % 5 chains (69 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7095 restraints for refining 3555 atoms. 5767 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2721 (Rfree = 0.000) for 3555 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 12: After refmac, R = 0.2539 (Rfree = 0.000) for 3482 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 13: After refmac, R = 0.2383 (Rfree = 0.000) for 3437 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.2238 (Rfree = 0.000) for 3411 atoms. Found 13 (16 requested) and removed 17 (8 requested) atoms. Cycle 15: After refmac, R = 0.2150 (Rfree = 0.000) for 3387 atoms. Found 11 (16 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.02 Search for helices and strands: 0 residues in 0 chains, 3488 seeds are put forward NCS extension: 41 residues added (0 deleted due to clashes), 3529 seeds are put forward Round 1: 256 peptides, 40 chains. Longest chain 17 peptides. Score 0.406 Round 2: 284 peptides, 36 chains. Longest chain 17 peptides. Score 0.500 Round 3: 290 peptides, 33 chains. Longest chain 21 peptides. Score 0.537 Round 4: 293 peptides, 32 chains. Longest chain 23 peptides. Score 0.551 Round 5: 288 peptides, 33 chains. Longest chain 17 peptides. Score 0.533 Taking the results from Round 4 Chains 34, Residues 261, Estimated correctness of the model 0.0 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7307 restraints for refining 3553 atoms. 6081 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2345 (Rfree = 0.000) for 3553 atoms. Found 15 (16 requested) and removed 28 (8 requested) atoms. Cycle 17: After refmac, R = 0.2143 (Rfree = 0.000) for 3500 atoms. Found 9 (16 requested) and removed 26 (8 requested) atoms. Cycle 18: After refmac, R = 0.2081 (Rfree = 0.000) for 3461 atoms. Found 10 (16 requested) and removed 19 (8 requested) atoms. Cycle 19: After refmac, R = 0.2080 (Rfree = 0.000) for 3434 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.2151 (Rfree = 0.000) for 3431 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.04 Search for helices and strands: 0 residues in 0 chains, 3551 seeds are put forward NCS extension: 30 residues added (11 deleted due to clashes), 3581 seeds are put forward Round 1: 264 peptides, 40 chains. Longest chain 16 peptides. Score 0.423 Round 2: 287 peptides, 35 chains. Longest chain 22 peptides. Score 0.514 Round 3: 302 peptides, 33 chains. Longest chain 27 peptides. Score 0.558 Round 4: 297 peptides, 34 chains. Longest chain 21 peptides. Score 0.541 Round 5: 295 peptides, 32 chains. Longest chain 27 peptides. Score 0.554 Taking the results from Round 3 Chains 33, Residues 269, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7660 restraints for refining 3551 atoms. 6571 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2566 (Rfree = 0.000) for 3551 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 22: After refmac, R = 0.2343 (Rfree = 0.000) for 3501 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 23: After refmac, R = 0.2202 (Rfree = 0.000) for 3475 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 24: After refmac, R = 0.2152 (Rfree = 0.000) for 3446 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 25: After refmac, R = 0.2066 (Rfree = 0.000) for 3432 atoms. Found 9 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.05 Search for helices and strands: 0 residues in 0 chains, 3546 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3566 seeds are put forward Round 1: 245 peptides, 38 chains. Longest chain 15 peptides. Score 0.401 Round 2: 281 peptides, 37 chains. Longest chain 17 peptides. Score 0.485 Round 3: 289 peptides, 35 chains. Longest chain 21 peptides. Score 0.518 Round 4: 277 peptides, 34 chains. Longest chain 15 peptides. Score 0.504 Round 5: 264 peptides, 33 chains. Longest chain 17 peptides. Score 0.488 Taking the results from Round 3 Chains 35, Residues 254, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7992 restraints for refining 3554 atoms. 6994 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2466 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 27: After refmac, R = 0.2347 (Rfree = 0.000) for 3516 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 28: After refmac, R = 0.2216 (Rfree = 0.000) for 3486 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.2175 (Rfree = 0.000) for 3467 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 30: After refmac, R = 0.2126 (Rfree = 0.000) for 3450 atoms. Found 15 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.02 Search for helices and strands: 0 residues in 0 chains, 3559 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 3591 seeds are put forward Round 1: 234 peptides, 38 chains. Longest chain 17 peptides. Score 0.377 Round 2: 262 peptides, 34 chains. Longest chain 17 peptides. Score 0.475 Round 3: 270 peptides, 35 chains. Longest chain 22 peptides. Score 0.482 Round 4: 267 peptides, 33 chains. Longest chain 23 peptides. Score 0.494 Round 5: 272 peptides, 33 chains. Longest chain 20 peptides. Score 0.504 Taking the results from Round 5 Chains 33, Residues 239, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 8034 restraints for refining 3553 atoms. 7111 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2277 (Rfree = 0.000) for 3553 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 32: After refmac, R = 0.2237 (Rfree = 0.000) for 3514 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 33: After refmac, R = 0.2255 (Rfree = 0.000) for 3492 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 34: After refmac, R = 0.2119 (Rfree = 0.000) for 3467 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 35: After refmac, R = 0.2044 (Rfree = 0.000) for 3455 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.72 3.03 Search for helices and strands: 0 residues in 0 chains, 3589 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3612 seeds are put forward Round 1: 237 peptides, 43 chains. Longest chain 16 peptides. Score 0.334 Round 2: 268 peptides, 39 chains. Longest chain 21 peptides. Score 0.441 Round 3: 274 peptides, 36 chains. Longest chain 18 peptides. Score 0.480 Round 4: 289 peptides, 34 chains. Longest chain 21 peptides. Score 0.527 Round 5: 282 peptides, 33 chains. Longest chain 22 peptides. Score 0.522 Taking the results from Round 4 Chains 35, Residues 255, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 7850 restraints for refining 3553 atoms. 6790 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2482 (Rfree = 0.000) for 3553 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 37: After refmac, R = 0.2370 (Rfree = 0.000) for 3518 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 38: After refmac, R = 0.2168 (Rfree = 0.000) for 3501 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 39: After refmac, R = 0.2186 (Rfree = 0.000) for 3482 atoms. Found 11 (16 requested) and removed 17 (8 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2082 (Rfree = 0.000) for 3458 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.72 3.03 Search for helices and strands: 0 residues in 0 chains, 3591 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3611 seeds are put forward Round 1: 221 peptides, 37 chains. Longest chain 15 peptides. Score 0.357 Round 2: 256 peptides, 37 chains. Longest chain 15 peptides. Score 0.435 Round 3: 275 peptides, 41 chains. Longest chain 22 peptides. Score 0.437 Round 4: 291 peptides, 36 chains. Longest chain 22 peptides. Score 0.513 Round 5: 288 peptides, 38 chains. Longest chain 23 peptides. Score 0.490 Taking the results from Round 4 Chains 36, Residues 255, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6886 reflections ( 99.59 % complete ) and 8029 restraints for refining 3555 atoms. 7045 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2431 (Rfree = 0.000) for 3555 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 42: After refmac, R = 0.2296 (Rfree = 0.000) for 3533 atoms. Found 10 (16 requested) and removed 16 (8 requested) atoms. Cycle 43: After refmac, R = 0.2255 (Rfree = 0.000) for 3515 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 44: After refmac, R = 0.2156 (Rfree = 0.000) for 3493 atoms. Found 14 (16 requested) and removed 14 (8 requested) atoms. Cycle 45: After refmac, R = 0.2153 (Rfree = 0.000) for 3481 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.02 Search for helices and strands: 0 residues in 0 chains, 3603 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3625 seeds are put forward Round 1: 239 peptides, 42 chains. Longest chain 12 peptides. Score 0.348 Round 2: 263 peptides, 35 chains. Longest chain 17 peptides. Score 0.468 Round 3: 268 peptides, 36 chains. Longest chain 21 peptides. Score 0.468 Round 4: 253 peptides, 35 chains. Longest chain 22 peptides. Score 0.447 Round 5: 268 peptides, 33 chains. Longest chain 18 peptides. Score 0.496 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 235, 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 2fg0-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6886 reflections ( 99.59 % complete ) and 8086 restraints for refining 3554 atoms. 7179 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2690 (Rfree = 0.000) for 3554 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2404 (Rfree = 0.000) for 3519 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2370 (Rfree = 0.000) for 3485 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2189 (Rfree = 0.000) for 3460 atoms. TimeTaking 45.82