Mon 24 Dec 01:09:15 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 2fea-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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/2fea-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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 01:09:19 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/2fea-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-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 363 and 0 Target number of residues in the AU: 363 Target solvent content: 0.6433 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-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: 4 Cell parameters: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3776 target number of atoms Had to go as low as 0.65 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: 22.949 3.601 Wilson plot Bfac: 73.95 6451 reflections ( 98.28 % complete ) and 0 restraints for refining 4181 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3273 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3002 (Rfree = 0.000) for 4181 atoms. Found 26 (26 requested) and removed 90 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 4192 seeds are put forward NCS extension: 0 residues added, 4192 seeds are put forward Round 1: 213 peptides, 39 chains. Longest chain 11 peptides. Score 0.357 Round 2: 247 peptides, 39 chains. Longest chain 15 peptides. Score 0.456 Round 3: 268 peptides, 40 chains. Longest chain 14 peptides. Score 0.499 Round 4: 271 peptides, 38 chains. Longest chain 18 peptides. Score 0.529 Round 5: 279 peptides, 39 chains. Longest chain 18 peptides. Score 0.538 Taking the results from Round 5 Chains 39, Residues 240, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6451 reflections ( 98.28 % complete ) and 7812 restraints for refining 3421 atoms. 6891 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2556 (Rfree = 0.000) for 3421 atoms. Found 17 (21 requested) and removed 33 (10 requested) atoms. Cycle 2: After refmac, R = 0.2440 (Rfree = 0.000) for 3370 atoms. Found 10 (21 requested) and removed 109 (10 requested) atoms. Cycle 3: After refmac, R = 0.2401 (Rfree = 0.000) for 3252 atoms. Found 9 (20 requested) and removed 24 (10 requested) atoms. Cycle 4: After refmac, R = 0.2258 (Rfree = 0.000) for 3226 atoms. Found 16 (20 requested) and removed 17 (10 requested) atoms. Cycle 5: After refmac, R = 0.2240 (Rfree = 0.000) for 3221 atoms. Found 18 (20 requested) and removed 25 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3374 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3394 seeds are put forward Round 1: 260 peptides, 47 chains. Longest chain 13 peptides. Score 0.396 Round 2: 270 peptides, 37 chains. Longest chain 19 peptides. Score 0.538 Round 3: 275 peptides, 41 chains. Longest chain 18 peptides. Score 0.506 Round 4: 274 peptides, 38 chains. Longest chain 21 peptides. Score 0.537 Round 5: 286 peptides, 39 chains. Longest chain 24 peptides. Score 0.555 Taking the results from Round 5 Chains 39, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7733 restraints for refining 3423 atoms. 6784 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2432 (Rfree = 0.000) for 3423 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 7: After refmac, R = 0.2131 (Rfree = 0.000) for 3401 atoms. Found 13 (21 requested) and removed 24 (10 requested) atoms. Cycle 8: After refmac, R = 0.2114 (Rfree = 0.000) for 3371 atoms. Found 12 (21 requested) and removed 20 (10 requested) atoms. Cycle 9: After refmac, R = 0.2080 (Rfree = 0.000) for 3354 atoms. Found 11 (21 requested) and removed 13 (10 requested) atoms. Cycle 10: After refmac, R = 0.1978 (Rfree = 0.000) for 3347 atoms. Found 10 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 3477 seeds are put forward NCS extension: 43 residues added (0 deleted due to clashes), 3520 seeds are put forward Round 1: 223 peptides, 41 chains. Longest chain 17 peptides. Score 0.362 Round 2: 264 peptides, 43 chains. Longest chain 17 peptides. Score 0.455 Round 3: 273 peptides, 37 chains. Longest chain 14 peptides. Score 0.545 Round 4: 278 peptides, 39 chains. Longest chain 15 peptides. Score 0.535 Round 5: 258 peptides, 35 chains. Longest chain 19 peptides. Score 0.530 Taking the results from Round 3 Chains 37, Residues 236, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6451 reflections ( 98.28 % complete ) and 7631 restraints for refining 3422 atoms. 6665 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2330 (Rfree = 0.000) for 3422 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 12: After refmac, R = 0.2112 (Rfree = 0.000) for 3394 atoms. Found 10 (21 requested) and removed 17 (10 requested) atoms. Cycle 13: After refmac, R = 0.2023 (Rfree = 0.000) for 3377 atoms. Found 7 (21 requested) and removed 12 (10 requested) atoms. Cycle 14: After refmac, R = 0.1994 (Rfree = 0.000) for 3368 atoms. Found 6 (21 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.1942 (Rfree = 0.000) for 3352 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3481 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3497 seeds are put forward Round 1: 224 peptides, 41 chains. Longest chain 11 peptides. Score 0.365 Round 2: 260 peptides, 38 chains. Longest chain 17 peptides. Score 0.502 Round 3: 247 peptides, 33 chains. Longest chain 21 peptides. Score 0.525 Round 4: 254 peptides, 35 chains. Longest chain 20 peptides. Score 0.520 Round 5: 252 peptides, 35 chains. Longest chain 26 peptides. Score 0.515 Taking the results from Round 3 Chains 33, Residues 214, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7845 restraints for refining 3422 atoms. 7007 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2265 (Rfree = 0.000) for 3422 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 17: After refmac, R = 0.2074 (Rfree = 0.000) for 3408 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 18: After refmac, R = 0.2008 (Rfree = 0.000) for 3398 atoms. Found 8 (21 requested) and removed 11 (10 requested) atoms. Cycle 19: After refmac, R = 0.1978 (Rfree = 0.000) for 3392 atoms. Found 5 (21 requested) and removed 15 (10 requested) atoms. Cycle 20: After refmac, R = 0.1949 (Rfree = 0.000) for 3382 atoms. Found 3 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3520 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 3545 seeds are put forward Round 1: 230 peptides, 41 chains. Longest chain 13 peptides. Score 0.383 Round 2: 239 peptides, 35 chains. Longest chain 20 peptides. Score 0.481 Round 3: 253 peptides, 37 chains. Longest chain 24 peptides. Score 0.495 Round 4: 241 peptides, 36 chains. Longest chain 13 peptides. Score 0.475 Round 5: 250 peptides, 37 chains. Longest chain 17 peptides. Score 0.487 Taking the results from Round 3 Chains 37, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7752 restraints for refining 3423 atoms. 6925 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2348 (Rfree = 0.000) for 3423 atoms. Found 16 (21 requested) and removed 12 (10 requested) atoms. Cycle 22: After refmac, R = 0.2113 (Rfree = 0.000) for 3416 atoms. Found 17 (21 requested) and removed 12 (10 requested) atoms. Cycle 23: After refmac, R = 0.2030 (Rfree = 0.000) for 3413 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. Cycle 24: After refmac, R = 0.1950 (Rfree = 0.000) for 3403 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.1862 (Rfree = 0.000) for 3392 atoms. Found 6 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3528 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3555 seeds are put forward Round 1: 208 peptides, 37 chains. Longest chain 11 peptides. Score 0.368 Round 2: 240 peptides, 36 chains. Longest chain 13 peptides. Score 0.472 Round 3: 246 peptides, 35 chains. Longest chain 15 peptides. Score 0.500 Round 4: 235 peptides, 36 chains. Longest chain 13 peptides. Score 0.459 Round 5: 250 peptides, 36 chains. Longest chain 24 peptides. Score 0.499 Taking the results from Round 3 Chains 35, Residues 211, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7848 restraints for refining 3423 atoms. 7039 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2223 (Rfree = 0.000) for 3423 atoms. Found 11 (21 requested) and removed 12 (10 requested) atoms. Cycle 27: After refmac, R = 0.2036 (Rfree = 0.000) for 3410 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. Cycle 28: After refmac, R = 0.1993 (Rfree = 0.000) for 3397 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.1966 (Rfree = 0.000) for 3386 atoms. Found 6 (21 requested) and removed 12 (10 requested) atoms. Cycle 30: After refmac, R = 0.1888 (Rfree = 0.000) for 3374 atoms. Found 6 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3514 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3528 seeds are put forward Round 1: 223 peptides, 42 chains. Longest chain 9 peptides. Score 0.349 Round 2: 213 peptides, 33 chains. Longest chain 22 peptides. Score 0.434 Round 3: 229 peptides, 35 chains. Longest chain 18 peptides. Score 0.454 Round 4: 232 peptides, 33 chains. Longest chain 18 peptides. Score 0.486 Round 5: 230 peptides, 37 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 4 Chains 33, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7980 restraints for refining 3423 atoms. 7217 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2121 (Rfree = 0.000) for 3423 atoms. Found 18 (21 requested) and removed 15 (10 requested) atoms. Cycle 32: After refmac, R = 0.1905 (Rfree = 0.000) for 3414 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.1838 (Rfree = 0.000) for 3403 atoms. Found 1 (21 requested) and removed 10 (10 requested) atoms. Cycle 34: After refmac, R = 0.1830 (Rfree = 0.000) for 3390 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1789 (Rfree = 0.000) for 3384 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3506 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3521 seeds are put forward Round 1: 196 peptides, 33 chains. Longest chain 13 peptides. Score 0.384 Round 2: 230 peptides, 37 chains. Longest chain 17 peptides. Score 0.433 Round 3: 208 peptides, 30 chains. Longest chain 19 peptides. Score 0.458 Round 4: 224 peptides, 36 chains. Longest chain 21 peptides. Score 0.428 Round 5: 231 peptides, 32 chains. Longest chain 22 peptides. Score 0.496 Taking the results from Round 5 Chains 32, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7786 restraints for refining 3419 atoms. 7022 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2110 (Rfree = 0.000) for 3419 atoms. Found 17 (21 requested) and removed 11 (10 requested) atoms. Cycle 37: After refmac, R = 0.1870 (Rfree = 0.000) for 3411 atoms. Found 8 (21 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.1798 (Rfree = 0.000) for 3397 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.1745 (Rfree = 0.000) for 3385 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. Cycle 40: After refmac, R = 0.1740 (Rfree = 0.000) for 3374 atoms. Found 1 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3487 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3509 seeds are put forward Round 1: 198 peptides, 36 chains. Longest chain 18 peptides. Score 0.351 Round 2: 219 peptides, 33 chains. Longest chain 20 peptides. Score 0.451 Round 3: 219 peptides, 34 chains. Longest chain 20 peptides. Score 0.439 Round 4: 239 peptides, 35 chains. Longest chain 20 peptides. Score 0.481 Round 5: 251 peptides, 33 chains. Longest chain 20 peptides. Score 0.535 Taking the results from Round 5 Chains 33, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7715 restraints for refining 3423 atoms. 6876 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2125 (Rfree = 0.000) for 3423 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 42: After refmac, R = 0.1917 (Rfree = 0.000) for 3411 atoms. Found 8 (21 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.1909 (Rfree = 0.000) for 3405 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. Cycle 44: After refmac, R = 0.1889 (Rfree = 0.000) for 3392 atoms. Found 4 (21 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.1839 (Rfree = 0.000) for 3381 atoms. Found 5 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3502 seeds are put forward NCS extension: 31 residues added (5 deleted due to clashes), 3533 seeds are put forward Round 1: 189 peptides, 36 chains. Longest chain 16 peptides. Score 0.322 Round 2: 218 peptides, 34 chains. Longest chain 18 peptides. Score 0.436 Round 3: 216 peptides, 34 chains. Longest chain 20 peptides. Score 0.430 Round 4: 221 peptides, 31 chains. Longest chain 21 peptides. Score 0.481 Round 5: 234 peptides, 34 chains. Longest chain 13 peptides. Score 0.480 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 190, 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 2fea-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6451 reflections ( 98.28 % complete ) and 8065 restraints for refining 3423 atoms. 7336 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2177 (Rfree = 0.000) for 3423 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1977 (Rfree = 0.000) for 3406 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1985 (Rfree = 0.000) for 3393 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2011 (Rfree = 0.000) for 3382 atoms. TimeTaking 44.1