Sun 23 Dec 22:22:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fea-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fea-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fea-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.6-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:48 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/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fea-3.6-parrot-hancs/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-hancs.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-hancs.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 4158 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3248 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2849 (Rfree = 0.000) for 4158 atoms. Found 26 (26 requested) and removed 67 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 4210 seeds are put forward NCS extension: 0 residues added, 4210 seeds are put forward Round 1: 208 peptides, 43 chains. Longest chain 9 peptides. Score 0.289 Round 2: 247 peptides, 38 chains. Longest chain 16 peptides. Score 0.467 Round 3: 259 peptides, 39 chains. Longest chain 16 peptides. Score 0.488 Round 4: 281 peptides, 41 chains. Longest chain 21 peptides. Score 0.521 Round 5: 279 peptides, 39 chains. Longest chain 15 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 ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7732 restraints for refining 3422 atoms. 6811 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2461 (Rfree = 0.000) for 3422 atoms. Found 17 (21 requested) and removed 28 (10 requested) atoms. Cycle 2: After refmac, R = 0.2378 (Rfree = 0.000) for 3365 atoms. Found 10 (21 requested) and removed 95 (10 requested) atoms. Cycle 3: After refmac, R = 0.2169 (Rfree = 0.000) for 3270 atoms. Found 13 (21 requested) and removed 12 (10 requested) atoms. Cycle 4: After refmac, R = 0.2188 (Rfree = 0.000) for 3265 atoms. Found 7 (20 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.2185 (Rfree = 0.000) for 3256 atoms. Found 5 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3408 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3430 seeds are put forward Round 1: 253 peptides, 44 chains. Longest chain 14 peptides. Score 0.412 Round 2: 277 peptides, 38 chains. Longest chain 22 peptides. Score 0.544 Round 3: 280 peptides, 36 chains. Longest chain 18 peptides. Score 0.572 Round 4: 279 peptides, 36 chains. Longest chain 19 peptides. Score 0.570 Round 5: 288 peptides, 36 chains. Longest chain 20 peptides. Score 0.590 Taking the results from Round 5 Chains 36, Residues 252, Estimated correctness of the model 10.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7830 restraints for refining 3421 atoms. 6858 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2347 (Rfree = 0.000) for 3421 atoms. Found 14 (21 requested) and removed 24 (10 requested) atoms. Cycle 7: After refmac, R = 0.2175 (Rfree = 0.000) for 3393 atoms. Found 4 (21 requested) and removed 16 (10 requested) atoms. Cycle 8: After refmac, R = 0.2199 (Rfree = 0.000) for 3374 atoms. Found 15 (21 requested) and removed 32 (10 requested) atoms. Cycle 9: After refmac, R = 0.2119 (Rfree = 0.000) for 3352 atoms. Found 12 (21 requested) and removed 18 (10 requested) atoms. Cycle 10: After refmac, R = 0.2078 (Rfree = 0.000) for 3341 atoms. Found 7 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3476 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 3495 seeds are put forward Round 1: 250 peptides, 42 chains. Longest chain 16 peptides. Score 0.428 Round 2: 282 peptides, 40 chains. Longest chain 15 peptides. Score 0.534 Round 3: 300 peptides, 38 chains. Longest chain 23 peptides. Score 0.596 Round 4: 278 peptides, 33 chains. Longest chain 24 peptides. Score 0.598 Round 5: 273 peptides, 30 chains. Longest chain 19 peptides. Score 0.617 Taking the results from Round 5 Chains 30, Residues 243, Estimated correctness of the model 21.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7925 restraints for refining 3423 atoms. 6983 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2323 (Rfree = 0.000) for 3423 atoms. Found 17 (21 requested) and removed 26 (10 requested) atoms. Cycle 12: After refmac, R = 0.2065 (Rfree = 0.000) for 3393 atoms. Found 11 (21 requested) and removed 16 (10 requested) atoms. Cycle 13: After refmac, R = 0.1958 (Rfree = 0.000) for 3380 atoms. Found 2 (21 requested) and removed 13 (10 requested) atoms. Cycle 14: After refmac, R = 0.1974 (Rfree = 0.000) for 3367 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.1990 (Rfree = 0.000) for 3354 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3470 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3489 seeds are put forward Round 1: 260 peptides, 41 chains. Longest chain 20 peptides. Score 0.467 Round 2: 270 peptides, 36 chains. Longest chain 16 peptides. Score 0.548 Round 3: 288 peptides, 34 chains. Longest chain 29 peptides. Score 0.610 Round 4: 285 peptides, 36 chains. Longest chain 18 peptides. Score 0.583 Round 5: 278 peptides, 36 chains. Longest chain 20 peptides. Score 0.567 Taking the results from Round 3 Chains 36, Residues 254, Estimated correctness of the model 18.4 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7179 restraints for refining 3423 atoms. 6088 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2319 (Rfree = 0.000) for 3423 atoms. Found 20 (21 requested) and removed 25 (10 requested) atoms. Cycle 17: After refmac, R = 0.2096 (Rfree = 0.000) for 3408 atoms. Found 11 (21 requested) and removed 12 (10 requested) atoms. Cycle 18: After refmac, R = 0.2000 (Rfree = 0.000) for 3404 atoms. Found 6 (21 requested) and removed 13 (10 requested) atoms. Cycle 19: After refmac, R = 0.1936 (Rfree = 0.000) for 3389 atoms. Found 5 (21 requested) and removed 10 (10 requested) atoms. Cycle 20: After refmac, R = 0.1929 (Rfree = 0.000) for 3379 atoms. Found 2 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3511 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3524 seeds are put forward Round 1: 246 peptides, 37 chains. Longest chain 16 peptides. Score 0.476 Round 2: 275 peptides, 34 chains. Longest chain 30 peptides. Score 0.581 Round 3: 295 peptides, 39 chains. Longest chain 17 peptides. Score 0.575 Round 4: 286 peptides, 38 chains. Longest chain 20 peptides. Score 0.565 Round 5: 281 peptides, 35 chains. Longest chain 21 peptides. Score 0.584 Taking the results from Round 5 Chains 35, Residues 246, Estimated correctness of the model 8.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7599 restraints for refining 3423 atoms. 6650 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2234 (Rfree = 0.000) for 3423 atoms. Found 10 (21 requested) and removed 29 (10 requested) atoms. Cycle 22: After refmac, R = 0.2027 (Rfree = 0.000) for 3390 atoms. Found 17 (21 requested) and removed 16 (10 requested) atoms. Cycle 23: After refmac, R = 0.1933 (Rfree = 0.000) for 3376 atoms. Found 7 (21 requested) and removed 13 (10 requested) atoms. Cycle 24: After refmac, R = 0.1861 (Rfree = 0.000) for 3363 atoms. Found 4 (21 requested) and removed 13 (10 requested) atoms. Cycle 25: After refmac, R = 0.1857 (Rfree = 0.000) for 3347 atoms. Found 5 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3452 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3472 seeds are put forward Round 1: 242 peptides, 43 chains. Longest chain 16 peptides. Score 0.393 Round 2: 252 peptides, 40 chains. Longest chain 17 peptides. Score 0.457 Round 3: 242 peptides, 35 chains. Longest chain 20 peptides. Score 0.489 Round 4: 267 peptides, 38 chains. Longest chain 19 peptides. Score 0.519 Round 5: 272 peptides, 40 chains. Longest chain 21 peptides. Score 0.510 Taking the results from Round 4 Chains 38, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7711 restraints for refining 3423 atoms. 6833 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2072 (Rfree = 0.000) for 3423 atoms. Found 17 (21 requested) and removed 34 (10 requested) atoms. Cycle 27: After refmac, R = 0.1904 (Rfree = 0.000) for 3382 atoms. Found 8 (21 requested) and removed 15 (10 requested) atoms. Cycle 28: After refmac, R = 0.1814 (Rfree = 0.000) for 3367 atoms. Found 6 (21 requested) and removed 13 (10 requested) atoms. Cycle 29: After refmac, R = 0.1826 (Rfree = 0.000) for 3355 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. Cycle 30: After refmac, R = 0.1827 (Rfree = 0.000) for 3342 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3453 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3479 seeds are put forward Round 1: 196 peptides, 38 chains. Longest chain 9 peptides. Score 0.318 Round 2: 230 peptides, 34 chains. Longest chain 14 peptides. Score 0.469 Round 3: 244 peptides, 37 chains. Longest chain 14 peptides. Score 0.471 Round 4: 244 peptides, 36 chains. Longest chain 21 peptides. Score 0.483 Round 5: 241 peptides, 33 chains. Longest chain 31 peptides. Score 0.510 Taking the results from Round 5 Chains 33, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7916 restraints for refining 3423 atoms. 7117 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2063 (Rfree = 0.000) for 3423 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 32: After refmac, R = 0.1963 (Rfree = 0.000) for 3424 atoms. Found 20 (21 requested) and removed 15 (10 requested) atoms. Cycle 33: After refmac, R = 0.1827 (Rfree = 0.000) for 3420 atoms. Found 10 (21 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.1800 (Rfree = 0.000) for 3408 atoms. Found 13 (21 requested) and removed 15 (10 requested) atoms. Cycle 35: After refmac, R = 0.1743 (Rfree = 0.000) for 3402 atoms. Found 10 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3533 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 3572 seeds are put forward Round 1: 223 peptides, 44 chains. Longest chain 9 peptides. Score 0.323 Round 2: 235 peptides, 39 chains. Longest chain 15 peptides. Score 0.422 Round 3: 248 peptides, 41 chains. Longest chain 16 peptides. Score 0.434 Round 4: 255 peptides, 41 chains. Longest chain 15 peptides. Score 0.454 Round 5: 256 peptides, 38 chains. Longest chain 22 peptides. Score 0.491 Taking the results from Round 5 Chains 38, Residues 218, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 7917 restraints for refining 3422 atoms. 7083 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2140 (Rfree = 0.000) for 3422 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 37: After refmac, R = 0.1982 (Rfree = 0.000) for 3419 atoms. Found 12 (21 requested) and removed 12 (10 requested) atoms. Cycle 38: After refmac, R = 0.1866 (Rfree = 0.000) for 3408 atoms. Found 11 (21 requested) and removed 17 (10 requested) atoms. Cycle 39: After refmac, R = 0.1774 (Rfree = 0.000) for 3399 atoms. Found 7 (21 requested) and removed 15 (10 requested) atoms. Cycle 40: After refmac, R = 0.1749 (Rfree = 0.000) for 3388 atoms. Found 6 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 3519 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 3548 seeds are put forward Round 1: 188 peptides, 38 chains. Longest chain 11 peptides. Score 0.292 Round 2: 209 peptides, 34 chains. Longest chain 16 peptides. Score 0.410 Round 3: 206 peptides, 32 chains. Longest chain 26 peptides. Score 0.427 Round 4: 202 peptides, 30 chains. Longest chain 17 peptides. Score 0.441 Round 5: 205 peptides, 29 chains. Longest chain 19 peptides. Score 0.462 Taking the results from Round 5 Chains 29, Residues 176, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6451 reflections ( 98.28 % complete ) and 8020 restraints for refining 3423 atoms. 7331 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1996 (Rfree = 0.000) for 3423 atoms. Found 13 (21 requested) and removed 17 (10 requested) atoms. Cycle 42: After refmac, R = 0.1940 (Rfree = 0.000) for 3404 atoms. Found 20 (21 requested) and removed 11 (10 requested) atoms. Cycle 43: After refmac, R = 0.1817 (Rfree = 0.000) for 3406 atoms. Found 9 (21 requested) and removed 14 (10 requested) atoms. Cycle 44: After refmac, R = 0.1677 (Rfree = 0.000) for 3399 atoms. Found 9 (21 requested) and removed 15 (10 requested) atoms. Cycle 45: After refmac, R = 0.1705 (Rfree = 0.000) for 3389 atoms. Found 10 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3501 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3524 seeds are put forward Round 1: 176 peptides, 36 chains. Longest chain 9 peptides. Score 0.280 Round 2: 203 peptides, 32 chains. Longest chain 15 peptides. Score 0.418 Round 3: 214 peptides, 33 chains. Longest chain 15 peptides. Score 0.437 Round 4: 199 peptides, 32 chains. Longest chain 18 peptides. Score 0.406 Round 5: 221 peptides, 33 chains. Longest chain 15 peptides. Score 0.457 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 188, 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 7896 restraints for refining 3423 atoms. 7177 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2054 (Rfree = 0.000) for 3423 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.1938 (Rfree = 0.000) for 3399 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.1831 (Rfree = 0.000) for 3389 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.1775 (Rfree = 0.000) for 3377 atoms. TimeTaking 55.35