Sun 23 Dec 22:23:02 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 2fno-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fno-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fno-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-4.0-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/2fno-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-4.0-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 22:23:12 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/2fno-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-4.0-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 366 and 0 Target number of residues in the AU: 366 Target solvent content: 0.6627 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-4.0-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3968 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: 106.006 4.000 Wilson plot Bfac: 86.43 5042 reflections ( 98.94 % complete ) and 0 restraints for refining 4366 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3519 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3636 (Rfree = 0.000) for 4366 atoms. Found 20 (20 requested) and removed 122 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 4340 seeds are put forward NCS extension: 0 residues added, 4340 seeds are put forward Round 1: 167 peptides, 37 chains. Longest chain 8 peptides. Score 0.232 Round 2: 206 peptides, 38 chains. Longest chain 11 peptides. Score 0.341 Round 3: 217 peptides, 38 chains. Longest chain 13 peptides. Score 0.372 Round 4: 216 peptides, 35 chains. Longest chain 15 peptides. Score 0.406 Round 5: 224 peptides, 37 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 4 Chains 35, Residues 181, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8479 restraints for refining 3582 atoms. 7746 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2861 (Rfree = 0.000) for 3582 atoms. Found 17 (17 requested) and removed 38 (8 requested) atoms. Cycle 2: After refmac, R = 0.2680 (Rfree = 0.000) for 3505 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 3: After refmac, R = 0.2447 (Rfree = 0.000) for 3460 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 4: After refmac, R = 0.1951 (Rfree = 0.000) for 3431 atoms. Found 11 (16 requested) and removed 16 (8 requested) atoms. Cycle 5: After refmac, R = 0.1812 (Rfree = 0.000) for 3422 atoms. Found 3 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 3531 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3546 seeds are put forward Round 1: 205 peptides, 42 chains. Longest chain 12 peptides. Score 0.287 Round 2: 231 peptides, 38 chains. Longest chain 13 peptides. Score 0.411 Round 3: 230 peptides, 36 chains. Longest chain 20 peptides. Score 0.432 Round 4: 240 peptides, 36 chains. Longest chain 15 peptides. Score 0.459 Round 5: 240 peptides, 39 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 4 Chains 36, Residues 204, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8434 restraints for refining 3583 atoms. 7629 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2433 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 7: After refmac, R = 0.2236 (Rfree = 0.000) for 3539 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 8: After refmac, R = 0.2235 (Rfree = 0.000) for 3507 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 9: After refmac, R = 0.2138 (Rfree = 0.000) for 3481 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 10: After refmac, R = 0.1728 (Rfree = 0.000) for 3464 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 3620 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3645 seeds are put forward Round 1: 188 peptides, 35 chains. Longest chain 11 peptides. Score 0.325 Round 2: 235 peptides, 40 chains. Longest chain 12 peptides. Score 0.399 Round 3: 231 peptides, 37 chains. Longest chain 18 peptides. Score 0.423 Round 4: 233 peptides, 36 chains. Longest chain 14 peptides. Score 0.440 Round 5: 236 peptides, 37 chains. Longest chain 17 peptides. Score 0.437 Taking the results from Round 4 Chains 36, Residues 197, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8493 restraints for refining 3583 atoms. 7722 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2285 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 12: After refmac, R = 0.2219 (Rfree = 0.000) for 3546 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 13: After refmac, R = 0.2176 (Rfree = 0.000) for 3524 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 14: After refmac, R = 0.2044 (Rfree = 0.000) for 3512 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 15: After refmac, R = 0.1616 (Rfree = 0.000) for 3503 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 3619 seeds are put forward NCS extension: 0 residues added, 3619 seeds are put forward Round 1: 187 peptides, 40 chains. Longest chain 10 peptides. Score 0.256 Round 2: 218 peptides, 40 chains. Longest chain 14 peptides. Score 0.351 Round 3: 216 peptides, 37 chains. Longest chain 14 peptides. Score 0.382 Round 4: 216 peptides, 37 chains. Longest chain 19 peptides. Score 0.382 Round 5: 220 peptides, 39 chains. Longest chain 10 peptides. Score 0.369 Taking the results from Round 4 Chains 37, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8597 restraints for refining 3583 atoms. 7918 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2249 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 17: After refmac, R = 0.2237 (Rfree = 0.000) for 3528 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 18: After refmac, R = 0.2131 (Rfree = 0.000) for 3501 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 19: After refmac, R = 0.1942 (Rfree = 0.000) for 3478 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 20: After refmac, R = 0.1496 (Rfree = 0.000) for 3470 atoms. Found 5 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 3606 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3627 seeds are put forward Round 1: 196 peptides, 40 chains. Longest chain 9 peptides. Score 0.285 Round 2: 195 peptides, 32 chains. Longest chain 15 peptides. Score 0.384 Round 3: 204 peptides, 35 chains. Longest chain 18 peptides. Score 0.372 Round 4: 206 peptides, 32 chains. Longest chain 19 peptides. Score 0.415 Round 5: 215 peptides, 35 chains. Longest chain 23 peptides. Score 0.403 Taking the results from Round 4 Chains 32, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8452 restraints for refining 3582 atoms. 7788 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2206 (Rfree = 0.000) for 3582 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 22: After refmac, R = 0.2244 (Rfree = 0.000) for 3545 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 23: After refmac, R = 0.2083 (Rfree = 0.000) for 3528 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 24: After refmac, R = 0.2033 (Rfree = 0.000) for 3512 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 25: After refmac, R = 0.2082 (Rfree = 0.000) for 3505 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 3679 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3708 seeds are put forward Round 1: 181 peptides, 38 chains. Longest chain 8 peptides. Score 0.264 Round 2: 207 peptides, 38 chains. Longest chain 10 peptides. Score 0.343 Round 3: 213 peptides, 37 chains. Longest chain 13 peptides. Score 0.373 Round 4: 212 peptides, 39 chains. Longest chain 10 peptides. Score 0.346 Round 5: 214 peptides, 34 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 5 Chains 34, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8552 restraints for refining 3582 atoms. 7866 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2284 (Rfree = 0.000) for 3582 atoms. Found 17 (17 requested) and removed 37 (8 requested) atoms. Cycle 27: After refmac, R = 0.2234 (Rfree = 0.000) for 3547 atoms. Found 16 (16 requested) and removed 34 (8 requested) atoms. Cycle 28: After refmac, R = 0.2147 (Rfree = 0.000) for 3523 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 29: After refmac, R = 0.1612 (Rfree = 0.000) for 3504 atoms. Found 5 (16 requested) and removed 19 (8 requested) atoms. Cycle 30: After refmac, R = 0.1551 (Rfree = 0.000) for 3488 atoms. Found 3 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.62 Search for helices and strands: 0 residues in 0 chains, 3615 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3628 seeds are put forward Round 1: 175 peptides, 36 chains. Longest chain 11 peptides. Score 0.272 Round 2: 186 peptides, 37 chains. Longest chain 10 peptides. Score 0.293 Round 3: 204 peptides, 34 chains. Longest chain 13 peptides. Score 0.385 Round 4: 205 peptides, 35 chains. Longest chain 14 peptides. Score 0.375 Round 5: 199 peptides, 34 chains. Longest chain 11 peptides. Score 0.371 Taking the results from Round 3 Chains 34, Residues 170, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8582 restraints for refining 3582 atoms. 7907 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1958 (Rfree = 0.000) for 3582 atoms. Found 17 (17 requested) and removed 69 (8 requested) atoms. Cycle 32: After refmac, R = 0.2090 (Rfree = 0.000) for 3513 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 33: After refmac, R = 0.2050 (Rfree = 0.000) for 3489 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 34: After refmac, R = 0.1956 (Rfree = 0.000) for 3474 atoms. Found 16 (16 requested) and removed 57 (8 requested) atoms. Cycle 35: After refmac, R = 0.2034 (Rfree = 0.000) for 3429 atoms. Found 16 (16 requested) and removed 45 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 3529 seeds are put forward NCS extension: 0 residues added, 3529 seeds are put forward Round 1: 169 peptides, 37 chains. Longest chain 7 peptides. Score 0.239 Round 2: 179 peptides, 32 chains. Longest chain 13 peptides. Score 0.337 Round 3: 178 peptides, 33 chains. Longest chain 12 peptides. Score 0.321 Round 4: 183 peptides, 32 chains. Longest chain 12 peptides. Score 0.349 Round 5: 188 peptides, 30 chains. Longest chain 13 peptides. Score 0.390 Taking the results from Round 5 Chains 30, Residues 158, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8406 restraints for refining 3583 atoms. 7757 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2224 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 68 (8 requested) atoms. Cycle 37: After refmac, R = 0.1888 (Rfree = 0.000) for 3517 atoms. Found 16 (16 requested) and removed 37 (8 requested) atoms. Cycle 38: After refmac, R = 0.1882 (Rfree = 0.000) for 3487 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 39: After refmac, R = 0.1498 (Rfree = 0.000) for 3468 atoms. Found 6 (16 requested) and removed 19 (8 requested) atoms. Cycle 40: After refmac, R = 0.1405 (Rfree = 0.000) for 3454 atoms. Found 2 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 3550 seeds are put forward NCS extension: 0 residues added, 3550 seeds are put forward Round 1: 157 peptides, 34 chains. Longest chain 7 peptides. Score 0.240 Round 2: 162 peptides, 33 chains. Longest chain 7 peptides. Score 0.270 Round 3: 173 peptides, 32 chains. Longest chain 11 peptides. Score 0.319 Round 4: 182 peptides, 31 chains. Longest chain 11 peptides. Score 0.359 Round 5: 176 peptides, 33 chains. Longest chain 10 peptides. Score 0.315 Taking the results from Round 4 Chains 32, Residues 151, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5042 reflections ( 98.94 % complete ) and 8292 restraints for refining 3583 atoms. 7673 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1950 (Rfree = 0.000) for 3583 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 42: After refmac, R = 0.1941 (Rfree = 0.000) for 3560 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 43: After refmac, R = 0.1892 (Rfree = 0.000) for 3539 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 44: After refmac, R = 0.1870 (Rfree = 0.000) for 3519 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 45: After refmac, R = 0.1745 (Rfree = 0.000) for 3502 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 3598 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3613 seeds are put forward Round 1: 147 peptides, 34 chains. Longest chain 8 peptides. Score 0.206 Round 2: 152 peptides, 28 chains. Longest chain 9 peptides. Score 0.308 Round 3: 166 peptides, 31 chains. Longest chain 9 peptides. Score 0.311 Round 4: 160 peptides, 29 chains. Longest chain 13 peptides. Score 0.319 Round 5: 160 peptides, 30 chains. Longest chain 11 peptides. Score 0.305 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 131, 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 2fno-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5042 reflections ( 98.94 % complete ) and 8770 restraints for refining 3583 atoms. 8275 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2125 (Rfree = 0.000) for 3583 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1986 (Rfree = 0.000) for 3562 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1920 (Rfree = 0.000) for 3546 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1834 (Rfree = 0.000) for 3531 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 58.55