null 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fno-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fno-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.8-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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fno-3.8-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 379 and 0 Target number of residues in the AU: 379 Target solvent content: 0.6507 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 78.04 5866 reflections ( 99.07 % complete ) and 0 restraints for refining 4404 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3398 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3471 (Rfree = 0.000) for 4404 atoms. Found 24 (24 requested) and removed 53 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 4488 seeds are put forward NCS extension: 0 residues added, 4488 seeds are put forward Round 1: 189 peptides, 41 chains. Longest chain 8 peptides. Score 0.250 Round 2: 227 peptides, 42 chains. Longest chain 10 peptides. Score 0.352 Round 3: 238 peptides, 42 chains. Longest chain 12 peptides. Score 0.383 Round 4: 236 peptides, 37 chains. Longest chain 14 peptides. Score 0.437 Round 5: 247 peptides, 38 chains. Longest chain 13 peptides. Score 0.454 Taking the results from Round 5 Chains 38, Residues 209, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8280 restraints for refining 3586 atoms. 7446 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2756 (Rfree = 0.000) for 3586 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 2: After refmac, R = 0.2446 (Rfree = 0.000) for 3514 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 3: After refmac, R = 0.2205 (Rfree = 0.000) for 3487 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 4: After refmac, R = 0.2262 (Rfree = 0.000) for 3485 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 5: After refmac, R = 0.1800 (Rfree = 0.000) for 3475 atoms. Found 10 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 3653 seeds are put forward NCS extension: 0 residues added, 3653 seeds are put forward Round 1: 228 peptides, 43 chains. Longest chain 9 peptides. Score 0.342 Round 2: 254 peptides, 42 chains. Longest chain 11 peptides. Score 0.426 Round 3: 248 peptides, 36 chains. Longest chain 18 peptides. Score 0.479 Round 4: 260 peptides, 39 chains. Longest chain 12 peptides. Score 0.476 Round 5: 236 peptides, 34 chains. Longest chain 14 peptides. Score 0.471 Taking the results from Round 3 Chains 36, Residues 212, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8287 restraints for refining 3588 atoms. 7459 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2336 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 26 (9 requested) atoms. Cycle 7: After refmac, R = 0.2322 (Rfree = 0.000) for 3550 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 8: After refmac, R = 0.2292 (Rfree = 0.000) for 3533 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 9: After refmac, R = 0.2049 (Rfree = 0.000) for 3520 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 10: After refmac, R = 0.1655 (Rfree = 0.000) for 3509 atoms. Found 2 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 3679 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3696 seeds are put forward Round 1: 221 peptides, 41 chains. Longest chain 12 peptides. Score 0.347 Round 2: 238 peptides, 40 chains. Longest chain 12 peptides. Score 0.407 Round 3: 233 peptides, 37 chains. Longest chain 12 peptides. Score 0.429 Round 4: 227 peptides, 32 chains. Longest chain 12 peptides. Score 0.471 Round 5: 231 peptides, 32 chains. Longest chain 12 peptides. Score 0.481 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 ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8432 restraints for refining 3587 atoms. 7668 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2169 (Rfree = 0.000) for 3587 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 12: After refmac, R = 0.2156 (Rfree = 0.000) for 3558 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 13: After refmac, R = 0.1928 (Rfree = 0.000) for 3547 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 14: After refmac, R = 0.2029 (Rfree = 0.000) for 3544 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 15: After refmac, R = 0.1948 (Rfree = 0.000) for 3543 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 3696 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3702 seeds are put forward Round 1: 212 peptides, 41 chains. Longest chain 10 peptides. Score 0.320 Round 2: 223 peptides, 37 chains. Longest chain 14 peptides. Score 0.401 Round 3: 226 peptides, 37 chains. Longest chain 12 peptides. Score 0.410 Round 4: 228 peptides, 40 chains. Longest chain 12 peptides. Score 0.379 Round 5: 229 peptides, 35 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 5 Chains 35, Residues 194, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8344 restraints for refining 3589 atoms. 7543 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2315 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 17: After refmac, R = 0.2023 (Rfree = 0.000) for 3564 atoms. Found 13 (19 requested) and removed 16 (9 requested) atoms. Cycle 18: After refmac, R = 0.1955 (Rfree = 0.000) for 3547 atoms. Found 18 (19 requested) and removed 18 (9 requested) atoms. Cycle 19: After refmac, R = 0.1946 (Rfree = 0.000) for 3539 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 20: After refmac, R = 0.1860 (Rfree = 0.000) for 3534 atoms. Found 14 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 3676 seeds are put forward NCS extension: 0 residues added, 3676 seeds are put forward Round 1: 197 peptides, 37 chains. Longest chain 15 peptides. Score 0.327 Round 2: 217 peptides, 34 chains. Longest chain 15 peptides. Score 0.421 Round 3: 203 peptides, 33 chains. Longest chain 15 peptides. Score 0.395 Round 4: 208 peptides, 34 chains. Longest chain 13 peptides. Score 0.396 Round 5: 222 peptides, 34 chains. Longest chain 15 peptides. Score 0.435 Taking the results from Round 5 Chains 34, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8474 restraints for refining 3586 atoms. 7756 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2124 (Rfree = 0.000) for 3586 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 22: After refmac, R = 0.2010 (Rfree = 0.000) for 3563 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 23: After refmac, R = 0.1981 (Rfree = 0.000) for 3557 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 24: After refmac, R = 0.1568 (Rfree = 0.000) for 3557 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. Cycle 25: After refmac, R = 0.1532 (Rfree = 0.000) for 3548 atoms. Found 5 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 3685 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3701 seeds are put forward Round 1: 205 peptides, 41 chains. Longest chain 12 peptides. Score 0.299 Round 2: 205 peptides, 31 chains. Longest chain 15 peptides. Score 0.425 Round 3: 223 peptides, 34 chains. Longest chain 14 peptides. Score 0.437 Round 4: 214 peptides, 33 chains. Longest chain 12 peptides. Score 0.425 Round 5: 208 peptides, 31 chains. Longest chain 17 peptides. Score 0.433 Taking the results from Round 3 Chains 34, Residues 189, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8316 restraints for refining 3589 atoms. 7573 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2233 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 27: After refmac, R = 0.2081 (Rfree = 0.000) for 3570 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 28: After refmac, R = 0.2026 (Rfree = 0.000) for 3567 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.2009 (Rfree = 0.000) for 3557 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 30: After refmac, R = 0.1996 (Rfree = 0.000) for 3553 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3698 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3712 seeds are put forward Round 1: 162 peptides, 35 chains. Longest chain 8 peptides. Score 0.243 Round 2: 196 peptides, 32 chains. Longest chain 11 peptides. Score 0.387 Round 3: 199 peptides, 34 chains. Longest chain 13 peptides. Score 0.371 Round 4: 197 peptides, 32 chains. Longest chain 14 peptides. Score 0.390 Round 5: 198 peptides, 33 chains. Longest chain 16 peptides. Score 0.380 Taking the results from Round 4 Chains 32, Residues 165, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8486 restraints for refining 3589 atoms. 7845 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2174 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 32: After refmac, R = 0.2109 (Rfree = 0.000) for 3581 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 33: After refmac, R = 0.2033 (Rfree = 0.000) for 3573 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 34: After refmac, R = 0.2072 (Rfree = 0.000) for 3568 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 35: After refmac, R = 0.2017 (Rfree = 0.000) for 3558 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 3678 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3698 seeds are put forward Round 1: 171 peptides, 37 chains. Longest chain 8 peptides. Score 0.245 Round 2: 170 peptides, 32 chains. Longest chain 9 peptides. Score 0.310 Round 3: 180 peptides, 32 chains. Longest chain 12 peptides. Score 0.340 Round 4: 190 peptides, 33 chains. Longest chain 12 peptides. Score 0.357 Round 5: 184 peptides, 32 chains. Longest chain 12 peptides. Score 0.352 Taking the results from Round 4 Chains 33, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8745 restraints for refining 3589 atoms. 8150 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2228 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 37: After refmac, R = 0.2236 (Rfree = 0.000) for 3575 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 38: After refmac, R = 0.2087 (Rfree = 0.000) for 3564 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 39: After refmac, R = 0.1985 (Rfree = 0.000) for 3555 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 40: After refmac, R = 0.1913 (Rfree = 0.000) for 3549 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 3665 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3681 seeds are put forward Round 1: 164 peptides, 33 chains. Longest chain 10 peptides. Score 0.277 Round 2: 198 peptides, 33 chains. Longest chain 18 peptides. Score 0.380 Round 3: 196 peptides, 33 chains. Longest chain 23 peptides. Score 0.375 Round 4: 188 peptides, 29 chains. Longest chain 18 peptides. Score 0.402 Round 5: 195 peptides, 31 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 4 Chains 31, Residues 159, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8601 restraints for refining 3589 atoms. 7971 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2159 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 42: After refmac, R = 0.2126 (Rfree = 0.000) for 3584 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 43: After refmac, R = 0.2004 (Rfree = 0.000) for 3574 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 44: After refmac, R = 0.2067 (Rfree = 0.000) for 3570 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.1924 (Rfree = 0.000) for 3570 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 3706 seeds are put forward NCS extension: 0 residues added, 3706 seeds are put forward Round 1: 138 peptides, 29 chains. Longest chain 8 peptides. Score 0.247 Round 2: 157 peptides, 29 chains. Longest chain 13 peptides. Score 0.310 Round 3: 156 peptides, 28 chains. Longest chain 15 peptides. Score 0.320 Round 4: 166 peptides, 28 chains. Longest chain 16 peptides. Score 0.351 Round 5: 164 peptides, 30 chains. Longest chain 11 peptides. Score 0.318 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 138, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5866 reflections ( 99.07 % complete ) and 8696 restraints for refining 3588 atoms. 8172 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2263 (Rfree = 0.000) for 3588 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2355 (Rfree = 0.000) for 3567 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2171 (Rfree = 0.000) for 3546 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2072 (Rfree = 0.000) for 3527 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:22:03 GMT 2018 Job finished. TimeTaking 59.01 Used memory is bytes: 9846320