Tue 25 Dec 19:27:55 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 2it9-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2it9-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2it9-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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/2it9-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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 ============================================================ Tue 25 Dec 19:28:05 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/2it9-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-3.6-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 393 and 0 Target number of residues in the AU: 393 Target solvent content: 0.6465 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-3.6-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.85 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: 67.879 3.600 Wilson plot Bfac: 75.92 7278 reflections ( 98.28 % complete ) and 0 restraints for refining 4479 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3761 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3064 (Rfree = 0.000) for 4479 atoms. Found 28 (28 requested) and removed 52 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 4544 seeds are put forward NCS extension: 0 residues added, 4544 seeds are put forward Round 1: 210 peptides, 41 chains. Longest chain 10 peptides. Score 0.312 Round 2: 276 peptides, 45 chains. Longest chain 14 peptides. Score 0.445 Round 3: 283 peptides, 38 chains. Longest chain 21 peptides. Score 0.535 Round 4: 284 peptides, 41 chains. Longest chain 18 peptides. Score 0.507 Round 5: 281 peptides, 41 chains. Longest chain 20 peptides. Score 0.499 Taking the results from Round 3 Chains 39, Residues 245, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8085 restraints for refining 3681 atoms. 7105 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2670 (Rfree = 0.000) for 3681 atoms. Found 18 (23 requested) and removed 27 (11 requested) atoms. Cycle 2: After refmac, R = 0.2538 (Rfree = 0.000) for 3628 atoms. Found 14 (23 requested) and removed 22 (11 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2330 (Rfree = 0.000) for 3596 atoms. Found 10 (23 requested) and removed 20 (11 requested) atoms. Cycle 4: After refmac, R = 0.2020 (Rfree = 0.000) for 3574 atoms. Found 6 (23 requested) and removed 18 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2174 (Rfree = 0.000) for 3556 atoms. Found 12 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3697 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 3725 seeds are put forward Round 1: 249 peptides, 45 chains. Longest chain 14 peptides. Score 0.374 Round 2: 272 peptides, 43 chains. Longest chain 12 peptides. Score 0.456 Round 3: 265 peptides, 38 chains. Longest chain 23 peptides. Score 0.493 Round 4: 293 peptides, 42 chains. Longest chain 18 peptides. Score 0.517 Round 5: 286 peptides, 46 chains. Longest chain 20 peptides. Score 0.459 Taking the results from Round 4 Chains 42, Residues 251, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8232 restraints for refining 3684 atoms. 7270 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2485 (Rfree = 0.000) for 3684 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 7: After refmac, R = 0.2337 (Rfree = 0.000) for 3648 atoms. Found 21 (23 requested) and removed 15 (11 requested) atoms. Cycle 8: After refmac, R = 0.2255 (Rfree = 0.000) for 3640 atoms. Found 19 (23 requested) and removed 20 (11 requested) atoms. Cycle 9: After refmac, R = 0.2239 (Rfree = 0.000) for 3626 atoms. Found 19 (23 requested) and removed 18 (11 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2138 (Rfree = 0.000) for 3615 atoms. Found 19 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3758 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3778 seeds are put forward Round 1: 230 peptides, 40 chains. Longest chain 13 peptides. Score 0.381 Round 2: 247 peptides, 37 chains. Longest chain 16 peptides. Score 0.460 Round 3: 261 peptides, 36 chains. Longest chain 24 peptides. Score 0.505 Round 4: 246 peptides, 40 chains. Longest chain 18 peptides. Score 0.423 Round 5: 261 peptides, 40 chains. Longest chain 27 peptides. Score 0.462 Taking the results from Round 3 Chains 36, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8226 restraints for refining 3684 atoms. 7362 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2238 (Rfree = 0.000) for 3684 atoms. Found 18 (23 requested) and removed 14 (11 requested) atoms. Cycle 12: After refmac, R = 0.2198 (Rfree = 0.000) for 3671 atoms. Found 10 (23 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.2080 (Rfree = 0.000) for 3642 atoms. Found 9 (23 requested) and removed 17 (11 requested) atoms. Cycle 14: After refmac, R = 0.1803 (Rfree = 0.000) for 3621 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1989 (Rfree = 0.000) for 3604 atoms. Found 14 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3720 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3740 seeds are put forward Round 1: 228 peptides, 41 chains. Longest chain 11 peptides. Score 0.363 Round 2: 254 peptides, 43 chains. Longest chain 13 peptides. Score 0.410 Round 3: 252 peptides, 45 chains. Longest chain 13 peptides. Score 0.382 Round 4: 264 peptides, 44 chains. Longest chain 17 peptides. Score 0.425 Round 5: 250 peptides, 42 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 4 Chains 44, Residues 220, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7278 reflections ( 98.28 % complete ) and 8354 restraints for refining 3684 atoms. 7518 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2264 (Rfree = 0.000) for 3684 atoms. Found 13 (23 requested) and removed 19 (11 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2271 (Rfree = 0.000) for 3658 atoms. Found 19 (23 requested) and removed 21 (11 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2078 (Rfree = 0.000) for 3631 atoms. Found 12 (23 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1830 (Rfree = 0.000) for 3618 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1818 (Rfree = 0.000) for 3595 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.26 Search for helices and strands: 0 residues in 0 chains, 3709 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3728 seeds are put forward Round 1: 200 peptides, 39 chains. Longest chain 9 peptides. Score 0.307 Round 2: 230 peptides, 42 chains. Longest chain 13 peptides. Score 0.357 Round 3: 247 peptides, 42 chains. Longest chain 15 peptides. Score 0.403 Round 4: 254 peptides, 44 chains. Longest chain 14 peptides. Score 0.399 Round 5: 258 peptides, 43 chains. Longest chain 12 peptides. Score 0.421 Taking the results from Round 5 Chains 43, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7278 reflections ( 98.28 % complete ) and 8367 restraints for refining 3683 atoms. 7550 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2251 (Rfree = 0.000) for 3683 atoms. Found 14 (23 requested) and removed 19 (11 requested) atoms. Cycle 22: After refmac, R = 0.2096 (Rfree = 0.000) for 3653 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.2086 (Rfree = 0.000) for 3642 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2084 (Rfree = 0.000) for 3634 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. Cycle 25: After refmac, R = 0.2060 (Rfree = 0.000) for 3618 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 3730 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3743 seeds are put forward Round 1: 202 peptides, 41 chains. Longest chain 12 peptides. Score 0.288 Round 2: 222 peptides, 40 chains. Longest chain 12 peptides. Score 0.358 Round 3: 231 peptides, 41 chains. Longest chain 10 peptides. Score 0.372 Round 4: 239 peptides, 45 chains. Longest chain 12 peptides. Score 0.346 Round 5: 246 peptides, 44 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 5 Chains 44, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8425 restraints for refining 3684 atoms. 7661 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2276 (Rfree = 0.000) for 3684 atoms. Found 12 (23 requested) and removed 13 (11 requested) atoms. Cycle 27: After refmac, R = 0.2016 (Rfree = 0.000) for 3667 atoms. Found 8 (23 requested) and removed 16 (11 requested) atoms. Cycle 28: After refmac, R = 0.1919 (Rfree = 0.000) for 3650 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1905 (Rfree = 0.000) for 3638 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1922 (Rfree = 0.000) for 3629 atoms. Found 4 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3703 seeds are put forward NCS extension: 0 residues added, 3703 seeds are put forward Round 1: 185 peptides, 38 chains. Longest chain 11 peptides. Score 0.275 Round 2: 212 peptides, 38 chains. Longest chain 11 peptides. Score 0.355 Round 3: 194 peptides, 35 chains. Longest chain 10 peptides. Score 0.340 Round 4: 208 peptides, 34 chains. Longest chain 13 peptides. Score 0.392 Round 5: 212 peptides, 38 chains. Longest chain 10 peptides. Score 0.355 Taking the results from Round 4 Chains 34, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8583 restraints for refining 3684 atoms. 7921 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2134 (Rfree = 0.000) for 3684 atoms. Found 9 (23 requested) and removed 15 (11 requested) atoms. Cycle 32: After refmac, R = 0.1977 (Rfree = 0.000) for 3670 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2043 (Rfree = 0.000) for 3656 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.2020 (Rfree = 0.000) for 3645 atoms. Found 18 (23 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2062 (Rfree = 0.000) for 3643 atoms. Found 20 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3753 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3773 seeds are put forward Round 1: 197 peptides, 43 chains. Longest chain 7 peptides. Score 0.247 Round 2: 211 peptides, 38 chains. Longest chain 11 peptides. Score 0.352 Round 3: 215 peptides, 40 chains. Longest chain 9 peptides. Score 0.339 Round 4: 218 peptides, 36 chains. Longest chain 11 peptides. Score 0.395 Round 5: 207 peptides, 36 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 4 Chains 36, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8296 restraints for refining 3684 atoms. 7604 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2054 (Rfree = 0.000) for 3684 atoms. Found 22 (23 requested) and removed 16 (11 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1855 (Rfree = 0.000) for 3684 atoms. Found 6 (23 requested) and removed 16 (11 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1872 (Rfree = 0.000) for 3665 atoms. Found 5 (23 requested) and removed 16 (11 requested) atoms. Cycle 39: After refmac, R = 0.1930 (Rfree = 0.000) for 3650 atoms. Found 15 (23 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1890 (Rfree = 0.000) for 3648 atoms. Found 11 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 3728 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3743 seeds are put forward Round 1: 178 peptides, 35 chains. Longest chain 10 peptides. Score 0.292 Round 2: 202 peptides, 39 chains. Longest chain 11 peptides. Score 0.313 Round 3: 208 peptides, 36 chains. Longest chain 11 peptides. Score 0.368 Round 4: 225 peptides, 36 chains. Longest chain 11 peptides. Score 0.414 Round 5: 205 peptides, 34 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 4 Chains 36, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7278 reflections ( 98.28 % complete ) and 8277 restraints for refining 3683 atoms. 7557 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2140 (Rfree = 0.000) for 3683 atoms. Found 17 (23 requested) and removed 18 (11 requested) atoms. Cycle 42: After refmac, R = 0.2178 (Rfree = 0.000) for 3662 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 43: After refmac, R = 0.2035 (Rfree = 0.000) for 3648 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 44: After refmac, R = 0.1919 (Rfree = 0.000) for 3648 atoms. Found 14 (23 requested) and removed 17 (11 requested) atoms. Cycle 45: After refmac, R = 0.1857 (Rfree = 0.000) for 3635 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3723 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3733 seeds are put forward Round 1: 167 peptides, 36 chains. Longest chain 8 peptides. Score 0.244 Round 2: 200 peptides, 40 chains. Longest chain 9 peptides. Score 0.295 Round 3: 200 peptides, 38 chains. Longest chain 9 peptides. Score 0.320 Round 4: 221 peptides, 38 chains. Longest chain 11 peptides. Score 0.380 Round 5: 220 peptides, 35 chains. Longest chain 13 peptides. Score 0.413 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 185, 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 2it9-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7278 reflections ( 98.28 % complete ) and 8214 restraints for refining 3684 atoms. 7509 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2118 (Rfree = 0.000) for 3684 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1944 (Rfree = 0.000) for 3659 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1916 (Rfree = 0.000) for 3638 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1907 (Rfree = 0.000) for 3623 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Writing output files ... TimeTaking 61.55