Sun 23 Dec 22:22:56 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 2f4p-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-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/2f4p-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-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 22:23:05 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/2f4p-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-3.2-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 411 and 0 Target number of residues in the AU: 411 Target solvent content: 0.6032 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-3.2-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.60 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: 21.543 3.200 Wilson plot Bfac: 53.61 9033 reflections ( 99.64 % complete ) and 0 restraints for refining 5230 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3166 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3145 (Rfree = 0.000) for 5230 atoms. Found 46 (46 requested) and removed 75 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.34 Search for helices and strands: 0 residues in 0 chains, 5267 seeds are put forward NCS extension: 0 residues added, 5267 seeds are put forward Round 1: 246 peptides, 45 chains. Longest chain 11 peptides. Score 0.377 Round 2: 320 peptides, 50 chains. Longest chain 15 peptides. Score 0.516 Round 3: 352 peptides, 46 chains. Longest chain 27 peptides. Score 0.625 Round 4: 363 peptides, 45 chains. Longest chain 18 peptides. Score 0.655 Round 5: 378 peptides, 46 chains. Longest chain 21 peptides. Score 0.674 Taking the results from Round 5 Chains 47, Residues 332, Estimated correctness of the model 59.5 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9228 restraints for refining 4294 atoms. 7878 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2759 (Rfree = 0.000) for 4294 atoms. Found 24 (38 requested) and removed 60 (19 requested) atoms. Cycle 2: After refmac, R = 0.2470 (Rfree = 0.000) for 4197 atoms. Found 22 (38 requested) and removed 39 (19 requested) atoms. Cycle 3: After refmac, R = 0.2306 (Rfree = 0.000) for 4163 atoms. Found 14 (37 requested) and removed 37 (18 requested) atoms. Cycle 4: After refmac, R = 0.2167 (Rfree = 0.000) for 4134 atoms. Found 14 (37 requested) and removed 31 (18 requested) atoms. Cycle 5: After refmac, R = 0.2015 (Rfree = 0.000) for 4107 atoms. Found 9 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4194 seeds are put forward NCS extension: 10 residues added (8 deleted due to clashes), 4204 seeds are put forward Round 1: 323 peptides, 44 chains. Longest chain 22 peptides. Score 0.583 Round 2: 363 peptides, 42 chains. Longest chain 39 peptides. Score 0.679 Round 3: 358 peptides, 39 chains. Longest chain 25 peptides. Score 0.694 Round 4: 353 peptides, 34 chains. Longest chain 26 peptides. Score 0.724 Round 5: 369 peptides, 37 chains. Longest chain 25 peptides. Score 0.727 Taking the results from Round 5 Chains 39, Residues 332, Estimated correctness of the model 70.7 % 3 chains (34 residues) have been docked in sequence Building loops using Loopy2018 39 chains (332 residues) following loop building 3 chains (34 residues) in sequence following loop building ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9022 restraints for refining 4294 atoms. 7594 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2405 (Rfree = 0.000) for 4294 atoms. Found 35 (38 requested) and removed 54 (19 requested) atoms. Cycle 7: After refmac, R = 0.2252 (Rfree = 0.000) for 4267 atoms. Found 16 (37 requested) and removed 33 (19 requested) atoms. Cycle 8: After refmac, R = 0.2149 (Rfree = 0.000) for 4244 atoms. Found 15 (36 requested) and removed 34 (19 requested) atoms. Cycle 9: After refmac, R = 0.2192 (Rfree = 0.000) for 4212 atoms. Found 20 (35 requested) and removed 26 (18 requested) atoms. Cycle 10: After refmac, R = 0.2057 (Rfree = 0.000) for 4199 atoms. Found 13 (34 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4288 seeds are put forward NCS extension: 17 residues added (12 deleted due to clashes), 4305 seeds are put forward Round 1: 304 peptides, 41 chains. Longest chain 18 peptides. Score 0.571 Round 2: 334 peptides, 39 chains. Longest chain 21 peptides. Score 0.651 Round 3: 352 peptides, 40 chains. Longest chain 30 peptides. Score 0.676 Round 4: 365 peptides, 41 chains. Longest chain 23 peptides. Score 0.690 Round 5: 376 peptides, 36 chains. Longest chain 33 peptides. Score 0.744 Taking the results from Round 5 Chains 37, Residues 340, Estimated correctness of the model 74.0 % 3 chains (49 residues) have been docked in sequence Building loops using Loopy2018 37 chains (340 residues) following loop building 3 chains (49 residues) in sequence following loop building ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 8837 restraints for refining 4293 atoms. 7314 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2372 (Rfree = 0.000) for 4293 atoms. Found 30 (34 requested) and removed 46 (19 requested) atoms. Cycle 12: After refmac, R = 0.2178 (Rfree = 0.000) for 4266 atoms. Found 10 (33 requested) and removed 28 (19 requested) atoms. Cycle 13: After refmac, R = 0.2061 (Rfree = 0.000) for 4239 atoms. Found 12 (33 requested) and removed 23 (19 requested) atoms. Cycle 14: After refmac, R = 0.2219 (Rfree = 0.000) for 4224 atoms. Found 20 (31 requested) and removed 26 (18 requested) atoms. Cycle 15: After refmac, R = 0.2057 (Rfree = 0.000) for 4208 atoms. Found 16 (30 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.99 3.28 Search for helices and strands: 0 residues in 0 chains, 4294 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4312 seeds are put forward Round 1: 312 peptides, 48 chains. Longest chain 23 peptides. Score 0.518 Round 2: 337 peptides, 37 chains. Longest chain 33 peptides. Score 0.674 Round 3: 341 peptides, 35 chains. Longest chain 42 peptides. Score 0.697 Round 4: 350 peptides, 38 chains. Longest chain 33 peptides. Score 0.688 Round 5: 352 peptides, 35 chains. Longest chain 36 peptides. Score 0.715 Taking the results from Round 5 Chains 36, Residues 317, Estimated correctness of the model 68.3 % 3 chains (44 residues) have been docked in sequence Building loops using Loopy2018 36 chains (317 residues) following loop building 3 chains (44 residues) in sequence following loop building ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9031 restraints for refining 4294 atoms. 7621 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2273 (Rfree = 0.000) for 4294 atoms. Found 30 (30 requested) and removed 33 (19 requested) atoms. Cycle 17: After refmac, R = 0.2171 (Rfree = 0.000) for 4278 atoms. Found 13 (30 requested) and removed 29 (19 requested) atoms. Cycle 18: After refmac, R = 0.2105 (Rfree = 0.000) for 4246 atoms. Found 10 (29 requested) and removed 24 (19 requested) atoms. Cycle 19: After refmac, R = 0.2015 (Rfree = 0.000) for 4225 atoms. Found 15 (27 requested) and removed 19 (18 requested) atoms. Cycle 20: After refmac, R = 0.1944 (Rfree = 0.000) for 4216 atoms. Found 12 (27 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4284 seeds are put forward NCS extension: 21 residues added (15 deleted due to clashes), 4305 seeds are put forward Round 1: 307 peptides, 45 chains. Longest chain 25 peptides. Score 0.537 Round 2: 336 peptides, 37 chains. Longest chain 33 peptides. Score 0.672 Round 3: 340 peptides, 39 chains. Longest chain 34 peptides. Score 0.662 Round 4: 330 peptides, 37 chains. Longest chain 31 peptides. Score 0.661 Round 5: 331 peptides, 39 chains. Longest chain 34 peptides. Score 0.646 Taking the results from Round 2 Chains 40, Residues 299, Estimated correctness of the model 59.0 % 4 chains (61 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 8725 restraints for refining 4294 atoms. 7334 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2086 (Rfree = 0.000) for 4294 atoms. Found 21 (27 requested) and removed 26 (19 requested) atoms. Cycle 22: After refmac, R = 0.1987 (Rfree = 0.000) for 4276 atoms. Found 19 (27 requested) and removed 26 (19 requested) atoms. Cycle 23: After refmac, R = 0.1844 (Rfree = 0.000) for 4267 atoms. Found 11 (27 requested) and removed 24 (19 requested) atoms. Cycle 24: After refmac, R = 0.1783 (Rfree = 0.000) for 4245 atoms. Found 10 (27 requested) and removed 20 (19 requested) atoms. Cycle 25: After refmac, R = 0.1724 (Rfree = 0.000) for 4228 atoms. Found 9 (27 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4323 seeds are put forward NCS extension: 25 residues added (8 deleted due to clashes), 4348 seeds are put forward Round 1: 289 peptides, 45 chains. Longest chain 23 peptides. Score 0.493 Round 2: 318 peptides, 44 chains. Longest chain 25 peptides. Score 0.572 Round 3: 309 peptides, 46 chains. Longest chain 16 peptides. Score 0.531 Round 4: 327 peptides, 40 chains. Longest chain 32 peptides. Score 0.629 Round 5: 333 peptides, 44 chains. Longest chain 25 peptides. Score 0.605 Taking the results from Round 4 Chains 42, Residues 287, Estimated correctness of the model 48.6 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9086 restraints for refining 4294 atoms. 7802 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1984 (Rfree = 0.000) for 4294 atoms. Found 21 (27 requested) and removed 26 (19 requested) atoms. Cycle 27: After refmac, R = 0.1905 (Rfree = 0.000) for 4283 atoms. Found 15 (27 requested) and removed 24 (19 requested) atoms. Cycle 28: After refmac, R = 0.2235 (Rfree = 0.000) for 4269 atoms. Found 27 (27 requested) and removed 23 (19 requested) atoms. Cycle 29: After refmac, R = 0.1668 (Rfree = 0.000) for 4270 atoms. Found 11 (27 requested) and removed 23 (19 requested) atoms. Cycle 30: After refmac, R = 0.2025 (Rfree = 0.000) for 4255 atoms. Found 27 (27 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 3.30 Search for helices and strands: 0 residues in 0 chains, 4356 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 4370 seeds are put forward Round 1: 276 peptides, 39 chains. Longest chain 29 peptides. Score 0.526 Round 2: 314 peptides, 44 chains. Longest chain 31 peptides. Score 0.563 Round 3: 330 peptides, 45 chains. Longest chain 22 peptides. Score 0.589 Round 4: 321 peptides, 41 chains. Longest chain 29 peptides. Score 0.608 Round 5: 316 peptides, 41 chains. Longest chain 31 peptides. Score 0.597 Taking the results from Round 4 Chains 42, Residues 280, Estimated correctness of the model 43.2 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9181 restraints for refining 4293 atoms. 7930 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1981 (Rfree = 0.000) for 4293 atoms. Found 27 (27 requested) and removed 27 (19 requested) atoms. Cycle 32: After refmac, R = 0.1784 (Rfree = 0.000) for 4284 atoms. Found 14 (27 requested) and removed 19 (19 requested) atoms. Cycle 33: After refmac, R = 0.1797 (Rfree = 0.000) for 4277 atoms. Found 13 (27 requested) and removed 21 (19 requested) atoms. Cycle 34: After refmac, R = 0.1735 (Rfree = 0.000) for 4268 atoms. Found 12 (27 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.1828 (Rfree = 0.000) for 4258 atoms. Found 24 (27 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4352 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4368 seeds are put forward Round 1: 302 peptides, 49 chains. Longest chain 29 peptides. Score 0.482 Round 2: 317 peptides, 47 chains. Longest chain 23 peptides. Score 0.540 Round 3: 307 peptides, 47 chains. Longest chain 19 peptides. Score 0.516 Round 4: 290 peptides, 41 chains. Longest chain 23 peptides. Score 0.539 Round 5: 291 peptides, 37 chains. Longest chain 29 peptides. Score 0.582 Taking the results from Round 5 Chains 38, Residues 254, Estimated correctness of the model 36.1 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9145 restraints for refining 4294 atoms. 8000 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1862 (Rfree = 0.000) for 4294 atoms. Found 27 (27 requested) and removed 25 (19 requested) atoms. Cycle 37: After refmac, R = 0.1668 (Rfree = 0.000) for 4290 atoms. Found 14 (27 requested) and removed 21 (19 requested) atoms. Cycle 38: After refmac, R = 0.1705 (Rfree = 0.000) for 4279 atoms. Found 19 (27 requested) and removed 21 (19 requested) atoms. Cycle 39: After refmac, R = 0.1584 (Rfree = 0.000) for 4275 atoms. Found 14 (27 requested) and removed 20 (19 requested) atoms. Cycle 40: After refmac, R = 0.1843 (Rfree = 0.000) for 4265 atoms. Found 27 (27 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.00 3.30 Search for helices and strands: 0 residues in 0 chains, 4365 seeds are put forward NCS extension: 24 residues added (17 deleted due to clashes), 4389 seeds are put forward Round 1: 257 peptides, 44 chains. Longest chain 18 peptides. Score 0.420 Round 2: 277 peptides, 35 chains. Longest chain 24 peptides. Score 0.571 Round 3: 290 peptides, 39 chains. Longest chain 21 peptides. Score 0.559 Round 4: 282 peptides, 38 chains. Longest chain 23 peptides. Score 0.551 Round 5: 271 peptides, 38 chains. Longest chain 35 peptides. Score 0.525 Taking the results from Round 2 Chains 35, Residues 242, Estimated correctness of the model 33.0 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9033 reflections ( 99.64 % complete ) and 9179 restraints for refining 4294 atoms. 8066 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1682 (Rfree = 0.000) for 4294 atoms. Found 23 (27 requested) and removed 28 (19 requested) atoms. Cycle 42: After refmac, R = 0.1560 (Rfree = 0.000) for 4283 atoms. Found 14 (27 requested) and removed 23 (19 requested) atoms. Cycle 43: After refmac, R = 0.1536 (Rfree = 0.000) for 4270 atoms. Found 14 (27 requested) and removed 19 (19 requested) atoms. Cycle 44: After refmac, R = 0.1949 (Rfree = 0.000) for 4262 atoms. Found 27 (27 requested) and removed 24 (19 requested) atoms. Cycle 45: After refmac, R = 0.1456 (Rfree = 0.000) for 4262 atoms. Found 15 (27 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.01 3.31 Search for helices and strands: 0 residues in 0 chains, 4370 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 4402 seeds are put forward Round 1: 245 peptides, 43 chains. Longest chain 16 peptides. Score 0.398 Round 2: 265 peptides, 40 chains. Longest chain 22 peptides. Score 0.488 Round 3: 268 peptides, 40 chains. Longest chain 16 peptides. Score 0.495 Round 4: 263 peptides, 38 chains. Longest chain 20 peptides. Score 0.505 Round 5: 265 peptides, 38 chains. Longest chain 20 peptides. Score 0.510 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 227, Estimated correctness of the model 14.5 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2f4p-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9033 reflections ( 99.64 % complete ) and 9487 restraints for refining 4293 atoms. 8570 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1729 (Rfree = 0.000) for 4293 atoms. Found 0 (27 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1818 (Rfree = 0.000) for 4269 atoms. Found 0 (27 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1541 (Rfree = 0.000) for 4245 atoms. Found 0 (27 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1396 (Rfree = 0.000) for 4223 atoms. TimeTaking 69.47