Starting phenix.real_space_refine on Thu Mar 14 14:05:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/03_2024/8exp_28658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/03_2024/8exp_28658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/03_2024/8exp_28658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/03_2024/8exp_28658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/03_2024/8exp_28658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exp_28658/03_2024/8exp_28658.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 38 5.16 5 C 5928 2.51 5 N 1484 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9024 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4511 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 10, 'TRANS': 528} Chain breaks: 2 Chain: "B" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4511 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 10, 'TRANS': 528} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.54 Number of scatterers: 9024 At special positions: 0 Unit cell: (73.9927, 106.477, 135.353, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 38 16.00 O 1572 8.00 N 1484 7.00 C 5928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 56.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 99 through 133 removed outlier: 3.514A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.611A pdb=" N ASN A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 removed outlier: 4.058A pdb=" N ILE A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 252 removed outlier: 3.890A pdb=" N ILE A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 5.479A pdb=" N ASN A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.798A pdb=" N SER A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.660A pdb=" N PHE A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 99 through 133 removed outlier: 3.515A pdb=" N LYS B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 194 through 208 removed outlier: 3.611A pdb=" N ASN B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 224 removed outlier: 4.058A pdb=" N ILE B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 3.890A pdb=" N ILE B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 removed outlier: 5.479A pdb=" N ASN B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.798A pdb=" N SER B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 379 through 382 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.660A pdb=" N PHE B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 484 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.440A pdb=" N GLU B 522 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 545 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR B 524 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 543 " --> pdb=" O TYR B 524 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS B 526 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B 541 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY B 528 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY B 539 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY B 530 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 372 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.967A pdb=" N TYR B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS B 517 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU B 523 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 6.638A pdb=" N VAL A 160 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE A 182 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG A 162 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.820A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 372 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 530 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY A 539 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY A 528 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 541 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS A 526 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 543 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR A 524 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 545 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A 522 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 517 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 523 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.820A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 372 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 530 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY A 539 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY A 528 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 541 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS A 526 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 543 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR A 524 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 545 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A 522 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N PHE B 90 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 527 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N THR B 92 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 529 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE B 94 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 531 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 137 removed outlier: 6.638A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG B 162 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 384 through 385 508 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1597 1.31 - 1.44: 2750 1.44 - 1.57: 4765 1.57 - 1.70: 50 1.70 - 1.83: 70 Bond restraints: 9232 Sorted by residual: bond pdb=" CG GLN B 487 " pdb=" CD GLN B 487 " ideal model delta sigma weight residual 1.516 1.379 0.137 2.50e-02 1.60e+03 3.02e+01 bond pdb=" CG GLN A 487 " pdb=" CD GLN A 487 " ideal model delta sigma weight residual 1.516 1.379 0.137 2.50e-02 1.60e+03 2.99e+01 bond pdb=" CB TYR A 552 " pdb=" CG TYR A 552 " ideal model delta sigma weight residual 1.512 1.393 0.119 2.20e-02 2.07e+03 2.91e+01 bond pdb=" CB TYR B 552 " pdb=" CG TYR B 552 " ideal model delta sigma weight residual 1.512 1.394 0.118 2.20e-02 2.07e+03 2.89e+01 bond pdb=" CB TYR B 521 " pdb=" CG TYR B 521 " ideal model delta sigma weight residual 1.512 1.407 0.105 2.20e-02 2.07e+03 2.29e+01 ... (remaining 9227 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.72: 297 106.72 - 113.53: 4712 113.53 - 120.34: 4005 120.34 - 127.16: 3322 127.16 - 133.97: 86 Bond angle restraints: 12422 Sorted by residual: angle pdb=" N ILE B 404 " pdb=" CA ILE B 404 " pdb=" C ILE B 404 " ideal model delta sigma weight residual 110.82 102.10 8.72 9.70e-01 1.06e+00 8.08e+01 angle pdb=" N ILE A 404 " pdb=" CA ILE A 404 " pdb=" C ILE A 404 " ideal model delta sigma weight residual 110.82 102.11 8.71 9.70e-01 1.06e+00 8.07e+01 angle pdb=" CA PHE B 313 " pdb=" CB PHE B 313 " pdb=" CG PHE B 313 " ideal model delta sigma weight residual 113.80 105.01 8.79 1.00e+00 1.00e+00 7.73e+01 angle pdb=" CA PHE A 313 " pdb=" CB PHE A 313 " pdb=" CG PHE A 313 " ideal model delta sigma weight residual 113.80 105.03 8.77 1.00e+00 1.00e+00 7.69e+01 angle pdb=" CA LYS B 354 " pdb=" C LYS B 354 " pdb=" N ILE B 355 " ideal model delta sigma weight residual 118.41 107.38 11.03 1.34e+00 5.57e-01 6.77e+01 ... (remaining 12417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 5230 15.75 - 31.50: 226 31.50 - 47.25: 42 47.25 - 63.01: 30 63.01 - 78.76: 6 Dihedral angle restraints: 5534 sinusoidal: 2308 harmonic: 3226 Sorted by residual: dihedral pdb=" C ASN A 302 " pdb=" N ASN A 302 " pdb=" CA ASN A 302 " pdb=" CB ASN A 302 " ideal model delta harmonic sigma weight residual -122.60 -114.90 -7.70 0 2.50e+00 1.60e-01 9.48e+00 dihedral pdb=" C ASN B 302 " pdb=" N ASN B 302 " pdb=" CA ASN B 302 " pdb=" CB ASN B 302 " ideal model delta harmonic sigma weight residual -122.60 -114.92 -7.68 0 2.50e+00 1.60e-01 9.43e+00 dihedral pdb=" CG LYS B 352 " pdb=" CD LYS B 352 " pdb=" CE LYS B 352 " pdb=" NZ LYS B 352 " ideal model delta sinusoidal sigma weight residual 180.00 127.15 52.85 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 5531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 742 0.075 - 0.149: 443 0.149 - 0.224: 143 0.224 - 0.299: 23 0.299 - 0.374: 7 Chirality restraints: 1358 Sorted by residual: chirality pdb=" CA PHE A 313 " pdb=" N PHE A 313 " pdb=" C PHE A 313 " pdb=" CB PHE A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA PHE B 313 " pdb=" N PHE B 313 " pdb=" C PHE B 313 " pdb=" CB PHE B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU B 400 " pdb=" CB LEU B 400 " pdb=" CD1 LEU B 400 " pdb=" CD2 LEU B 400 " both_signs ideal model delta sigma weight residual False -2.59 -2.92 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1355 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 463 " -0.064 2.00e-02 2.50e+03 3.41e-02 2.33e+01 pdb=" CG TYR A 463 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 463 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 463 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR A 463 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 463 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 463 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 463 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 463 " 0.064 2.00e-02 2.50e+03 3.41e-02 2.33e+01 pdb=" CG TYR B 463 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 463 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 463 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR B 463 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 463 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 463 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 463 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 540 " -0.062 2.00e-02 2.50e+03 3.01e-02 2.26e+01 pdb=" CG TRP B 540 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 540 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 540 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP B 540 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 540 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 540 " 0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 540 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 540 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP B 540 " -0.023 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 93 2.60 - 3.18: 8700 3.18 - 3.75: 14641 3.75 - 4.33: 21209 4.33 - 4.90: 32042 Nonbonded interactions: 76685 Sorted by model distance: nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.031 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.031 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.039 2.230 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.040 2.230 nonbonded pdb=" CE MET A 266 " pdb=" CE MET B 266 " model vdw 2.109 3.880 ... (remaining 76680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.060 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.860 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4467 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.137 9232 Z= 1.212 Angle : 1.741 11.026 12422 Z= 1.196 Chirality : 0.099 0.374 1358 Planarity : 0.008 0.037 1520 Dihedral : 10.687 78.757 3454 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.38 % Favored : 96.44 % Rotamer: Outliers : 0.60 % Allowed : 1.39 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1066 helix: 0.31 (0.19), residues: 564 sheet: 0.61 (0.44), residues: 138 loop : -0.63 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.008 TRP B 540 HIS 0.008 0.003 HIS A 549 PHE 0.031 0.007 PHE B 313 TYR 0.064 0.009 TYR A 463 ARG 0.006 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 295 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.8887 (mt) cc_final: 0.8678 (mp) REVERT: A 19 LEU cc_start: 0.9464 (mt) cc_final: 0.9164 (mt) REVERT: A 103 ASP cc_start: 0.8144 (m-30) cc_final: 0.7872 (m-30) REVERT: A 127 TYR cc_start: 0.8533 (t80) cc_final: 0.7905 (t80) REVERT: A 143 LYS cc_start: 0.8616 (tttt) cc_final: 0.8193 (tttp) REVERT: A 220 PHE cc_start: 0.7908 (m-80) cc_final: 0.7547 (m-80) REVERT: A 224 MET cc_start: 0.8780 (mpp) cc_final: 0.8216 (mpp) REVERT: A 263 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 265 ILE cc_start: 0.9198 (mm) cc_final: 0.8990 (mm) REVERT: A 300 GLU cc_start: 0.7976 (tp30) cc_final: 0.7646 (tp30) REVERT: A 316 ILE cc_start: 0.8464 (mt) cc_final: 0.8232 (mm) REVERT: A 317 PHE cc_start: 0.8448 (m-80) cc_final: 0.8063 (m-10) REVERT: A 322 MET cc_start: 0.8742 (mtm) cc_final: 0.8485 (mtm) REVERT: A 404 ILE cc_start: 0.5036 (mt) cc_final: 0.4045 (mm) REVERT: B 19 LEU cc_start: 0.9478 (mt) cc_final: 0.9109 (mt) REVERT: B 127 TYR cc_start: 0.8418 (t80) cc_final: 0.7708 (t80) REVERT: B 143 LYS cc_start: 0.8450 (tttt) cc_final: 0.8065 (tttp) REVERT: B 180 ILE cc_start: 0.8138 (mt) cc_final: 0.7836 (mm) REVERT: B 220 PHE cc_start: 0.7891 (m-80) cc_final: 0.7539 (m-80) REVERT: B 224 MET cc_start: 0.8768 (mpp) cc_final: 0.8285 (mpp) REVERT: B 227 ASN cc_start: 0.8067 (t0) cc_final: 0.7865 (t0) REVERT: B 300 GLU cc_start: 0.7970 (tp30) cc_final: 0.7383 (tm-30) REVERT: B 316 ILE cc_start: 0.8487 (mt) cc_final: 0.8287 (mm) REVERT: B 317 PHE cc_start: 0.8426 (m-80) cc_final: 0.8161 (m-10) REVERT: B 321 LEU cc_start: 0.8761 (mt) cc_final: 0.8551 (mt) REVERT: B 404 ILE cc_start: 0.5004 (mt) cc_final: 0.4113 (mm) outliers start: 6 outliers final: 1 residues processed: 301 average time/residue: 0.2579 time to fit residues: 100.4168 Evaluate side-chains 184 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 153 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN A 557 HIS B 153 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 537 ASN B 557 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4679 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9232 Z= 0.325 Angle : 0.737 7.564 12422 Z= 0.409 Chirality : 0.049 0.199 1358 Planarity : 0.005 0.043 1520 Dihedral : 5.515 23.730 1174 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1066 helix: 0.67 (0.21), residues: 564 sheet: 0.73 (0.48), residues: 124 loop : -0.96 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 440 HIS 0.008 0.003 HIS A 282 PHE 0.020 0.002 PHE B 21 TYR 0.025 0.002 TYR A 394 ARG 0.007 0.001 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9459 (mt) cc_final: 0.9132 (mt) REVERT: A 143 LYS cc_start: 0.8861 (tttt) cc_final: 0.8424 (tttp) REVERT: A 224 MET cc_start: 0.7986 (mpp) cc_final: 0.7778 (mmm) REVERT: A 226 TYR cc_start: 0.6151 (p90) cc_final: 0.5924 (p90) REVERT: A 265 ILE cc_start: 0.8857 (mm) cc_final: 0.8635 (mm) REVERT: A 300 GLU cc_start: 0.8634 (tp30) cc_final: 0.7867 (tm-30) REVERT: A 321 LEU cc_start: 0.9001 (mt) cc_final: 0.8577 (mt) REVERT: B 12 PHE cc_start: 0.8757 (t80) cc_final: 0.8180 (t80) REVERT: B 19 LEU cc_start: 0.9482 (mt) cc_final: 0.9253 (mt) REVERT: B 137 TYR cc_start: 0.7322 (p90) cc_final: 0.7114 (p90) REVERT: B 143 LYS cc_start: 0.8732 (tttt) cc_final: 0.8283 (tttp) REVERT: B 224 MET cc_start: 0.8003 (mpp) cc_final: 0.7761 (mmm) REVERT: B 227 ASN cc_start: 0.7676 (t0) cc_final: 0.7349 (t0) REVERT: B 265 ILE cc_start: 0.8984 (mp) cc_final: 0.8630 (mp) REVERT: B 300 GLU cc_start: 0.8670 (tp30) cc_final: 0.7809 (tm-30) REVERT: B 321 LEU cc_start: 0.9088 (mt) cc_final: 0.8737 (mt) REVERT: B 495 MET cc_start: 0.5224 (mtt) cc_final: 0.4882 (mtp) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.2173 time to fit residues: 65.3960 Evaluate side-chains 175 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 40.0000 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN B 158 ASN B 278 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4592 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9232 Z= 0.196 Angle : 0.591 9.514 12422 Z= 0.324 Chirality : 0.044 0.173 1358 Planarity : 0.003 0.036 1520 Dihedral : 4.982 20.825 1174 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1066 helix: 1.08 (0.22), residues: 566 sheet: 0.58 (0.46), residues: 138 loop : -0.69 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 110 HIS 0.003 0.001 HIS B 282 PHE 0.042 0.002 PHE A 14 TYR 0.014 0.002 TYR B 366 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9458 (mt) cc_final: 0.9069 (mt) REVERT: A 126 LEU cc_start: 0.8959 (mt) cc_final: 0.8738 (mt) REVERT: A 137 TYR cc_start: 0.7082 (p90) cc_final: 0.6804 (p90) REVERT: A 143 LYS cc_start: 0.8756 (tttt) cc_final: 0.8389 (tttp) REVERT: A 150 LEU cc_start: 0.8669 (tp) cc_final: 0.8442 (tp) REVERT: A 224 MET cc_start: 0.8393 (mpp) cc_final: 0.7971 (mmm) REVERT: A 233 VAL cc_start: 0.8233 (t) cc_final: 0.7941 (p) REVERT: A 265 ILE cc_start: 0.8971 (mm) cc_final: 0.8766 (mm) REVERT: A 300 GLU cc_start: 0.8919 (tp30) cc_final: 0.7865 (tm-30) REVERT: A 321 LEU cc_start: 0.9124 (mt) cc_final: 0.8692 (mt) REVERT: B 9 ILE cc_start: 0.8572 (mt) cc_final: 0.7528 (mt) REVERT: B 12 PHE cc_start: 0.8702 (t80) cc_final: 0.8170 (t80) REVERT: B 143 LYS cc_start: 0.8523 (tttt) cc_final: 0.8095 (tttp) REVERT: B 150 LEU cc_start: 0.8427 (tp) cc_final: 0.8098 (tp) REVERT: B 200 LEU cc_start: 0.9296 (mt) cc_final: 0.9082 (mt) REVERT: B 233 VAL cc_start: 0.7940 (t) cc_final: 0.7532 (p) REVERT: B 265 ILE cc_start: 0.8884 (mp) cc_final: 0.8515 (mp) REVERT: B 293 ARG cc_start: 0.7440 (mtt90) cc_final: 0.7093 (mtm-85) REVERT: B 300 GLU cc_start: 0.8936 (tp30) cc_final: 0.7989 (tm-30) REVERT: B 321 LEU cc_start: 0.9068 (mt) cc_final: 0.8754 (mt) REVERT: B 365 MET cc_start: -0.2009 (tpt) cc_final: -0.3340 (tpt) REVERT: B 495 MET cc_start: 0.5022 (mtt) cc_final: 0.4611 (mtp) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2183 time to fit residues: 63.3155 Evaluate side-chains 173 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN B 278 ASN B 285 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4775 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9232 Z= 0.301 Angle : 0.686 7.929 12422 Z= 0.378 Chirality : 0.046 0.167 1358 Planarity : 0.004 0.043 1520 Dihedral : 5.192 21.686 1174 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1066 helix: 0.80 (0.21), residues: 578 sheet: 0.38 (0.50), residues: 110 loop : -1.31 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 99 HIS 0.006 0.002 HIS B 205 PHE 0.026 0.003 PHE A 21 TYR 0.027 0.002 TYR A 394 ARG 0.004 0.001 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.8892 (mt) cc_final: 0.8645 (mt) REVERT: A 128 LEU cc_start: 0.9034 (mt) cc_final: 0.8803 (mt) REVERT: A 143 LYS cc_start: 0.8855 (tttt) cc_final: 0.8520 (tttp) REVERT: A 210 ASP cc_start: 0.8451 (m-30) cc_final: 0.8224 (m-30) REVERT: A 265 ILE cc_start: 0.8979 (mm) cc_final: 0.8764 (mm) REVERT: A 300 GLU cc_start: 0.9231 (tp30) cc_final: 0.8244 (tm-30) REVERT: A 321 LEU cc_start: 0.9248 (mt) cc_final: 0.8808 (mt) REVERT: A 579 MET cc_start: 0.1934 (mmm) cc_final: 0.1139 (mmt) REVERT: B 5 LEU cc_start: 0.8448 (mp) cc_final: 0.8168 (mp) REVERT: B 9 ILE cc_start: 0.8542 (mt) cc_final: 0.7466 (mt) REVERT: B 12 PHE cc_start: 0.8658 (t80) cc_final: 0.8298 (t80) REVERT: B 15 ILE cc_start: 0.9209 (mm) cc_final: 0.8658 (mm) REVERT: B 143 LYS cc_start: 0.8823 (tttt) cc_final: 0.8341 (tttp) REVERT: B 150 LEU cc_start: 0.8786 (tp) cc_final: 0.8540 (tp) REVERT: B 300 GLU cc_start: 0.9214 (tp30) cc_final: 0.8174 (tm-30) REVERT: B 321 LEU cc_start: 0.9252 (mt) cc_final: 0.9003 (mt) REVERT: B 365 MET cc_start: -0.1810 (tpt) cc_final: -0.2848 (tpt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2055 time to fit residues: 56.8357 Evaluate side-chains 168 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 278 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 278 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4715 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9232 Z= 0.223 Angle : 0.604 5.705 12422 Z= 0.330 Chirality : 0.044 0.178 1358 Planarity : 0.004 0.038 1520 Dihedral : 5.006 21.200 1174 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1066 helix: 0.99 (0.21), residues: 582 sheet: 0.45 (0.52), residues: 110 loop : -1.42 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 110 HIS 0.004 0.001 HIS B 282 PHE 0.018 0.002 PHE B 491 TYR 0.015 0.002 TYR A 552 ARG 0.006 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8409 (t80) cc_final: 0.7978 (t80) REVERT: A 143 LYS cc_start: 0.8973 (tttt) cc_final: 0.8580 (tttp) REVERT: A 224 MET cc_start: 0.8127 (mtp) cc_final: 0.7894 (mmm) REVERT: A 233 VAL cc_start: 0.8083 (t) cc_final: 0.7611 (p) REVERT: A 265 ILE cc_start: 0.8958 (mm) cc_final: 0.8756 (mm) REVERT: A 300 GLU cc_start: 0.9026 (tp30) cc_final: 0.8095 (tm-30) REVERT: A 321 LEU cc_start: 0.9240 (mt) cc_final: 0.8979 (mt) REVERT: A 365 MET cc_start: -0.3315 (tpt) cc_final: -0.4222 (tpt) REVERT: B 5 LEU cc_start: 0.8329 (mp) cc_final: 0.8107 (mp) REVERT: B 9 ILE cc_start: 0.8484 (mt) cc_final: 0.7370 (mt) REVERT: B 12 PHE cc_start: 0.8656 (t80) cc_final: 0.8378 (t80) REVERT: B 15 ILE cc_start: 0.9285 (mm) cc_final: 0.9051 (mm) REVERT: B 143 LYS cc_start: 0.8737 (tttt) cc_final: 0.8238 (tttp) REVERT: B 150 LEU cc_start: 0.8751 (tp) cc_final: 0.8538 (tp) REVERT: B 224 MET cc_start: 0.8075 (mtp) cc_final: 0.7796 (mmm) REVERT: B 300 GLU cc_start: 0.9024 (tp30) cc_final: 0.8092 (tm-30) REVERT: B 321 LEU cc_start: 0.9316 (mt) cc_final: 0.9035 (mt) REVERT: B 325 GLN cc_start: 0.8486 (pm20) cc_final: 0.8282 (pm20) REVERT: B 342 PRO cc_start: 0.3720 (Cg_exo) cc_final: 0.3470 (Cg_endo) REVERT: B 365 MET cc_start: -0.1332 (tpt) cc_final: -0.2294 (tpt) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2150 time to fit residues: 60.9631 Evaluate side-chains 173 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN B 278 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4710 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9232 Z= 0.200 Angle : 0.597 6.829 12422 Z= 0.321 Chirality : 0.043 0.158 1358 Planarity : 0.003 0.037 1520 Dihedral : 4.889 20.335 1174 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1066 helix: 1.19 (0.22), residues: 584 sheet: 0.55 (0.53), residues: 110 loop : -1.44 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 110 HIS 0.005 0.001 HIS A 205 PHE 0.012 0.001 PHE A 491 TYR 0.013 0.002 TYR A 552 ARG 0.004 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8361 (t80) cc_final: 0.7986 (t80) REVERT: A 15 ILE cc_start: 0.9081 (mm) cc_final: 0.8674 (mm) REVERT: A 138 LEU cc_start: 0.7392 (tp) cc_final: 0.6935 (tt) REVERT: A 143 LYS cc_start: 0.8891 (tttt) cc_final: 0.8410 (tptt) REVERT: A 210 ASP cc_start: 0.8311 (m-30) cc_final: 0.7864 (m-30) REVERT: A 224 MET cc_start: 0.8282 (mtp) cc_final: 0.7874 (mmm) REVERT: A 233 VAL cc_start: 0.8137 (t) cc_final: 0.7693 (p) REVERT: A 321 LEU cc_start: 0.9260 (mt) cc_final: 0.8908 (mt) REVERT: A 365 MET cc_start: -0.3441 (tpt) cc_final: -0.4213 (tpt) REVERT: B 5 LEU cc_start: 0.8233 (mp) cc_final: 0.8019 (mp) REVERT: B 9 ILE cc_start: 0.8813 (mt) cc_final: 0.7918 (mt) REVERT: B 15 ILE cc_start: 0.9205 (mm) cc_final: 0.8910 (mm) REVERT: B 143 LYS cc_start: 0.8696 (tttt) cc_final: 0.8203 (tttp) REVERT: B 150 LEU cc_start: 0.8702 (tp) cc_final: 0.8404 (tp) REVERT: B 224 MET cc_start: 0.8047 (mtp) cc_final: 0.7741 (mmm) REVERT: B 321 LEU cc_start: 0.9252 (mt) cc_final: 0.8931 (mt) REVERT: B 342 PRO cc_start: 0.3298 (Cg_exo) cc_final: 0.3003 (Cg_endo) REVERT: B 365 MET cc_start: -0.1144 (tpt) cc_final: -0.2083 (tpt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2049 time to fit residues: 56.7156 Evaluate side-chains 171 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4720 moved from start: 0.6747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9232 Z= 0.215 Angle : 0.610 8.006 12422 Z= 0.330 Chirality : 0.044 0.158 1358 Planarity : 0.004 0.036 1520 Dihedral : 4.866 19.508 1174 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1066 helix: 1.27 (0.22), residues: 584 sheet: 0.44 (0.52), residues: 110 loop : -1.49 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 99 HIS 0.005 0.001 HIS A 205 PHE 0.023 0.002 PHE B 12 TYR 0.018 0.002 TYR B 441 ARG 0.004 0.000 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8319 (t80) cc_final: 0.7941 (t80) REVERT: A 15 ILE cc_start: 0.9098 (mm) cc_final: 0.8735 (mm) REVERT: A 138 LEU cc_start: 0.7452 (tp) cc_final: 0.7116 (tt) REVERT: A 143 LYS cc_start: 0.8922 (tttt) cc_final: 0.8541 (tptt) REVERT: A 217 PHE cc_start: 0.8936 (t80) cc_final: 0.8450 (t80) REVERT: A 224 MET cc_start: 0.8325 (mtp) cc_final: 0.7936 (mmm) REVERT: A 227 ASN cc_start: 0.7509 (t0) cc_final: 0.7250 (t0) REVERT: A 265 ILE cc_start: 0.9018 (mm) cc_final: 0.8815 (mm) REVERT: A 321 LEU cc_start: 0.9333 (mt) cc_final: 0.9059 (mt) REVERT: A 365 MET cc_start: -0.3543 (tpt) cc_final: -0.4271 (tpt) REVERT: B 5 LEU cc_start: 0.8241 (mp) cc_final: 0.7794 (mm) REVERT: B 9 ILE cc_start: 0.8638 (mt) cc_final: 0.7864 (mt) REVERT: B 12 PHE cc_start: 0.8216 (t80) cc_final: 0.7776 (t80) REVERT: B 15 ILE cc_start: 0.9156 (mm) cc_final: 0.8923 (mm) REVERT: B 143 LYS cc_start: 0.8764 (tttt) cc_final: 0.8263 (tttp) REVERT: B 150 LEU cc_start: 0.8638 (tp) cc_final: 0.8399 (tp) REVERT: B 224 MET cc_start: 0.8138 (mtp) cc_final: 0.7753 (mmm) REVERT: B 227 ASN cc_start: 0.7245 (t0) cc_final: 0.7001 (t0) REVERT: B 321 LEU cc_start: 0.9314 (mt) cc_final: 0.8999 (mt) REVERT: B 342 PRO cc_start: 0.3003 (Cg_exo) cc_final: 0.2743 (Cg_endo) REVERT: B 365 MET cc_start: -0.3168 (tpt) cc_final: -0.4844 (tpt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2116 time to fit residues: 56.1999 Evaluate side-chains 158 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.0370 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4667 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9232 Z= 0.166 Angle : 0.581 7.828 12422 Z= 0.311 Chirality : 0.043 0.150 1358 Planarity : 0.003 0.036 1520 Dihedral : 4.731 19.042 1174 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1066 helix: 1.45 (0.22), residues: 584 sheet: 0.31 (0.52), residues: 110 loop : -1.43 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 99 HIS 0.004 0.001 HIS A 201 PHE 0.016 0.001 PHE A 121 TYR 0.017 0.001 TYR B 441 ARG 0.002 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8076 (t80) cc_final: 0.7746 (t80) REVERT: A 15 ILE cc_start: 0.9032 (mm) cc_final: 0.8774 (mm) REVERT: A 143 LYS cc_start: 0.8988 (tttt) cc_final: 0.8617 (tptt) REVERT: A 210 ASP cc_start: 0.8264 (m-30) cc_final: 0.7827 (m-30) REVERT: A 233 VAL cc_start: 0.8444 (t) cc_final: 0.8042 (p) REVERT: A 265 ILE cc_start: 0.8976 (mm) cc_final: 0.8772 (mm) REVERT: A 321 LEU cc_start: 0.9296 (mt) cc_final: 0.8960 (mt) REVERT: A 365 MET cc_start: -0.3645 (tpt) cc_final: -0.4331 (tpt) REVERT: A 579 MET cc_start: 0.2314 (mmm) cc_final: 0.1771 (mtt) REVERT: B 5 LEU cc_start: 0.8201 (mp) cc_final: 0.7931 (mm) REVERT: B 9 ILE cc_start: 0.8636 (mt) cc_final: 0.7826 (mt) REVERT: B 12 PHE cc_start: 0.8168 (t80) cc_final: 0.7846 (t80) REVERT: B 143 LYS cc_start: 0.8818 (tttt) cc_final: 0.8353 (tttp) REVERT: B 150 LEU cc_start: 0.8595 (tp) cc_final: 0.8337 (tp) REVERT: B 224 MET cc_start: 0.8222 (mtp) cc_final: 0.7602 (mmm) REVERT: B 227 ASN cc_start: 0.7604 (t0) cc_final: 0.7382 (t0) REVERT: B 321 LEU cc_start: 0.9272 (mt) cc_final: 0.8967 (mt) REVERT: B 365 MET cc_start: -0.2997 (tpt) cc_final: -0.4680 (tpt) REVERT: B 579 MET cc_start: 0.2077 (mmm) cc_final: 0.1789 (mmm) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2019 time to fit residues: 54.2028 Evaluate side-chains 165 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 chunk 86 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4782 moved from start: 0.7272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9232 Z= 0.259 Angle : 0.661 7.457 12422 Z= 0.357 Chirality : 0.045 0.222 1358 Planarity : 0.004 0.034 1520 Dihedral : 4.968 18.990 1174 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1066 helix: 1.21 (0.22), residues: 588 sheet: 0.19 (0.52), residues: 110 loop : -1.64 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 99 HIS 0.007 0.001 HIS B 205 PHE 0.022 0.002 PHE A 121 TYR 0.020 0.002 TYR B 441 ARG 0.005 0.001 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5888 (mmm) cc_final: 0.5330 (mmt) REVERT: A 15 ILE cc_start: 0.9244 (mm) cc_final: 0.8965 (mm) REVERT: A 143 LYS cc_start: 0.8961 (tttt) cc_final: 0.8564 (tptt) REVERT: A 227 ASN cc_start: 0.7329 (t0) cc_final: 0.7091 (t0) REVERT: A 265 ILE cc_start: 0.8967 (mm) cc_final: 0.8744 (mm) REVERT: A 365 MET cc_start: -0.3613 (tpt) cc_final: -0.4208 (tpt) REVERT: A 373 TYR cc_start: 0.3087 (m-80) cc_final: 0.2843 (m-80) REVERT: B 9 ILE cc_start: 0.8843 (mt) cc_final: 0.8061 (mt) REVERT: B 12 PHE cc_start: 0.8213 (t80) cc_final: 0.7984 (t80) REVERT: B 143 LYS cc_start: 0.8889 (tttt) cc_final: 0.8455 (tttp) REVERT: B 224 MET cc_start: 0.7912 (mtp) cc_final: 0.7195 (tpp) REVERT: B 227 ASN cc_start: 0.7770 (t0) cc_final: 0.7481 (t0) REVERT: B 319 PHE cc_start: 0.7947 (t80) cc_final: 0.7715 (t80) REVERT: B 321 LEU cc_start: 0.9289 (mt) cc_final: 0.9000 (mt) REVERT: B 365 MET cc_start: -0.2949 (tpt) cc_final: -0.4490 (tpt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2064 time to fit residues: 49.9388 Evaluate side-chains 153 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 105 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4717 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9232 Z= 0.190 Angle : 0.614 7.550 12422 Z= 0.327 Chirality : 0.043 0.200 1358 Planarity : 0.003 0.035 1520 Dihedral : 4.807 19.303 1174 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1066 helix: 1.39 (0.22), residues: 586 sheet: 0.19 (0.51), residues: 110 loop : -1.64 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 99 HIS 0.003 0.001 HIS A 205 PHE 0.021 0.002 PHE B 491 TYR 0.018 0.001 TYR B 441 ARG 0.003 0.000 ARG B 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5689 (mmm) cc_final: 0.5136 (mmt) REVERT: A 123 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7045 (ptmm) REVERT: A 143 LYS cc_start: 0.9013 (tttt) cc_final: 0.8658 (tptt) REVERT: A 217 PHE cc_start: 0.8974 (t80) cc_final: 0.8367 (t80) REVERT: A 224 MET cc_start: 0.8359 (mtp) cc_final: 0.7377 (tpp) REVERT: A 233 VAL cc_start: 0.8251 (t) cc_final: 0.7897 (p) REVERT: A 265 ILE cc_start: 0.8934 (mm) cc_final: 0.8720 (mm) REVERT: A 321 LEU cc_start: 0.9359 (mt) cc_final: 0.9092 (mt) REVERT: A 373 TYR cc_start: 0.2921 (m-80) cc_final: 0.2616 (m-80) REVERT: B 9 ILE cc_start: 0.8803 (mt) cc_final: 0.8079 (mt) REVERT: B 123 LYS cc_start: 0.7392 (ttpt) cc_final: 0.6903 (ptmm) REVERT: B 143 LYS cc_start: 0.8983 (tttt) cc_final: 0.8682 (tttp) REVERT: B 224 MET cc_start: 0.8220 (mtp) cc_final: 0.7274 (tpp) REVERT: B 227 ASN cc_start: 0.7641 (t0) cc_final: 0.7413 (t0) REVERT: B 321 LEU cc_start: 0.9274 (mt) cc_final: 0.8998 (mt) REVERT: B 365 MET cc_start: -0.2972 (tpt) cc_final: -0.4529 (tpt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1862 time to fit residues: 46.9837 Evaluate side-chains 158 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.204151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.138152 restraints weight = 22151.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143040 restraints weight = 13379.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.146173 restraints weight = 9275.710| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9232 Z= 0.170 Angle : 0.614 12.343 12422 Z= 0.321 Chirality : 0.043 0.179 1358 Planarity : 0.003 0.035 1520 Dihedral : 4.639 18.193 1174 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1066 helix: 1.52 (0.22), residues: 586 sheet: 0.22 (0.52), residues: 110 loop : -1.61 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 99 HIS 0.004 0.001 HIS A 201 PHE 0.019 0.001 PHE B 491 TYR 0.018 0.001 TYR B 441 ARG 0.003 0.000 ARG A 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.59 seconds wall clock time: 36 minutes 25.21 seconds (2185.21 seconds total)