Starting phenix.real_space_refine on Sat Apr 13 01:34:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4h_31711/04_2024/7v4h_31711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4h_31711/04_2024/7v4h_31711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4h_31711/04_2024/7v4h_31711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4h_31711/04_2024/7v4h_31711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4h_31711/04_2024/7v4h_31711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4h_31711/04_2024/7v4h_31711.pdb" } resolution = 2.9 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= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 17300 2.51 5 N 4750 2.21 5 O 5210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ASP 14": "OD1" <-> "OD2" Residue "J TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F GLU 199": "OE1" <-> "OE2" Residue "F TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "H PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 339": "OD1" <-> "OD2" Residue "I ASP 67": "OD1" <-> "OD2" Residue "I GLU 199": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27340 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "F" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "G" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "H" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Chain: "I" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2734 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 22, 'TRANS': 329} Time building chain proxies: 14.04, per 1000 atoms: 0.51 Number of scatterers: 27340 At special positions: 0 Unit cell: (134.33, 136.35, 107.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 5210 8.00 N 4750 7.00 C 17300 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: 9.48 Conformation dependent library (CDL) restraints added in 5.1 seconds 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 26 sheets defined 32.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.529A pdb=" N LEU J 50 " --> pdb=" O PRO J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 removed outlier: 3.591A pdb=" N ALA J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 123 Processing helix chain 'J' and resid 168 through 183 removed outlier: 3.567A pdb=" N VAL J 172 " --> pdb=" O GLY J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 229 removed outlier: 3.902A pdb=" N TYR J 219 " --> pdb=" O TRP J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 276 through 284 Processing helix chain 'J' and resid 294 through 298 removed outlier: 3.579A pdb=" N GLU J 297 " --> pdb=" O GLY J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 324 Processing helix chain 'J' and resid 339 through 349 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.698A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.682A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 229 removed outlier: 3.640A pdb=" N TYR A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.535A pdb=" N GLU A 297 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.661A pdb=" N ALA B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.773A pdb=" N GLU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.545A pdb=" N VAL B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 229 removed outlier: 3.632A pdb=" N TYR B 219 " --> pdb=" O TRP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 274 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 294 through 298 removed outlier: 3.508A pdb=" N GLU B 297 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 106 through 115 removed outlier: 3.747A pdb=" N ALA C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.711A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 229 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 262 through 274 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 339 through 353 removed outlier: 3.688A pdb=" N THR C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 353 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.691A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 123 removed outlier: 3.772A pdb=" N GLU D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.544A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.317A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR D 219 " --> pdb=" O TRP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 removed outlier: 3.600A pdb=" N ASN D 259 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 Processing helix chain 'D' and resid 276 through 284 Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.600A pdb=" N GLU D 297 " --> pdb=" O GLY D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 removed outlier: 3.565A pdb=" N GLU D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 11 through 15 removed outlier: 3.941A pdb=" N ASP E 14 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.673A pdb=" N LEU E 50 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 116 through 123 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.508A pdb=" N VAL E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 229 removed outlier: 4.138A pdb=" N GLY E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE E 227 " --> pdb=" O ARG E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 removed outlier: 4.082A pdb=" N VAL E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 284 Processing helix chain 'E' and resid 318 through 325 Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'F' and resid 11 through 15 removed outlier: 3.889A pdb=" N ASP F 14 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 removed outlier: 3.634A pdb=" N LEU F 50 " --> pdb=" O PRO F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 207 through 229 removed outlier: 4.177A pdb=" N GLY F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP F 215 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 261 through 274 removed outlier: 4.137A pdb=" N VAL F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 283 Processing helix chain 'F' and resid 287 through 292 removed outlier: 3.525A pdb=" N ARG F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'G' and resid 11 through 15 removed outlier: 3.896A pdb=" N ASP G 14 " --> pdb=" O ASN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 removed outlier: 3.569A pdb=" N LEU G 50 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 Processing helix chain 'G' and resid 116 through 123 Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 207 through 229 removed outlier: 4.134A pdb=" N GLY G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 261 through 274 removed outlier: 4.127A pdb=" N VAL G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 283 Processing helix chain 'G' and resid 287 through 292 removed outlier: 3.639A pdb=" N ARG G 291 " --> pdb=" O GLY G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 325 Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'H' and resid 11 through 15 removed outlier: 3.887A pdb=" N ASP H 14 " --> pdb=" O ASN H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.688A pdb=" N LEU H 50 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 115 Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.532A pdb=" N VAL H 172 " --> pdb=" O GLY H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 229 removed outlier: 4.082A pdb=" N GLY H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE H 227 " --> pdb=" O ARG H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 274 removed outlier: 3.991A pdb=" N VAL H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 284 Processing helix chain 'H' and resid 318 through 325 removed outlier: 3.658A pdb=" N GLU H 322 " --> pdb=" O GLY H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 352 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.664A pdb=" N LEU I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 115 Processing helix chain 'I' and resid 116 through 123 Processing helix chain 'I' and resid 168 through 183 removed outlier: 3.526A pdb=" N VAL I 172 " --> pdb=" O GLY I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 229 removed outlier: 4.134A pdb=" N GLY I 211 " --> pdb=" O GLY I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 259 Processing helix chain 'I' and resid 262 through 274 removed outlier: 3.888A pdb=" N ILE I 266 " --> pdb=" O GLY I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 283 Processing helix chain 'I' and resid 287 through 292 removed outlier: 3.641A pdb=" N ARG I 291 " --> pdb=" O GLY I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 325 Processing helix chain 'I' and resid 339 through 352 Processing sheet with id=AA1, first strand: chain 'J' and resid 33 through 40 removed outlier: 6.445A pdb=" N ILE J 20 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL J 90 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU J 22 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS J 92 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE J 24 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR J 94 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ILE J 26 " --> pdb=" O THR J 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU J 89 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE J 77 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE J 91 " --> pdb=" O GLN J 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP J 53 " --> pdb=" O ILE J 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 186 through 191 removed outlier: 5.684A pdb=" N GLN J 201 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU J 199 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN J 197 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR J 126 " --> pdb=" O PRO J 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 186 through 191 removed outlier: 5.684A pdb=" N GLN J 201 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU J 199 " --> pdb=" O ILE J 189 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLY J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN J 197 " --> pdb=" O GLY J 191 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR J 126 " --> pdb=" O PRO J 204 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 307 " --> pdb=" O VAL J 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.543A pdb=" N ILE A 20 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 90 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU A 22 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N CYS A 92 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 24 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 94 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE A 26 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 89 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 77 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 91 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 5.919A pdb=" N GLN A 201 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 189 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU A 199 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY A 191 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 197 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR A 126 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 206 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 124 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 186 through 191 removed outlier: 5.919A pdb=" N GLN A 201 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 189 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU A 199 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY A 191 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 197 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR A 126 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 206 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 124 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 307 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 40 removed outlier: 6.458A pdb=" N ILE B 20 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 90 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS B 92 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 24 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR B 94 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N ILE B 26 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 89 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE B 77 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 91 " --> pdb=" O GLN B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 186 through 191 removed outlier: 5.800A pdb=" N GLN B 201 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE B 189 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU B 199 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY B 191 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN B 197 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 126 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 191 removed outlier: 5.800A pdb=" N GLN B 201 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE B 189 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU B 199 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY B 191 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN B 197 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 126 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 307 " --> pdb=" O VAL B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 40 removed outlier: 6.456A pdb=" N ILE C 20 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL C 90 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU C 22 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N CYS C 92 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 24 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR C 94 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ILE C 26 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 89 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 77 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 91 " --> pdb=" O GLN C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 191 removed outlier: 5.688A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 126 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 191 removed outlier: 5.688A pdb=" N GLN C 201 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 189 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 199 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY C 191 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLN C 197 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 126 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 307 " --> pdb=" O VAL C 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 40 removed outlier: 6.497A pdb=" N ILE D 20 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL D 90 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU D 22 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS D 92 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE D 24 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR D 94 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ILE D 26 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 89 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE D 77 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE D 91 " --> pdb=" O GLN D 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 186 through 191 removed outlier: 5.865A pdb=" N GLN D 201 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN D 197 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 186 through 191 removed outlier: 5.865A pdb=" N GLN D 201 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU D 199 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN D 197 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 33 through 40 removed outlier: 6.333A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE E 26 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 89 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE E 77 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE E 91 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 230 through 233 Processing sheet with id=AB9, first strand: chain 'E' and resid 230 through 233 removed outlier: 6.391A pdb=" N TYR E 126 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN E 197 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY E 191 " --> pdb=" O GLN E 197 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU E 199 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE E 189 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN E 201 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 187 " --> pdb=" O THR G 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR G 39 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLY E 191 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER G 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE G 20 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL G 90 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU G 22 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS G 92 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE G 24 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR G 94 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE G 26 " --> pdb=" O THR G 94 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU G 89 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE G 77 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE G 91 " --> pdb=" O GLN G 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.526A pdb=" N ILE F 91 " --> pdb=" O GLN F 75 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE F 77 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 89 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE F 20 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL F 90 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU F 22 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS F 92 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 24 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR F 94 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE F 26 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER F 35 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY G 191 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY G 188 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR G 126 " --> pdb=" O PRO G 204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.526A pdb=" N ILE F 91 " --> pdb=" O GLN F 75 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE F 77 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 89 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE F 20 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL F 90 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU F 22 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS F 92 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 24 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR F 94 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE F 26 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER F 35 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY G 191 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY G 188 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR G 126 " --> pdb=" O PRO G 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 230 through 233 Processing sheet with id=AC4, first strand: chain 'F' and resid 230 through 233 removed outlier: 6.288A pdb=" N TYR F 126 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY F 188 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY F 191 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N SER H 35 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE H 20 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL H 90 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU H 22 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS H 92 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE H 24 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR H 94 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ILE H 26 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU H 89 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE H 77 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE H 91 " --> pdb=" O GLN H 75 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 231 through 233 Processing sheet with id=AC6, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.277A pdb=" N TYR H 126 " --> pdb=" O PRO H 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY H 188 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLY H 191 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N SER I 35 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE I 20 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL I 90 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU I 22 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS I 92 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE I 24 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR I 94 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ILE I 26 " --> pdb=" O THR I 94 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU I 89 " --> pdb=" O ILE I 77 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE I 77 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE I 91 " --> pdb=" O GLN I 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 186 through 191 removed outlier: 5.922A pdb=" N GLN I 201 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU I 199 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLN I 197 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR I 126 " --> pdb=" O PRO I 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 186 through 191 removed outlier: 5.922A pdb=" N GLN I 201 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU I 199 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLN I 197 " --> pdb=" O GLY I 191 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR I 126 " --> pdb=" O PRO I 204 " (cutoff:3.500A) 1180 hydrogen bonds defined for protein. 3303 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: 9.57 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9053 1.34 - 1.45: 4195 1.45 - 1.57: 14692 1.57 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 28070 Sorted by residual: bond pdb=" CB TRP J 53 " pdb=" CG TRP J 53 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.54e+00 bond pdb=" C GLY D 99 " pdb=" N GLU D 100 " ideal model delta sigma weight residual 1.331 1.295 0.036 2.07e-02 2.33e+03 2.97e+00 bond pdb=" CB TRP I 53 " pdb=" CG TRP I 53 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.58e+00 bond pdb=" CB GLU E 199 " pdb=" CG GLU E 199 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB TRP F 53 " pdb=" CG TRP F 53 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.34e+00 ... (remaining 28065 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.91: 1080 106.91 - 113.71: 14947 113.71 - 120.50: 10647 120.50 - 127.30: 11031 127.30 - 134.10: 475 Bond angle restraints: 38180 Sorted by residual: angle pdb=" CA TRP D 53 " pdb=" CB TRP D 53 " pdb=" CG TRP D 53 " ideal model delta sigma weight residual 113.60 120.31 -6.71 1.90e+00 2.77e-01 1.25e+01 angle pdb=" CA TRP C 53 " pdb=" CB TRP C 53 " pdb=" CG TRP C 53 " ideal model delta sigma weight residual 113.60 120.30 -6.70 1.90e+00 2.77e-01 1.24e+01 angle pdb=" N GLY E 188 " pdb=" CA GLY E 188 " pdb=" C GLY E 188 " ideal model delta sigma weight residual 110.96 114.97 -4.01 1.19e+00 7.06e-01 1.13e+01 angle pdb=" N TRP H 53 " pdb=" CA TRP H 53 " pdb=" C TRP H 53 " ideal model delta sigma weight residual 109.18 113.84 -4.66 1.42e+00 4.96e-01 1.08e+01 angle pdb=" N TRP I 53 " pdb=" CA TRP I 53 " pdb=" C TRP I 53 " ideal model delta sigma weight residual 109.18 113.74 -4.56 1.42e+00 4.96e-01 1.03e+01 ... (remaining 38175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14934 17.48 - 34.97: 1213 34.97 - 52.45: 238 52.45 - 69.93: 37 69.93 - 87.42: 28 Dihedral angle restraints: 16450 sinusoidal: 6540 harmonic: 9910 Sorted by residual: dihedral pdb=" CA MET C 338 " pdb=" C MET C 338 " pdb=" N ASP C 339 " pdb=" CA ASP C 339 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA MET J 338 " pdb=" C MET J 338 " pdb=" N ASP J 339 " pdb=" CA ASP J 339 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU E 199 " pdb=" C GLU E 199 " pdb=" N PHE E 200 " pdb=" CA PHE E 200 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 16447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2347 0.034 - 0.067: 1109 0.067 - 0.101: 327 0.101 - 0.135: 190 0.135 - 0.169: 17 Chirality restraints: 3990 Sorted by residual: chirality pdb=" CA ILE H 139 " pdb=" N ILE H 139 " pdb=" C ILE H 139 " pdb=" CB ILE H 139 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA TRP I 53 " pdb=" N TRP I 53 " pdb=" C TRP I 53 " pdb=" CB TRP I 53 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA VAL B 230 " pdb=" N VAL B 230 " pdb=" C VAL B 230 " pdb=" CB VAL B 230 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 3987 not shown) Planarity restraints: 5030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 53 " -0.043 2.00e-02 2.50e+03 2.99e-02 2.23e+01 pdb=" CG TRP D 53 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP D 53 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 53 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 53 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 53 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 53 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 53 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 53 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 53 " -0.033 2.00e-02 2.50e+03 1.84e-02 8.47e+00 pdb=" CG TRP I 53 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP I 53 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP I 53 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 53 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP I 53 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 53 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 53 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP I 53 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 53 " 0.031 2.00e-02 2.50e+03 1.74e-02 7.58e+00 pdb=" CG TRP H 53 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP H 53 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 53 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 53 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 53 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 53 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 53 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 53 " 0.002 2.00e-02 2.50e+03 ... (remaining 5027 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 291 2.65 - 3.21: 24342 3.21 - 3.77: 41309 3.77 - 4.34: 60277 4.34 - 4.90: 100624 Nonbonded interactions: 226843 Sorted by model distance: nonbonded pdb=" ND2 ASN A 190 " pdb=" OE2 GLU A 199 " model vdw 2.083 2.520 nonbonded pdb=" OD2 ASP C 46 " pdb=" OG SER C 48 " model vdw 2.149 2.440 nonbonded pdb=" NH2 ARG E 84 " pdb=" O ASP G 6 " model vdw 2.168 2.520 nonbonded pdb=" O GLY H 318 " pdb=" OG1 THR H 321 " model vdw 2.169 2.440 nonbonded pdb=" O THR I 293 " pdb=" OG1 THR I 298 " model vdw 2.170 2.440 ... (remaining 226838 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic 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: 8.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 27.580 Check model and map are aligned: 0.400 Set scattering table: 0.280 Process input model: 71.080 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.004 0.058 28070 Z= 0.251 Angle : 0.589 8.080 38180 Z= 0.316 Chirality : 0.046 0.169 3990 Planarity : 0.005 0.063 5030 Dihedral : 13.651 87.417 10210 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.11 (0.14), residues: 3500 helix: -0.42 (0.15), residues: 1110 sheet: -0.56 (0.19), residues: 790 loop : -0.92 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP D 53 HIS 0.003 0.001 HIS E 280 PHE 0.016 0.001 PHE G 200 TYR 0.024 0.002 TYR A 176 ARG 0.006 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.387 Fit side-chains REVERT: D 56 ASP cc_start: 0.7882 (t70) cc_final: 0.7617 (t70) REVERT: I 199 GLU cc_start: 0.7787 (tt0) cc_final: 0.7511 (tt0) outliers start: 0 outliers final: 1 residues processed: 268 average time/residue: 1.3734 time to fit residues: 431.9857 Evaluate side-chains 193 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 0.5980 chunk 265 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 274 optimal weight: 0.0970 chunk 106 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 30.0000 chunk 317 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 GLN ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN H 136 GLN I 9 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28070 Z= 0.254 Angle : 0.570 8.571 38180 Z= 0.298 Chirality : 0.046 0.155 3990 Planarity : 0.005 0.063 5030 Dihedral : 4.660 29.123 3863 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.73 % Allowed : 6.76 % Favored : 91.51 % 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: -0.62 (0.14), residues: 3500 helix: 0.51 (0.15), residues: 1130 sheet: -0.48 (0.19), residues: 790 loop : -0.97 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP D 53 HIS 0.003 0.001 HIS E 280 PHE 0.018 0.001 PHE G 200 TYR 0.022 0.002 TYR A 176 ARG 0.005 0.000 ARG H 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 209 time to evaluate : 3.050 Fit side-chains REVERT: J 53 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.7179 (m-10) REVERT: J 136 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: B 136 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: D 56 ASP cc_start: 0.7896 (t70) cc_final: 0.7641 (t70) REVERT: H 140 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7684 (mm110) REVERT: I 140 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7700 (mp10) outliers start: 49 outliers final: 26 residues processed: 235 average time/residue: 1.3214 time to fit residues: 367.2510 Evaluate side-chains 216 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 318 optimal weight: 7.9990 chunk 343 optimal weight: 30.0000 chunk 283 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 108 optimal weight: 0.2980 chunk 255 optimal weight: 9.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN E 280 HIS F 9 ASN F 140 GLN G 9 ASN G 108 HIS G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 28070 Z= 0.428 Angle : 0.646 9.590 38180 Z= 0.336 Chirality : 0.049 0.161 3990 Planarity : 0.005 0.067 5030 Dihedral : 4.986 26.306 3860 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.22 % Allowed : 9.79 % Favored : 87.99 % 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: -0.82 (0.14), residues: 3500 helix: 0.38 (0.15), residues: 1130 sheet: -0.60 (0.19), residues: 790 loop : -1.12 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 53 HIS 0.006 0.001 HIS E 280 PHE 0.020 0.002 PHE B 200 TYR 0.035 0.002 TYR A 176 ARG 0.004 0.000 ARG H 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 196 time to evaluate : 3.101 Fit side-chains REVERT: B 136 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: H 140 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7735 (mm110) REVERT: I 84 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7279 (mpt-90) outliers start: 63 outliers final: 46 residues processed: 234 average time/residue: 1.3718 time to fit residues: 378.2178 Evaluate side-chains 238 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 190 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 141 TRP Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 319 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 302 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28070 Z= 0.251 Angle : 0.551 8.965 38180 Z= 0.287 Chirality : 0.046 0.159 3990 Planarity : 0.005 0.065 5030 Dihedral : 4.634 23.523 3860 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.54 % Allowed : 11.94 % Favored : 85.53 % 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: -0.63 (0.14), residues: 3500 helix: 0.64 (0.15), residues: 1130 sheet: -0.64 (0.18), residues: 800 loop : -0.99 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 53 HIS 0.003 0.001 HIS H 280 PHE 0.015 0.001 PHE G 200 TYR 0.023 0.001 TYR A 176 ARG 0.003 0.000 ARG I 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 204 time to evaluate : 3.171 Fit side-chains REVERT: J 136 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: B 136 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: C 136 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: D 136 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: E 84 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7201 (mpt-90) REVERT: E 271 GLU cc_start: 0.4841 (OUTLIER) cc_final: 0.4228 (mp0) REVERT: H 84 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7083 (mpt-90) REVERT: H 140 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7700 (mm110) REVERT: I 84 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7022 (mpt180) REVERT: I 140 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7548 (mm110) outliers start: 72 outliers final: 45 residues processed: 256 average time/residue: 1.3535 time to fit residues: 407.5416 Evaluate side-chains 250 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 251 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 303 optimal weight: 7.9990 chunk 85 optimal weight: 0.0970 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28070 Z= 0.286 Angle : 0.569 9.177 38180 Z= 0.296 Chirality : 0.046 0.156 3990 Planarity : 0.005 0.065 5030 Dihedral : 4.670 23.303 3860 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.13 % Allowed : 12.75 % Favored : 84.12 % 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: -0.61 (0.14), residues: 3500 helix: 0.66 (0.15), residues: 1130 sheet: -0.62 (0.18), residues: 800 loop : -1.00 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 53 HIS 0.003 0.001 HIS G 249 PHE 0.017 0.002 PHE G 200 TYR 0.027 0.002 TYR A 176 ARG 0.003 0.000 ARG H 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 198 time to evaluate : 3.335 Fit side-chains REVERT: J 136 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: B 136 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: C 136 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: D 136 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: E 84 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7231 (mpt-90) REVERT: E 271 GLU cc_start: 0.4982 (OUTLIER) cc_final: 0.4268 (mp0) REVERT: H 84 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7135 (mpt-90) REVERT: I 84 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7151 (mpt180) REVERT: I 140 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7544 (mm110) outliers start: 89 outliers final: 59 residues processed: 261 average time/residue: 1.3363 time to fit residues: 411.0952 Evaluate side-chains 260 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 193 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 141 TRP Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 141 TRP Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 3.9990 chunk 304 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 198 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 338 optimal weight: 0.6980 chunk 281 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN G 244 ASN H 9 ASN I 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28070 Z= 0.300 Angle : 0.576 9.236 38180 Z= 0.299 Chirality : 0.047 0.158 3990 Planarity : 0.005 0.066 5030 Dihedral : 4.705 23.439 3860 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.56 % Allowed : 13.10 % Favored : 83.35 % 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: -0.60 (0.14), residues: 3500 helix: 0.68 (0.15), residues: 1130 sheet: -0.63 (0.18), residues: 800 loop : -1.00 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 53 HIS 0.003 0.001 HIS G 249 PHE 0.017 0.002 PHE B 200 TYR 0.027 0.002 TYR A 176 ARG 0.003 0.000 ARG H 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 197 time to evaluate : 2.979 Fit side-chains REVERT: J 136 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: B 136 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: C 136 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: D 136 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: E 84 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7337 (mpt-90) REVERT: E 271 GLU cc_start: 0.5028 (OUTLIER) cc_final: 0.4215 (mp0) REVERT: H 84 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7443 (mpt-90) REVERT: H 140 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7644 (mm110) REVERT: I 84 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7290 (mpt-90) REVERT: I 140 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7587 (mm110) outliers start: 101 outliers final: 71 residues processed: 269 average time/residue: 1.3304 time to fit residues: 423.8033 Evaluate side-chains 270 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 191 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 141 TRP Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 280 HIS Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 141 TRP Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 285 optimal weight: 4.9990 chunk 189 optimal weight: 0.4980 chunk 337 optimal weight: 0.5980 chunk 211 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 ASN E 140 GLN F 9 ASN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28070 Z= 0.137 Angle : 0.488 7.960 38180 Z= 0.254 Chirality : 0.044 0.152 3990 Planarity : 0.004 0.060 5030 Dihedral : 4.214 22.104 3860 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.32 % Allowed : 14.89 % Favored : 82.78 % 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: -0.31 (0.14), residues: 3500 helix: 1.00 (0.16), residues: 1130 sheet: -0.49 (0.17), residues: 860 loop : -0.88 (0.17), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 53 HIS 0.003 0.000 HIS H 280 PHE 0.014 0.001 PHE G 200 TYR 0.016 0.001 TYR F 95 ARG 0.004 0.000 ARG H 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 223 time to evaluate : 3.103 Fit side-chains REVERT: B 136 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8545 (mp10) REVERT: E 271 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.4163 (mp0) REVERT: H 9 ASN cc_start: 0.7952 (m-40) cc_final: 0.7749 (m110) REVERT: H 84 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.6685 (mpt-90) REVERT: H 140 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7633 (mm110) outliers start: 66 outliers final: 38 residues processed: 271 average time/residue: 1.2256 time to fit residues: 397.2069 Evaluate side-chains 251 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 214 optimal weight: 0.2980 chunk 229 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 265 optimal weight: 9.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN F 140 GLN G 9 ASN G 140 GLN I 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28070 Z= 0.405 Angle : 0.630 9.570 38180 Z= 0.326 Chirality : 0.048 0.165 3990 Planarity : 0.005 0.066 5030 Dihedral : 4.830 26.011 3860 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.35 % Allowed : 14.93 % Favored : 81.73 % 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: -0.55 (0.14), residues: 3500 helix: 0.72 (0.15), residues: 1120 sheet: -0.56 (0.18), residues: 790 loop : -0.97 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 53 HIS 0.004 0.001 HIS H 280 PHE 0.021 0.002 PHE B 200 TYR 0.033 0.002 TYR A 176 ARG 0.007 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 204 time to evaluate : 3.184 Fit side-chains REVERT: J 136 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: B 136 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8208 (mt0) REVERT: E 84 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7054 (mpt-90) REVERT: E 271 GLU cc_start: 0.5063 (OUTLIER) cc_final: 0.4178 (mp0) REVERT: H 140 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7707 (mm110) REVERT: I 84 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6813 (mpt180) outliers start: 95 outliers final: 66 residues processed: 274 average time/residue: 1.2196 time to fit residues: 399.5824 Evaluate side-chains 271 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 200 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 141 TRP Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 112 LYS Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 233 SER Chi-restraints excluded: chain H residue 280 HIS Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 141 TRP Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 7.9990 chunk 323 optimal weight: 1.9990 chunk 294 optimal weight: 0.0470 chunk 314 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 136 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 284 optimal weight: 0.0870 chunk 297 optimal weight: 0.6980 chunk 313 optimal weight: 4.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 ASN F 9 ASN F 140 GLN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28070 Z= 0.140 Angle : 0.495 8.043 38180 Z= 0.257 Chirality : 0.044 0.152 3990 Planarity : 0.005 0.061 5030 Dihedral : 4.272 21.697 3860 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.46 % Allowed : 15.92 % Favored : 81.62 % 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 (0.14), residues: 3500 helix: 0.99 (0.16), residues: 1130 sheet: -0.52 (0.17), residues: 870 loop : -0.87 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 53 HIS 0.011 0.000 HIS H 280 PHE 0.014 0.001 PHE G 200 TYR 0.016 0.001 TYR F 95 ARG 0.004 0.000 ARG H 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 207 time to evaluate : 3.402 Fit side-chains REVERT: C 305 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6039 (tp) REVERT: D 305 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6075 (tp) REVERT: E 84 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.6968 (mpt-90) REVERT: E 271 GLU cc_start: 0.5032 (OUTLIER) cc_final: 0.4129 (mp0) REVERT: H 84 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.6959 (mpt-90) REVERT: H 140 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7652 (mm110) REVERT: I 140 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7518 (mp10) outliers start: 70 outliers final: 52 residues processed: 259 average time/residue: 1.2370 time to fit residues: 383.4131 Evaluate side-chains 261 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 204 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 280 HIS Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 141 TRP Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 202 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 348 optimal weight: 6.9990 chunk 320 optimal weight: 0.9980 chunk 277 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 140 GLN F 9 ASN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28070 Z= 0.341 Angle : 0.596 9.365 38180 Z= 0.308 Chirality : 0.047 0.156 3990 Planarity : 0.005 0.064 5030 Dihedral : 4.678 24.127 3860 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.46 % Allowed : 16.09 % Favored : 81.44 % 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: -0.47 (0.14), residues: 3500 helix: 0.76 (0.15), residues: 1130 sheet: -0.56 (0.18), residues: 790 loop : -0.89 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 53 HIS 0.005 0.001 HIS H 280 PHE 0.019 0.002 PHE B 200 TYR 0.028 0.002 TYR A 176 ARG 0.004 0.000 ARG E 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 201 time to evaluate : 3.052 Fit side-chains REVERT: J 136 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: D 305 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6068 (tp) REVERT: E 84 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7130 (mpt180) REVERT: E 271 GLU cc_start: 0.5040 (OUTLIER) cc_final: 0.4128 (mp0) REVERT: H 84 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7345 (mpt-90) REVERT: H 140 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7680 (mm110) REVERT: I 84 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.6895 (mpt180) REVERT: I 140 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7621 (mp10) outliers start: 70 outliers final: 54 residues processed: 256 average time/residue: 1.2741 time to fit residues: 387.8065 Evaluate side-chains 258 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 198 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 TRP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 345 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 53 TRP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 GLU Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 141 TRP Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 280 HIS Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 141 TRP Chi-restraints excluded: chain I residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 256 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 278 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 285 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN E 9 ASN E 140 GLN F 9 ASN G 9 ASN G 140 GLN H 9 ASN I 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.184954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126247 restraints weight = 29865.132| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.19 r_work: 0.3263 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28070 Z= 0.148 Angle : 0.500 8.082 38180 Z= 0.259 Chirality : 0.044 0.150 3990 Planarity : 0.004 0.062 5030 Dihedral : 4.267 23.630 3860 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.32 % Allowed : 16.09 % Favored : 81.58 % 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: -0.27 (0.14), residues: 3500 helix: 1.03 (0.16), residues: 1130 sheet: -0.52 (0.17), residues: 860 loop : -0.81 (0.17), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 53 HIS 0.008 0.000 HIS H 280 PHE 0.014 0.001 PHE G 200 TYR 0.016 0.001 TYR F 95 ARG 0.004 0.000 ARG H 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8179.72 seconds wall clock time: 152 minutes 13.00 seconds (9133.00 seconds total)