Starting phenix.real_space_refine on Wed Apr 10 16:13:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/04_2024/8q3n_18130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/04_2024/8q3n_18130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/04_2024/8q3n_18130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/04_2024/8q3n_18130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/04_2024/8q3n_18130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3n_18130/04_2024/8q3n_18130_updated.pdb" } resolution = 2.63 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= 0.006 sd= 0.053 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 102 5.16 5 C 12486 2.51 5 N 3540 2.21 5 O 3768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19912 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "F" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.58, per 1000 atoms: 0.53 Number of scatterers: 19912 At special positions: 0 Unit cell: (116.48, 134.784, 144.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 12 15.00 Mg 4 11.99 O 3768 8.00 N 3540 7.00 C 12486 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.46 Conformation dependent library (CDL) restraints added in 3.5 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 13 sheets defined 43.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 11 through 21 Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 154 through 165 removed outlier: 4.041A pdb=" N THR A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 236 through 256 removed outlier: 3.656A pdb=" N HIS A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 292 through 303 removed outlier: 3.859A pdb=" N ARG A 296 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.792A pdb=" N GLY A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 303 " --> pdb=" O PHE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.796A pdb=" N ARG B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 129' Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 236 through 256 removed outlier: 3.693A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.214A pdb=" N ARG B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.516A pdb=" N ALA B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 368 through 371 No H-bonds generated for 'chain 'B' and resid 368 through 371' Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 392 through 404 Processing helix chain 'B' and resid 409 through 416 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 11 through 21 Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.714A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.584A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 129' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 154 through 165 Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 236 through 256 removed outlier: 3.725A pdb=" N HIS C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 291 through 303 removed outlier: 4.228A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Proline residue: C 297 - end of helix removed outlier: 3.547A pdb=" N ALA C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 368 through 371 No H-bonds generated for 'chain 'C' and resid 368 through 371' Processing helix chain 'C' and resid 374 through 388 Processing helix chain 'C' and resid 392 through 405 removed outlier: 3.985A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 Processing helix chain 'D' and resid 3 through 6 No H-bonds generated for 'chain 'D' and resid 3 through 6' Processing helix chain 'D' and resid 11 through 21 Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.677A pdb=" N ARG D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 129' Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 155 through 165 removed outlier: 4.171A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 198 Processing helix chain 'D' and resid 213 through 222 Processing helix chain 'D' and resid 236 through 256 removed outlier: 3.733A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 291 through 303 removed outlier: 4.160A pdb=" N ARG D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Proline residue: D 297 - end of helix Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 368 through 371 No H-bonds generated for 'chain 'D' and resid 368 through 371' Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 392 through 405 removed outlier: 3.870A pdb=" N MET D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 416 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 11 through 21 Processing helix chain 'E' and resid 31 through 43 Processing helix chain 'E' and resid 83 through 88 Processing helix chain 'E' and resid 124 through 127 No H-bonds generated for 'chain 'E' and resid 124 through 127' Processing helix chain 'E' and resid 154 through 165 Processing helix chain 'E' and resid 184 through 198 Processing helix chain 'E' and resid 213 through 222 Processing helix chain 'E' and resid 236 through 256 removed outlier: 3.695A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 277 Processing helix chain 'E' and resid 291 through 303 removed outlier: 4.105A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix removed outlier: 3.558A pdb=" N ALA E 303 " --> pdb=" O ARG E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 347 through 351 Processing helix chain 'E' and resid 368 through 370 No H-bonds generated for 'chain 'E' and resid 368 through 370' Processing helix chain 'E' and resid 374 through 388 Processing helix chain 'E' and resid 392 through 404 Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 32 through 45 removed outlier: 3.950A pdb=" N SER F 45 " --> pdb=" O GLN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 154 through 165 removed outlier: 4.168A pdb=" N LEU F 162 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 198 Processing helix chain 'F' and resid 213 through 222 Processing helix chain 'F' and resid 236 through 255 Processing helix chain 'F' and resid 267 through 277 Processing helix chain 'F' and resid 291 through 301 removed outlier: 3.771A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 327 through 334 Processing helix chain 'F' and resid 347 through 350 No H-bonds generated for 'chain 'F' and resid 347 through 350' Processing helix chain 'F' and resid 374 through 389 Proline residue: F 389 - end of helix Processing helix chain 'F' and resid 392 through 405 Processing helix chain 'F' and resid 409 through 417 Processing sheet with id= A, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.733A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE A 49 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 341 through 344 removed outlier: 7.832A pdb=" N GLY A 174 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 315 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 176 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA A 317 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA A 178 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA A 319 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 203 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 263 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N MET A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU A 226 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU A 208 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 228 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ASP A 210 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER A 230 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 79 through 81 removed outlier: 3.855A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS B 100 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL B 116 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 341 through 344 removed outlier: 7.893A pdb=" N GLY B 174 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE B 315 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE B 176 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 317 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA B 178 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA B 319 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 318 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU B 226 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU B 208 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 228 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASP B 210 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N SER B 230 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.844A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS C 100 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL C 116 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 341 through 344 removed outlier: 7.809A pdb=" N GLY C 174 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE C 315 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE C 176 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 317 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA C 178 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ALA C 319 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU C 226 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU C 208 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 228 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ASP C 210 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N SER C 230 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 79 through 81 removed outlier: 3.806A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS D 100 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL D 116 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 341 through 344 removed outlier: 7.866A pdb=" N GLY D 174 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE D 315 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE D 176 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA D 317 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA D 178 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA D 319 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU D 226 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU D 208 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL D 228 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ASP D 210 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N SER D 230 " --> pdb=" O ASP D 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 79 through 81 removed outlier: 3.761A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 342 through 344 removed outlier: 6.697A pdb=" N LEU E 175 " --> pdb=" O LEU E 343 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE E 176 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA E 317 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA E 178 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ALA E 319 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL E 203 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU E 263 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N MET E 205 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU E 226 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU E 208 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL E 228 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ASP E 210 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N SER E 230 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 96 through 101 removed outlier: 3.737A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 315 through 321 Processing sheet with id= M, first strand: chain 'F' and resid 260 through 263 removed outlier: 6.141A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU F 226 " --> pdb=" O VAL F 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 744 hydrogen bonds defined for protein. 2148 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: 5.68 Time building geometry restraints manager: 8.09 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: 6759 1.34 - 1.46: 3970 1.46 - 1.58: 9268 1.58 - 1.70: 19 1.70 - 1.82: 198 Bond restraints: 20214 Sorted by residual: bond pdb=" CB PRO F 167 " pdb=" CG PRO F 167 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.77e+00 bond pdb=" CB LYS F 257 " pdb=" CG LYS F 257 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB ASP C 322 " pdb=" CG ASP C 322 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.62e+00 bond pdb=" CB LYS A 348 " pdb=" CG LYS A 348 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CG PRO F 167 " pdb=" CD PRO F 167 " ideal model delta sigma weight residual 1.503 1.462 0.041 3.40e-02 8.65e+02 1.45e+00 ... (remaining 20209 not shown) Histogram of bond angle deviations from ideal: 94.97 - 103.19: 199 103.19 - 111.40: 9081 111.40 - 119.62: 8437 119.62 - 127.83: 9418 127.83 - 136.05: 117 Bond angle restraints: 27252 Sorted by residual: angle pdb=" CA PRO F 167 " pdb=" N PRO F 167 " pdb=" CD PRO F 167 " ideal model delta sigma weight residual 112.00 104.97 7.03 1.40e+00 5.10e-01 2.52e+01 angle pdb=" C LYS F 379 " pdb=" N MET F 380 " pdb=" CA MET F 380 " ideal model delta sigma weight residual 121.58 112.00 9.58 1.95e+00 2.63e-01 2.41e+01 angle pdb=" CA MET F 380 " pdb=" CB MET F 380 " pdb=" CG MET F 380 " ideal model delta sigma weight residual 114.10 123.23 -9.13 2.00e+00 2.50e-01 2.08e+01 angle pdb=" N MET F 380 " pdb=" CA MET F 380 " pdb=" CB MET F 380 " ideal model delta sigma weight residual 110.41 117.79 -7.38 1.68e+00 3.54e-01 1.93e+01 angle pdb=" CB MET D 416 " pdb=" CG MET D 416 " pdb=" SD MET D 416 " ideal model delta sigma weight residual 112.70 124.76 -12.06 3.00e+00 1.11e-01 1.62e+01 ... (remaining 27247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12189 35.65 - 71.30: 302 71.30 - 106.94: 15 106.94 - 142.59: 5 142.59 - 178.24: 5 Dihedral angle restraints: 12516 sinusoidal: 5304 harmonic: 7212 Sorted by residual: dihedral pdb=" O2A ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PA ADP D1000 " pdb=" PB ADP D1000 " ideal model delta sinusoidal sigma weight residual -60.00 118.24 -178.24 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PA ADP C1000 " pdb=" PB ADP C1000 " ideal model delta sinusoidal sigma weight residual -60.00 115.43 -175.43 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP D1000 " pdb=" O5' ADP D1000 " pdb=" PA ADP D1000 " pdb=" O2A ADP D1000 " ideal model delta sinusoidal sigma weight residual 300.00 129.32 170.68 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 12513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2528 0.052 - 0.103: 466 0.103 - 0.154: 100 0.154 - 0.206: 1 0.206 - 0.257: 1 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CA MET F 380 " pdb=" N MET F 380 " pdb=" C MET F 380 " pdb=" CB MET F 380 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU F 188 " pdb=" CB LEU F 188 " pdb=" CD1 LEU F 188 " pdb=" CD2 LEU F 188 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA ASP B 322 " pdb=" N ASP B 322 " pdb=" C ASP B 322 " pdb=" CB ASP B 322 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 3093 not shown) Planarity restraints: 3528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 166 " 0.078 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO F 167 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 381 " -0.022 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP E 381 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP E 381 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 381 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 381 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 381 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 381 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 381 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 322 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ASP C 322 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP C 322 " 0.015 2.00e-02 2.50e+03 pdb=" N THR C 323 " 0.013 2.00e-02 2.50e+03 ... (remaining 3525 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 236 2.57 - 3.15: 16263 3.15 - 3.74: 32038 3.74 - 4.32: 43664 4.32 - 4.90: 72626 Nonbonded interactions: 164827 Sorted by model distance: nonbonded pdb=" O2B ADP C1000 " pdb="MG MG C1001 " model vdw 1.991 2.170 nonbonded pdb=" O2B ADP D1000 " pdb="MG MG D1001 " model vdw 1.996 2.170 nonbonded pdb=" O1B ADP B1000 " pdb="MG MG B1001 " model vdw 2.017 2.170 nonbonded pdb=" O3B ADP E1000 " pdb="MG MG E1001 " model vdw 2.038 2.170 nonbonded pdb=" OG1 THR C 185 " pdb="MG MG C1001 " model vdw 2.052 2.170 ... (remaining 164822 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' and (resid 1 through 418 or resid 1000)) selection = (chain 'C' and (resid 1 through 418 or resid 1000)) selection = (chain 'D' and (resid 1 through 418 or resid 1000)) selection = (chain 'E' and (resid 1 through 418 or resid 1000)) selection = chain 'F' } 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.440 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 52.310 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.120 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.003 0.097 20214 Z= 0.230 Angle : 0.642 12.058 27252 Z= 0.310 Chirality : 0.041 0.257 3096 Planarity : 0.004 0.114 3528 Dihedral : 16.080 178.238 7848 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.54 % Allowed : 17.36 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.95 (0.17), residues: 2496 helix: 1.30 (0.16), residues: 1148 sheet: 0.58 (0.27), residues: 367 loop : -0.02 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 381 HIS 0.008 0.001 HIS A 42 PHE 0.009 0.001 PHE E 398 TYR 0.023 0.001 TYR E 197 ARG 0.013 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8798 (pm20) cc_final: 0.8447 (pm20) REVERT: C 374 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7980 (tm-30) REVERT: C 378 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8540 (mm-40) REVERT: E 21 MET cc_start: 0.7838 (tmt) cc_final: 0.7359 (ttt) REVERT: E 41 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: F 1 MET cc_start: 0.1851 (pmm) cc_final: 0.0364 (ptp) REVERT: F 21 MET cc_start: 0.4325 (tpt) cc_final: 0.3066 (tmm) REVERT: F 36 PHE cc_start: 0.4259 (t80) cc_final: 0.3882 (t80) REVERT: F 120 ASN cc_start: 0.1079 (m110) cc_final: 0.0834 (m-40) REVERT: F 396 MET cc_start: 0.2199 (mpt) cc_final: 0.0653 (tpt) outliers start: 33 outliers final: 27 residues processed: 267 average time/residue: 1.5278 time to fit residues: 455.2227 Evaluate side-chains 254 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 374 GLN D 378 GLN E 220 GLN E 388 HIS F 193 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20214 Z= 0.285 Angle : 0.568 8.100 27252 Z= 0.270 Chirality : 0.042 0.174 3096 Planarity : 0.004 0.061 3528 Dihedral : 10.317 179.953 2843 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.31 % Allowed : 15.18 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.90 (0.17), residues: 2496 helix: 1.24 (0.16), residues: 1149 sheet: 0.58 (0.26), residues: 366 loop : -0.03 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 381 HIS 0.005 0.001 HIS E 388 PHE 0.015 0.001 PHE F 64 TYR 0.020 0.001 TYR F 72 ARG 0.006 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 235 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7923 (ppp) cc_final: 0.7631 (pmm) REVERT: B 59 GLN cc_start: 0.8791 (pm20) cc_final: 0.8385 (pm20) REVERT: B 326 LYS cc_start: 0.8648 (ptmm) cc_final: 0.8344 (pttt) REVERT: B 374 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8603 (tp40) REVERT: C 32 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8839 (mp10) REVERT: C 322 ASP cc_start: 0.8002 (t0) cc_final: 0.7601 (t0) REVERT: F 1 MET cc_start: 0.2033 (pmm) cc_final: 0.0493 (ptp) REVERT: F 21 MET cc_start: 0.4360 (tpt) cc_final: 0.3089 (tmm) REVERT: F 396 MET cc_start: 0.2130 (OUTLIER) cc_final: 0.0648 (mmm) outliers start: 71 outliers final: 39 residues processed: 283 average time/residue: 1.4648 time to fit residues: 463.8205 Evaluate side-chains 270 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 230 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 396 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 185 optimal weight: 0.2980 chunk 152 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 223 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 221 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 220 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20214 Z= 0.150 Angle : 0.544 7.991 27252 Z= 0.256 Chirality : 0.040 0.177 3096 Planarity : 0.003 0.047 3528 Dihedral : 9.704 178.683 2821 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.84 % Allowed : 16.48 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.95 (0.17), residues: 2496 helix: 1.28 (0.16), residues: 1150 sheet: 0.56 (0.26), residues: 373 loop : 0.02 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 381 HIS 0.008 0.001 HIS F 256 PHE 0.016 0.001 PHE F 64 TYR 0.017 0.001 TYR A 80 ARG 0.008 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9190 (mp10) cc_final: 0.8988 (mp10) REVERT: A 193 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: A 244 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: B 59 GLN cc_start: 0.8796 (pm20) cc_final: 0.8364 (pm20) REVERT: B 244 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8470 (mm-30) REVERT: B 326 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8206 (pttt) REVERT: C 32 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8845 (mp10) REVERT: C 322 ASP cc_start: 0.7996 (t0) cc_final: 0.7508 (t0) REVERT: D 374 GLN cc_start: 0.8080 (tp40) cc_final: 0.7778 (tm-30) REVERT: E 326 LYS cc_start: 0.9064 (mppt) cc_final: 0.8838 (mppt) REVERT: E 329 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: F 1 MET cc_start: 0.2321 (pmm) cc_final: 0.0756 (ptp) REVERT: F 21 MET cc_start: 0.4367 (tpt) cc_final: 0.3121 (tmm) REVERT: F 73 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.5731 (pp) REVERT: F 111 PHE cc_start: 0.7003 (m-80) cc_final: 0.6697 (m-10) REVERT: F 396 MET cc_start: 0.2136 (OUTLIER) cc_final: 0.0676 (mmm) outliers start: 61 outliers final: 34 residues processed: 285 average time/residue: 1.5471 time to fit residues: 490.3494 Evaluate side-chains 267 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 396 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 224 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 chunk 117 optimal weight: 0.4980 chunk 212 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 220 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20214 Z= 0.292 Angle : 0.570 8.338 27252 Z= 0.270 Chirality : 0.042 0.189 3096 Planarity : 0.003 0.057 3528 Dihedral : 9.544 177.515 2817 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.03 % Allowed : 17.04 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.91 (0.17), residues: 2496 helix: 1.20 (0.16), residues: 1154 sheet: 0.54 (0.26), residues: 373 loop : 0.04 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 381 HIS 0.005 0.001 HIS F 256 PHE 0.016 0.001 PHE F 64 TYR 0.017 0.001 TYR E 197 ARG 0.008 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 234 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7965 (ppp) cc_final: 0.7715 (pmm) REVERT: A 21 MET cc_start: 0.7480 (ppp) cc_final: 0.7244 (ppp) REVERT: A 244 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: B 59 GLN cc_start: 0.8796 (pm20) cc_final: 0.8381 (pm20) REVERT: B 109 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8107 (ptt90) REVERT: B 244 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8449 (mm-30) REVERT: B 326 LYS cc_start: 0.8669 (ptmm) cc_final: 0.8422 (ptmm) REVERT: C 32 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8838 (mp10) REVERT: C 322 ASP cc_start: 0.8198 (t0) cc_final: 0.7716 (t0) REVERT: D 374 GLN cc_start: 0.8224 (tp40) cc_final: 0.7870 (tp40) REVERT: E 41 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: E 326 LYS cc_start: 0.9136 (mppt) cc_final: 0.8901 (mppt) REVERT: E 329 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: E 341 MET cc_start: 0.8784 (ptm) cc_final: 0.8290 (pp-130) REVERT: F 1 MET cc_start: 0.2333 (pmm) cc_final: 0.0558 (ptp) REVERT: F 21 MET cc_start: 0.4356 (tpt) cc_final: 0.3101 (tmm) REVERT: F 36 PHE cc_start: 0.2957 (t80) cc_final: 0.2689 (t80) REVERT: F 73 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.5781 (pp) REVERT: F 111 PHE cc_start: 0.7005 (m-80) cc_final: 0.6631 (m-10) REVERT: F 390 MET cc_start: 0.3145 (pp-130) cc_final: 0.0912 (mtp) outliers start: 65 outliers final: 38 residues processed: 277 average time/residue: 1.5088 time to fit residues: 466.8064 Evaluate side-chains 280 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 237 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 275 ASN C 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 20214 Z= 0.472 Angle : 0.638 8.784 27252 Z= 0.306 Chirality : 0.044 0.196 3096 Planarity : 0.004 0.057 3528 Dihedral : 9.574 179.683 2815 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.19 % Allowed : 16.62 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.66 (0.17), residues: 2496 helix: 0.99 (0.16), residues: 1153 sheet: 0.36 (0.25), residues: 399 loop : -0.05 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 381 HIS 0.004 0.001 HIS E 239 PHE 0.018 0.001 PHE F 300 TYR 0.017 0.002 TYR E 197 ARG 0.011 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 239 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9274 (mp10) cc_final: 0.9049 (mp10) REVERT: A 244 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: B 59 GLN cc_start: 0.8805 (pm20) cc_final: 0.8407 (pm20) REVERT: B 244 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8438 (mm-30) REVERT: B 326 LYS cc_start: 0.8767 (ptmm) cc_final: 0.8553 (ptmt) REVERT: B 362 ARG cc_start: 0.8871 (ttm110) cc_final: 0.8220 (mtm-85) REVERT: B 374 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8409 (OUTLIER) REVERT: C 32 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8847 (mp10) REVERT: C 322 ASP cc_start: 0.8400 (t0) cc_final: 0.7987 (t0) REVERT: D 374 GLN cc_start: 0.8408 (tp40) cc_final: 0.8047 (tp40) REVERT: E 32 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8252 (mm-40) REVERT: E 41 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8311 (tm-30) REVERT: E 326 LYS cc_start: 0.9195 (mppt) cc_final: 0.8939 (mppt) REVERT: E 329 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: E 341 MET cc_start: 0.8906 (ptm) cc_final: 0.8368 (pp-130) REVERT: F 1 MET cc_start: 0.2595 (pmm) cc_final: 0.0947 (ptp) REVERT: F 21 MET cc_start: 0.4433 (tpt) cc_final: 0.3211 (tmm) REVERT: F 36 PHE cc_start: 0.3475 (t80) cc_final: 0.3230 (t80) REVERT: F 49 ILE cc_start: 0.3237 (OUTLIER) cc_final: 0.2975 (pp) REVERT: F 50 PHE cc_start: 0.7355 (t80) cc_final: 0.6878 (t80) REVERT: F 73 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.5787 (pp) REVERT: F 111 PHE cc_start: 0.6851 (m-80) cc_final: 0.6596 (m-10) REVERT: F 390 MET cc_start: 0.3071 (pp-130) cc_final: 0.0763 (mtp) outliers start: 90 outliers final: 48 residues processed: 304 average time/residue: 1.5369 time to fit residues: 522.9780 Evaluate side-chains 280 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 228 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 416 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.6980 chunk 214 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 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 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20214 Z= 0.191 Angle : 0.595 10.094 27252 Z= 0.278 Chirality : 0.041 0.198 3096 Planarity : 0.003 0.055 3528 Dihedral : 9.250 179.365 2810 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.07 % Allowed : 18.02 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.78 (0.17), residues: 2496 helix: 1.13 (0.16), residues: 1143 sheet: 0.47 (0.26), residues: 354 loop : -0.04 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.004 0.000 HIS F 256 PHE 0.023 0.001 PHE F 300 TYR 0.017 0.001 TYR E 197 ARG 0.011 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 237 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7938 (ppp) cc_final: 0.7682 (pmm) REVERT: A 21 MET cc_start: 0.7475 (ppp) cc_final: 0.7251 (ppp) REVERT: A 244 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: A 396 MET cc_start: 0.9577 (tpt) cc_final: 0.9367 (tpp) REVERT: B 59 GLN cc_start: 0.8808 (pm20) cc_final: 0.8394 (pm20) REVERT: B 244 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8397 (mm-30) REVERT: B 259 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8259 (p0) REVERT: B 326 LYS cc_start: 0.8698 (ptmm) cc_final: 0.8433 (ptmm) REVERT: C 32 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8850 (mp10) REVERT: C 322 ASP cc_start: 0.8372 (t0) cc_final: 0.7915 (t0) REVERT: D 374 GLN cc_start: 0.8324 (tp40) cc_final: 0.8044 (tp40) REVERT: E 32 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8206 (mm-40) REVERT: E 41 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8244 (tm-30) REVERT: E 172 GLN cc_start: 0.8479 (mt0) cc_final: 0.8277 (pt0) REVERT: E 326 LYS cc_start: 0.9213 (mppt) cc_final: 0.8955 (mppt) REVERT: E 329 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: E 341 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8464 (pp-130) REVERT: F 1 MET cc_start: 0.2774 (pmm) cc_final: 0.1161 (ptp) REVERT: F 21 MET cc_start: 0.4170 (tpt) cc_final: 0.2864 (tmm) REVERT: F 36 PHE cc_start: 0.3517 (t80) cc_final: 0.3310 (t80) REVERT: F 49 ILE cc_start: 0.3381 (OUTLIER) cc_final: 0.3169 (pp) REVERT: F 50 PHE cc_start: 0.7406 (t80) cc_final: 0.6917 (t80) REVERT: F 73 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.5877 (pp) REVERT: F 275 ASN cc_start: 0.9074 (t0) cc_final: 0.8810 (t0) REVERT: F 390 MET cc_start: 0.3102 (pp-130) cc_final: 0.0776 (mtp) outliers start: 66 outliers final: 40 residues processed: 283 average time/residue: 1.4736 time to fit residues: 466.0702 Evaluate side-chains 284 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 237 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 144 optimal weight: 0.0770 chunk 109 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN E 193 GLN E 220 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20214 Z= 0.191 Angle : 0.597 10.711 27252 Z= 0.280 Chirality : 0.041 0.208 3096 Planarity : 0.003 0.054 3528 Dihedral : 8.771 178.764 2810 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.75 % Allowed : 18.81 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.83 (0.17), residues: 2496 helix: 1.15 (0.16), residues: 1146 sheet: 0.43 (0.26), residues: 368 loop : 0.02 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.000 HIS F 256 PHE 0.027 0.001 PHE F 300 TYR 0.022 0.001 TYR A 80 ARG 0.012 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7866 (ppp) cc_final: 0.7589 (pmm) REVERT: A 32 GLN cc_start: 0.9259 (mp10) cc_final: 0.9018 (mp10) REVERT: A 244 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: A 396 MET cc_start: 0.9577 (tpt) cc_final: 0.9365 (tpp) REVERT: B 41 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8832 (tp40) REVERT: B 59 GLN cc_start: 0.8795 (pm20) cc_final: 0.8368 (pm20) REVERT: B 244 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8400 (mm-30) REVERT: B 259 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8242 (p0) REVERT: B 326 LYS cc_start: 0.8702 (ptmm) cc_final: 0.8429 (ptmm) REVERT: B 362 ARG cc_start: 0.8965 (mtp85) cc_final: 0.8741 (ttp-110) REVERT: C 32 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8853 (mp10) REVERT: C 322 ASP cc_start: 0.8405 (t0) cc_final: 0.7936 (t0) REVERT: D 374 GLN cc_start: 0.8449 (tp40) cc_final: 0.8162 (tp40) REVERT: E 29 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8264 (pmt) REVERT: E 32 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8240 (mm-40) REVERT: E 41 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8259 (tm-30) REVERT: E 172 GLN cc_start: 0.8449 (mt0) cc_final: 0.8239 (pt0) REVERT: E 326 LYS cc_start: 0.9253 (mppt) cc_final: 0.8994 (mppt) REVERT: E 329 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: E 341 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8459 (pp-130) REVERT: F 1 MET cc_start: 0.2824 (pmm) cc_final: 0.1156 (ptp) REVERT: F 21 MET cc_start: 0.4110 (tpt) cc_final: 0.2852 (tmm) REVERT: F 36 PHE cc_start: 0.3881 (t80) cc_final: 0.3637 (t80) REVERT: F 50 PHE cc_start: 0.7441 (t80) cc_final: 0.6957 (t80) REVERT: F 73 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.5850 (pp) REVERT: F 390 MET cc_start: 0.3070 (pp-130) cc_final: 0.0699 (mtp) outliers start: 59 outliers final: 40 residues processed: 287 average time/residue: 1.5549 time to fit residues: 496.4911 Evaluate side-chains 285 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.4980 chunk 94 optimal weight: 0.0270 chunk 141 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS E 193 GLN E 220 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20214 Z= 0.157 Angle : 0.600 11.285 27252 Z= 0.280 Chirality : 0.041 0.214 3096 Planarity : 0.003 0.054 3528 Dihedral : 8.356 179.361 2808 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.33 % Allowed : 19.27 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.93 (0.17), residues: 2496 helix: 1.22 (0.16), residues: 1142 sheet: 0.50 (0.26), residues: 366 loop : 0.10 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.000 HIS F 42 PHE 0.025 0.001 PHE F 300 TYR 0.020 0.001 TYR E 197 ARG 0.012 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7639 (ppp) cc_final: 0.7425 (ppp) REVERT: A 32 GLN cc_start: 0.9246 (mp10) cc_final: 0.9000 (mp10) REVERT: A 220 GLN cc_start: 0.8768 (mt0) cc_final: 0.8272 (mp10) REVERT: A 244 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: A 353 ARG cc_start: 0.8649 (tpp-160) cc_final: 0.8275 (mmm-85) REVERT: B 41 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8702 (tp40) REVERT: B 59 GLN cc_start: 0.8796 (pm20) cc_final: 0.8357 (pm20) REVERT: B 244 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8407 (mm-30) REVERT: B 326 LYS cc_start: 0.8682 (ptmm) cc_final: 0.8409 (ptmm) REVERT: C 32 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8857 (mp10) REVERT: C 186 MET cc_start: 0.9227 (mtp) cc_final: 0.8945 (mtm) REVERT: C 322 ASP cc_start: 0.8413 (t0) cc_final: 0.7939 (t0) REVERT: D 374 GLN cc_start: 0.8381 (tp40) cc_final: 0.8007 (tp40) REVERT: E 29 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8221 (pmt) REVERT: E 32 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: E 41 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8274 (tm-30) REVERT: E 59 GLN cc_start: 0.8896 (pm20) cc_final: 0.8670 (pp30) REVERT: E 326 LYS cc_start: 0.9265 (mppt) cc_final: 0.9042 (mppt) REVERT: E 329 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: E 341 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8362 (pp-130) REVERT: F 1 MET cc_start: 0.2936 (pmm) cc_final: 0.1253 (ptp) REVERT: F 21 MET cc_start: 0.4231 (tpt) cc_final: 0.2894 (tmm) REVERT: F 50 PHE cc_start: 0.7357 (t80) cc_final: 0.6950 (t80) REVERT: F 73 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.5868 (pp) REVERT: F 390 MET cc_start: 0.3070 (pp-130) cc_final: 0.0669 (mtp) outliers start: 50 outliers final: 36 residues processed: 287 average time/residue: 1.6355 time to fit residues: 520.2592 Evaluate side-chains 276 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 207 optimal weight: 40.0000 chunk 220 optimal weight: 30.0000 chunk 132 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 193 GLN E 220 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20214 Z= 0.292 Angle : 0.635 11.771 27252 Z= 0.299 Chirality : 0.042 0.255 3096 Planarity : 0.004 0.058 3528 Dihedral : 8.077 169.294 2808 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.56 % Allowed : 19.37 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.86 (0.17), residues: 2496 helix: 1.10 (0.16), residues: 1149 sheet: 0.51 (0.26), residues: 360 loop : 0.11 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 381 HIS 0.003 0.001 HIS E 239 PHE 0.035 0.001 PHE F 300 TYR 0.022 0.001 TYR A 80 ARG 0.013 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 231 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7482 (ppp) cc_final: 0.7271 (ppp) REVERT: A 244 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: B 41 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8759 (tp40) REVERT: B 59 GLN cc_start: 0.8794 (pm20) cc_final: 0.8375 (pm20) REVERT: B 244 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8384 (mm-30) REVERT: B 326 LYS cc_start: 0.8724 (ptmm) cc_final: 0.8439 (ptmm) REVERT: C 32 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8843 (mp10) REVERT: C 322 ASP cc_start: 0.8490 (t0) cc_final: 0.8040 (t0) REVERT: D 374 GLN cc_start: 0.8447 (tp40) cc_final: 0.8034 (tp40) REVERT: E 29 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8232 (pmt) REVERT: E 32 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8198 (mm-40) REVERT: E 41 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8364 (tm-30) REVERT: E 326 LYS cc_start: 0.9254 (mppt) cc_final: 0.9026 (mppt) REVERT: E 329 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: E 341 MET cc_start: 0.8740 (ptm) cc_final: 0.8416 (pp-130) REVERT: F 1 MET cc_start: 0.2924 (pmm) cc_final: 0.1376 (ptp) REVERT: F 20 ASN cc_start: 0.6147 (m-40) cc_final: 0.5845 (m-40) REVERT: F 21 MET cc_start: 0.4310 (tpt) cc_final: 0.2839 (tmm) REVERT: F 50 PHE cc_start: 0.7394 (t80) cc_final: 0.6994 (t80) REVERT: F 73 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.5883 (pp) REVERT: F 390 MET cc_start: 0.3139 (pp-130) cc_final: 0.0691 (mtp) outliers start: 55 outliers final: 42 residues processed: 270 average time/residue: 1.5236 time to fit residues: 458.3791 Evaluate side-chains 286 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 239 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 245 optimal weight: 50.0000 chunk 225 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 41 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 193 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20214 Z= 0.203 Angle : 0.623 12.422 27252 Z= 0.291 Chirality : 0.041 0.247 3096 Planarity : 0.003 0.060 3528 Dihedral : 7.467 147.013 2808 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.33 % Allowed : 19.74 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.93 (0.17), residues: 2496 helix: 1.19 (0.16), residues: 1136 sheet: 0.54 (0.26), residues: 360 loop : 0.13 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 381 HIS 0.003 0.000 HIS F 256 PHE 0.020 0.001 PHE F 300 TYR 0.019 0.001 TYR E 197 ARG 0.013 0.000 ARG E 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9261 (mp10) cc_final: 0.9002 (mp10) REVERT: A 185 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8914 (p) REVERT: A 244 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: A 353 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8244 (mmm-85) REVERT: B 41 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8800 (tp40) REVERT: B 59 GLN cc_start: 0.8808 (pm20) cc_final: 0.8372 (pm20) REVERT: B 244 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8392 (mm-30) REVERT: B 326 LYS cc_start: 0.8695 (ptmm) cc_final: 0.8450 (ptmt) REVERT: C 32 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8845 (mp10) REVERT: C 322 ASP cc_start: 0.8490 (t0) cc_final: 0.8049 (t0) REVERT: D 374 GLN cc_start: 0.8386 (tp40) cc_final: 0.7883 (tp40) REVERT: D 378 GLN cc_start: 0.8796 (mt0) cc_final: 0.8489 (mt0) REVERT: E 29 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8181 (pmt) REVERT: E 32 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8198 (mm-40) REVERT: E 41 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8272 (tm-30) REVERT: E 59 GLN cc_start: 0.8908 (pm20) cc_final: 0.8615 (pp30) REVERT: E 326 LYS cc_start: 0.9256 (mppt) cc_final: 0.9003 (mppt) REVERT: E 329 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: E 341 MET cc_start: 0.8671 (ptm) cc_final: 0.8433 (pp-130) REVERT: F 1 MET cc_start: 0.2991 (pmm) cc_final: 0.1402 (ptp) REVERT: F 20 ASN cc_start: 0.6138 (m-40) cc_final: 0.5840 (m-40) REVERT: F 21 MET cc_start: 0.4243 (tpt) cc_final: 0.2831 (tmm) REVERT: F 50 PHE cc_start: 0.7435 (t80) cc_final: 0.7078 (t80) REVERT: F 73 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6064 (pp) REVERT: F 390 MET cc_start: 0.3118 (pp-130) cc_final: 0.0688 (mtp) outliers start: 50 outliers final: 40 residues processed: 273 average time/residue: 1.5569 time to fit residues: 473.8134 Evaluate side-chains 283 residues out of total 2148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 381 TRP Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 200 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 378 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN E 388 HIS ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.123010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077895 restraints weight = 41414.514| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.57 r_work: 0.2818 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20214 Z= 0.203 Angle : 0.630 12.377 27252 Z= 0.294 Chirality : 0.041 0.239 3096 Planarity : 0.004 0.058 3528 Dihedral : 6.995 126.605 2808 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.28 % Allowed : 19.88 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.95 (0.17), residues: 2496 helix: 1.19 (0.16), residues: 1137 sheet: 0.56 (0.26), residues: 360 loop : 0.15 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 381 HIS 0.003 0.000 HIS F 256 PHE 0.025 0.001 PHE F 300 TYR 0.025 0.001 TYR A 80 ARG 0.015 0.000 ARG B 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8030.83 seconds wall clock time: 144 minutes 14.34 seconds (8654.34 seconds total)