Starting phenix.real_space_refine on Mon Feb 19 00:17:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/02_2024/8emw_28267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/02_2024/8emw_28267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/02_2024/8emw_28267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/02_2024/8emw_28267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/02_2024/8emw_28267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/02_2024/8emw_28267.pdb" } resolution = 3.5 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11633 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 79 5.16 5 C 7373 2.51 5 N 2034 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 782": "OD1" <-> "OD2" Residue "A PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11714 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5926 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 47, 'TRANS': 695} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2512 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2516 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 339 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.06, per 1000 atoms: 0.52 Number of scatterers: 11714 At special positions: 0 Unit cell: (83.061, 132.562, 119.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 79 16.00 O 2227 8.00 N 2034 7.00 C 7373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.14 Conformation dependent library (CDL) restraints added in 2.4 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2832 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 30 sheets defined 21.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.545A pdb=" N ARG A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.509A pdb=" N TRP A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 157 through 163 removed outlier: 3.873A pdb=" N GLN A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.766A pdb=" N LYS A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.969A pdb=" N VAL A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.612A pdb=" N LYS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.762A pdb=" N ASP A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.667A pdb=" N PHE A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.009A pdb=" N LEU A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 347 through 357 removed outlier: 4.021A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.578A pdb=" N GLU A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.714A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS A 429 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 removed outlier: 4.006A pdb=" N LEU A 437 " --> pdb=" O GLY A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 437' Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.542A pdb=" N THR A 592 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 593 " --> pdb=" O MET A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 593' Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.635A pdb=" N ALA A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.665A pdb=" N PHE A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.698A pdb=" N ASN A 666 " --> pdb=" O GLN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.698A pdb=" N ARG A 874 " --> pdb=" O ASP A 870 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN A 875 " --> pdb=" O GLN A 871 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 877 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA A 878 " --> pdb=" O ARG A 874 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 4.170A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.029A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.800A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.535A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'D' and resid 9 through 21 removed outlier: 3.600A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.513A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.604A pdb=" N SER A 26 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N THR A 42 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 55 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 54 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 3.989A pdb=" N ASP A 71 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 104 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 330 through 331 removed outlier: 7.430A pdb=" N SER A 330 " --> pdb=" O LEU A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA8, first strand: chain 'A' and resid 408 through 411 removed outlier: 6.601A pdb=" N VAL A 408 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LYS A 466 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 410 " --> pdb=" O LYS A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 620 through 621 removed outlier: 6.441A pdb=" N PHE A 620 " --> pdb=" O TYR A 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.376A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 839 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.376A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 745 through 752 removed outlier: 5.097A pdb=" N GLU A 800 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 805 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 824 through 826 removed outlier: 5.553A pdb=" N LEU A 825 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.018A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.846A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.272A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.733A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.569A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.623A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.663A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.732A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.572A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.572A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 111 through 112 removed outlier: 3.589A pdb=" N VAL C 112 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC8, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.902A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 167 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.630A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AD2, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.683A pdb=" N SER C 277 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 320 removed outlier: 3.534A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 768 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: 3.99 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3660 1.33 - 1.45: 2007 1.45 - 1.57: 6153 1.57 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 11939 Sorted by residual: bond pdb=" CA SER A 37 " pdb=" CB SER A 37 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.58e-02 4.01e+03 8.68e+00 bond pdb=" N ASP C 291 " pdb=" CA ASP C 291 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.26e-02 6.30e+03 6.27e+00 bond pdb=" N ASP C 290 " pdb=" CA ASP C 290 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.11e+00 bond pdb=" N ASP A 125 " pdb=" CA ASP A 125 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 5.98e+00 bond pdb=" N SER A 37 " pdb=" CA SER A 37 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.63e+00 ... (remaining 11934 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.71: 248 105.71 - 112.81: 6231 112.81 - 119.91: 4229 119.91 - 127.02: 5336 127.02 - 134.12: 134 Bond angle restraints: 16178 Sorted by residual: angle pdb=" N THR A 127 " pdb=" CA THR A 127 " pdb=" C THR A 127 " ideal model delta sigma weight residual 113.89 105.90 7.99 1.58e+00 4.01e-01 2.56e+01 angle pdb=" C ASN A 39 " pdb=" CA ASN A 39 " pdb=" CB ASN A 39 " ideal model delta sigma weight residual 113.45 103.94 9.51 1.98e+00 2.55e-01 2.31e+01 angle pdb=" C ASP C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" N ASP C 291 " pdb=" CA ASP C 291 " pdb=" C ASP C 291 " ideal model delta sigma weight residual 112.92 108.08 4.84 1.23e+00 6.61e-01 1.55e+01 angle pdb=" C TYR C 289 " pdb=" CA TYR C 289 " pdb=" CB TYR C 289 " ideal model delta sigma weight residual 114.10 105.86 8.24 2.11e+00 2.25e-01 1.53e+01 ... (remaining 16173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6314 17.36 - 34.73: 738 34.73 - 52.09: 135 52.09 - 69.46: 14 69.46 - 86.82: 15 Dihedral angle restraints: 7216 sinusoidal: 2845 harmonic: 4371 Sorted by residual: dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO A 702 " pdb=" C PRO A 702 " pdb=" N GLU A 703 " pdb=" CA GLU A 703 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASN C 313 " pdb=" C ASN C 313 " pdb=" N ARG C 314 " pdb=" CA ARG C 314 " ideal model delta harmonic sigma weight residual -180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1512 0.071 - 0.142: 283 0.142 - 0.212: 24 0.212 - 0.283: 6 0.283 - 0.354: 1 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CA ASP A 126 " pdb=" N ASP A 126 " pdb=" C ASP A 126 " pdb=" CB ASP A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASN A 39 " pdb=" N ASN A 39 " pdb=" C ASN A 39 " pdb=" CB ASN A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL A 347 " pdb=" CA VAL A 347 " pdb=" CG1 VAL A 347 " pdb=" CG2 VAL A 347 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1823 not shown) Planarity restraints: 2098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 370 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 371 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 369 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 370 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 455 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 456 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.038 5.00e-02 4.00e+02 ... (remaining 2095 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2838 2.78 - 3.31: 9861 3.31 - 3.84: 18694 3.84 - 4.37: 21694 4.37 - 4.90: 37965 Nonbonded interactions: 91052 Sorted by model distance: nonbonded pdb=" OH TYR A 240 " pdb=" OD2 ASP C 186 " model vdw 2.248 2.440 nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.262 2.440 nonbonded pdb=" O VAL A 361 " pdb=" OG SER A 411 " model vdw 2.275 2.440 nonbonded pdb=" OG SER C 161 " pdb=" O THR C 165 " model vdw 2.280 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.288 2.440 ... (remaining 91047 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 'B' and (resid 4 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 41 or (resid 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 51 or (resi \ d 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throug \ h 152 or (resid 153 and (name N or name CA or name C or name O or name CB )) or \ resid 154 through 174 or (resid 175 and (name N or name CA or name C or name O o \ r name CB )) or resid 176 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB )) or resid 198 through 291 or (resid 292 and (name N \ or name CA or name C or name O or name CB )) or resid 293 through 340)) selection = (chain 'C' and (resid 4 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 213 or (resid 214 through 215 an \ d (name N or name CA or name C or name O or name CB )) or resid 216 through 258 \ or (resid 259 and (name N or name CA or name C or name O or name CB )) or resid \ 260 through 282 or (resid 283 and (name N or name CA or name C or name O or name \ CB )) or resid 284 through 340)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.000 Extract box with map and model: 9.460 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.120 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.008 0.104 11939 Z= 0.536 Angle : 0.908 9.878 16178 Z= 0.503 Chirality : 0.056 0.354 1826 Planarity : 0.007 0.102 2098 Dihedral : 15.242 86.819 4384 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.17), residues: 1486 helix: -4.92 (0.10), residues: 308 sheet: -3.25 (0.24), residues: 374 loop : -2.74 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.011 0.002 HIS A 332 PHE 0.033 0.003 PHE B 199 TYR 0.021 0.003 TYR A 692 ARG 0.006 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8030 (p0) cc_final: 0.7789 (p0) REVERT: A 173 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8117 (tppt) REVERT: A 215 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7707 (ttp80) REVERT: A 236 LYS cc_start: 0.7854 (tptt) cc_final: 0.7580 (mttp) REVERT: A 247 MET cc_start: 0.7560 (ttp) cc_final: 0.7159 (ttp) REVERT: A 290 GLN cc_start: 0.7581 (mt0) cc_final: 0.7325 (mt0) REVERT: A 341 LEU cc_start: 0.8880 (mp) cc_final: 0.8677 (mp) REVERT: A 374 GLU cc_start: 0.8306 (pm20) cc_final: 0.7672 (pm20) REVERT: A 460 MET cc_start: 0.8644 (ttp) cc_final: 0.8215 (ttp) REVERT: A 577 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7189 (mm-30) REVERT: A 583 GLU cc_start: 0.7749 (tt0) cc_final: 0.7542 (mt-10) REVERT: A 870 ASP cc_start: 0.7837 (t0) cc_final: 0.7603 (t0) REVERT: B 12 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 325 MET cc_start: 0.7238 (mmp) cc_final: 0.6568 (mtp) REVERT: B 340 ASN cc_start: 0.8139 (t0) cc_final: 0.7894 (t0) REVERT: C 78 LYS cc_start: 0.8212 (tttm) cc_final: 0.7940 (mtpp) REVERT: C 188 MET cc_start: 0.7864 (mmm) cc_final: 0.7557 (mmm) REVERT: C 312 ASP cc_start: 0.7021 (p0) cc_final: 0.6798 (p0) REVERT: D 44 HIS cc_start: 0.7815 (m-70) cc_final: 0.7613 (m-70) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2959 time to fit residues: 98.2811 Evaluate side-chains 176 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 124 GLN A 163 GLN A 379 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN A 871 GLN B 35 ASN B 91 HIS B 239 ASN B 268 ASN B 340 ASN C 16 ASN C 230 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11939 Z= 0.212 Angle : 0.567 7.417 16178 Z= 0.300 Chirality : 0.043 0.146 1826 Planarity : 0.005 0.056 2098 Dihedral : 5.354 23.022 1630 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.05 % Allowed : 16.89 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.18), residues: 1486 helix: -3.49 (0.20), residues: 325 sheet: -2.85 (0.24), residues: 377 loop : -2.32 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.002 0.001 HIS B 54 PHE 0.016 0.001 PHE A 636 TYR 0.016 0.001 TYR A 822 ARG 0.003 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 1.253 Fit side-chains REVERT: A 46 ASP cc_start: 0.7919 (p0) cc_final: 0.7641 (p0) REVERT: A 58 ASN cc_start: 0.8484 (p0) cc_final: 0.8224 (p0) REVERT: A 173 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7912 (tppt) REVERT: A 215 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7415 (ttp-170) REVERT: A 236 LYS cc_start: 0.7776 (tptt) cc_final: 0.7509 (mttp) REVERT: A 252 GLN cc_start: 0.8276 (mt0) cc_final: 0.8061 (mt0) REVERT: A 283 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 290 GLN cc_start: 0.7596 (mt0) cc_final: 0.7332 (mt0) REVERT: A 374 GLU cc_start: 0.8156 (pm20) cc_final: 0.7798 (pm20) REVERT: A 439 ILE cc_start: 0.8635 (pt) cc_final: 0.8356 (mt) REVERT: A 577 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 736 GLN cc_start: 0.8659 (mp10) cc_final: 0.8312 (mp10) REVERT: A 870 ASP cc_start: 0.8100 (t0) cc_final: 0.7684 (t0) REVERT: B 12 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7505 (tm-30) REVERT: B 45 MET cc_start: 0.7828 (mtm) cc_final: 0.7488 (mtm) REVERT: B 325 MET cc_start: 0.7148 (mmp) cc_final: 0.6417 (mtp) REVERT: C 78 LYS cc_start: 0.8129 (tttm) cc_final: 0.7825 (mtpp) REVERT: C 82 TRP cc_start: 0.8511 (m100) cc_final: 0.8265 (m100) REVERT: C 156 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6929 (mm-40) REVERT: C 188 MET cc_start: 0.7914 (mmm) cc_final: 0.7666 (mmm) REVERT: C 234 PHE cc_start: 0.7855 (m-80) cc_final: 0.7564 (m-80) REVERT: C 312 ASP cc_start: 0.7160 (p0) cc_final: 0.6953 (p0) REVERT: D 44 HIS cc_start: 0.7809 (m-70) cc_final: 0.7569 (m-70) outliers start: 26 outliers final: 19 residues processed: 231 average time/residue: 0.2733 time to fit residues: 90.2150 Evaluate side-chains 212 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 HIS A 830 ASN A 871 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 11939 Z= 0.465 Angle : 0.666 9.690 16178 Z= 0.346 Chirality : 0.047 0.152 1826 Planarity : 0.005 0.062 2098 Dihedral : 5.523 26.707 1630 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.79 % Allowed : 19.97 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.19), residues: 1486 helix: -2.77 (0.23), residues: 324 sheet: -2.81 (0.24), residues: 370 loop : -2.22 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 169 HIS 0.007 0.001 HIS A 808 PHE 0.027 0.002 PHE A 636 TYR 0.020 0.002 TYR A 692 ARG 0.004 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 189 time to evaluate : 1.413 Fit side-chains REVERT: A 46 ASP cc_start: 0.8184 (p0) cc_final: 0.7877 (p0) REVERT: A 58 ASN cc_start: 0.8530 (p0) cc_final: 0.8208 (p0) REVERT: A 173 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7994 (tppt) REVERT: A 215 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7556 (ttp80) REVERT: A 236 LYS cc_start: 0.8138 (tptt) cc_final: 0.7603 (mttp) REVERT: A 374 GLU cc_start: 0.8171 (pm20) cc_final: 0.7802 (pm20) REVERT: A 439 ILE cc_start: 0.8675 (pt) cc_final: 0.8402 (mt) REVERT: A 869 MET cc_start: 0.7815 (mmp) cc_final: 0.7022 (mmp) REVERT: A 870 ASP cc_start: 0.8195 (t0) cc_final: 0.7748 (t0) REVERT: B 45 MET cc_start: 0.7954 (mtm) cc_final: 0.7523 (mtm) REVERT: B 325 MET cc_start: 0.7306 (mmp) cc_final: 0.6458 (mtp) REVERT: C 82 TRP cc_start: 0.8668 (m100) cc_final: 0.8365 (m100) REVERT: C 156 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6945 (mm-40) REVERT: C 253 PHE cc_start: 0.8339 (m-10) cc_final: 0.8058 (m-10) outliers start: 48 outliers final: 39 residues processed: 221 average time/residue: 0.2518 time to fit residues: 78.8695 Evaluate side-chains 220 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 757 ASP Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 830 ASN A 871 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11939 Z= 0.233 Angle : 0.554 9.174 16178 Z= 0.285 Chirality : 0.043 0.140 1826 Planarity : 0.004 0.059 2098 Dihedral : 4.951 24.613 1630 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.55 % Allowed : 22.26 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.19), residues: 1486 helix: -2.21 (0.25), residues: 324 sheet: -2.58 (0.25), residues: 371 loop : -2.07 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS A 379 PHE 0.018 0.001 PHE B 199 TYR 0.013 0.001 TYR A 692 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7966 (p0) cc_final: 0.7692 (p0) REVERT: A 58 ASN cc_start: 0.8548 (p0) cc_final: 0.8232 (p0) REVERT: A 121 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7257 (ttt) REVERT: A 125 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7875 (t0) REVERT: A 173 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7912 (tppt) REVERT: A 215 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7462 (ttp-170) REVERT: A 236 LYS cc_start: 0.8027 (tptt) cc_final: 0.7558 (mttp) REVERT: A 263 LEU cc_start: 0.8759 (tt) cc_final: 0.8203 (mm) REVERT: A 374 GLU cc_start: 0.8026 (pm20) cc_final: 0.7153 (pm20) REVERT: A 391 ASP cc_start: 0.7638 (m-30) cc_final: 0.7431 (t0) REVERT: A 460 MET cc_start: 0.8181 (ttp) cc_final: 0.7880 (ttm) REVERT: A 577 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7252 (mm-30) REVERT: A 870 ASP cc_start: 0.8117 (t0) cc_final: 0.7663 (t0) REVERT: B 45 MET cc_start: 0.7803 (mtm) cc_final: 0.7483 (mtm) REVERT: B 325 MET cc_start: 0.7270 (mmp) cc_final: 0.6607 (mtp) REVERT: C 156 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6915 (mm-40) REVERT: C 253 PHE cc_start: 0.8209 (m-10) cc_final: 0.7953 (m-10) REVERT: D 14 LYS cc_start: 0.8492 (tmtt) cc_final: 0.7974 (ttmt) outliers start: 45 outliers final: 32 residues processed: 238 average time/residue: 0.2355 time to fit residues: 79.8384 Evaluate side-chains 231 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 99 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN A 871 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11939 Z= 0.274 Angle : 0.566 9.912 16178 Z= 0.288 Chirality : 0.044 0.138 1826 Planarity : 0.004 0.062 2098 Dihedral : 4.886 26.635 1630 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.34 % Allowed : 22.65 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.20), residues: 1486 helix: -1.90 (0.26), residues: 324 sheet: -2.52 (0.25), residues: 372 loop : -1.97 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS A 808 PHE 0.019 0.002 PHE B 199 TYR 0.014 0.001 TYR A 692 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7945 (p0) cc_final: 0.7666 (p0) REVERT: A 121 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7201 (ttt) REVERT: A 173 LYS cc_start: 0.8420 (ttpt) cc_final: 0.7947 (tppt) REVERT: A 236 LYS cc_start: 0.8085 (tptt) cc_final: 0.7564 (mttp) REVERT: A 252 GLN cc_start: 0.8154 (mt0) cc_final: 0.7570 (mt0) REVERT: A 374 GLU cc_start: 0.8055 (pm20) cc_final: 0.7505 (pm20) REVERT: A 460 MET cc_start: 0.8223 (ttp) cc_final: 0.7898 (ttm) REVERT: A 577 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7301 (mm-30) REVERT: A 869 MET cc_start: 0.7698 (mmp) cc_final: 0.6947 (mmp) REVERT: A 870 ASP cc_start: 0.8111 (t0) cc_final: 0.7699 (t0) REVERT: B 45 MET cc_start: 0.7815 (mtm) cc_final: 0.7303 (mtm) REVERT: B 325 MET cc_start: 0.7296 (mmp) cc_final: 0.6602 (mtp) REVERT: G 38 MET cc_start: 0.8292 (mmm) cc_final: 0.8051 (tpp) REVERT: C 13 GLN cc_start: 0.8720 (tt0) cc_final: 0.8435 (pt0) REVERT: C 82 TRP cc_start: 0.8648 (m100) cc_final: 0.8260 (m-10) REVERT: C 188 MET cc_start: 0.8078 (mmm) cc_final: 0.7755 (mmt) REVERT: C 253 PHE cc_start: 0.8218 (m-10) cc_final: 0.7946 (m-10) REVERT: D 44 HIS cc_start: 0.7648 (m90) cc_final: 0.6989 (m90) outliers start: 55 outliers final: 44 residues processed: 233 average time/residue: 0.2398 time to fit residues: 79.6990 Evaluate side-chains 233 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 144 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN B 239 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11939 Z= 0.217 Angle : 0.541 8.464 16178 Z= 0.275 Chirality : 0.043 0.151 1826 Planarity : 0.004 0.061 2098 Dihedral : 4.641 25.167 1630 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.03 % Allowed : 23.99 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.20), residues: 1486 helix: -1.59 (0.27), residues: 329 sheet: -2.43 (0.25), residues: 376 loop : -1.76 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.002 0.001 HIS A 379 PHE 0.018 0.001 PHE A 381 TYR 0.013 0.001 TYR G 40 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 197 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7837 (p0) cc_final: 0.7562 (p0) REVERT: A 104 MET cc_start: 0.8050 (ttt) cc_final: 0.7782 (ttt) REVERT: A 121 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7128 (ttt) REVERT: A 173 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7926 (tppt) REVERT: A 215 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7437 (ttp80) REVERT: A 236 LYS cc_start: 0.8017 (tptt) cc_final: 0.7535 (mttp) REVERT: A 252 GLN cc_start: 0.8138 (mt0) cc_final: 0.7635 (mt0) REVERT: A 374 GLU cc_start: 0.8040 (pm20) cc_final: 0.7161 (pm20) REVERT: A 577 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 870 ASP cc_start: 0.8035 (t0) cc_final: 0.7684 (t0) REVERT: B 45 MET cc_start: 0.7805 (mtm) cc_final: 0.7449 (mtm) REVERT: B 325 MET cc_start: 0.7212 (mmp) cc_final: 0.6582 (mtp) REVERT: C 13 GLN cc_start: 0.8762 (tt0) cc_final: 0.8488 (pt0) REVERT: C 82 TRP cc_start: 0.8592 (m100) cc_final: 0.8204 (m-10) REVERT: C 188 MET cc_start: 0.8090 (mmm) cc_final: 0.7810 (mmt) REVERT: C 220 GLN cc_start: 0.7613 (mp-120) cc_final: 0.7284 (mp10) REVERT: C 253 PHE cc_start: 0.8165 (m-10) cc_final: 0.7864 (m-10) REVERT: C 318 LEU cc_start: 0.8995 (tt) cc_final: 0.8782 (tt) REVERT: D 14 LYS cc_start: 0.8452 (tmtt) cc_final: 0.8009 (ttmt) REVERT: D 44 HIS cc_start: 0.7569 (m90) cc_final: 0.6939 (m90) outliers start: 51 outliers final: 38 residues processed: 231 average time/residue: 0.2556 time to fit residues: 84.5162 Evaluate side-chains 229 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 121 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN B 13 GLN B 156 GLN C 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11939 Z= 0.135 Angle : 0.509 9.367 16178 Z= 0.258 Chirality : 0.042 0.265 1826 Planarity : 0.003 0.060 2098 Dihedral : 4.245 28.547 1630 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.60 % Allowed : 25.81 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.21), residues: 1486 helix: -1.17 (0.28), residues: 329 sheet: -2.20 (0.25), residues: 372 loop : -1.57 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.003 0.001 HIS A 379 PHE 0.015 0.001 PHE A 381 TYR 0.015 0.001 TYR G 40 ARG 0.008 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7519 (p0) cc_final: 0.7258 (p0) REVERT: A 173 LYS cc_start: 0.8260 (ttpt) cc_final: 0.7798 (tppt) REVERT: A 236 LYS cc_start: 0.7895 (tptt) cc_final: 0.7470 (mttp) REVERT: A 374 GLU cc_start: 0.7880 (pm20) cc_final: 0.7369 (pm20) REVERT: A 577 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 585 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6569 (t0) REVERT: A 634 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7115 (mpp) REVERT: A 869 MET cc_start: 0.7251 (mmp) cc_final: 0.6647 (mmp) REVERT: B 45 MET cc_start: 0.7785 (mtm) cc_final: 0.7263 (mtm) REVERT: B 297 TRP cc_start: 0.8758 (m100) cc_final: 0.8248 (m100) REVERT: B 325 MET cc_start: 0.7188 (mmp) cc_final: 0.6558 (mtp) REVERT: G 44 HIS cc_start: 0.7176 (m-70) cc_final: 0.6939 (m-70) REVERT: C 13 GLN cc_start: 0.8790 (tt0) cc_final: 0.8552 (pt0) REVERT: C 82 TRP cc_start: 0.8537 (m100) cc_final: 0.8246 (m-10) REVERT: C 209 LYS cc_start: 0.6472 (mttt) cc_final: 0.6065 (mttt) REVERT: D 14 LYS cc_start: 0.8437 (tmtt) cc_final: 0.8054 (ttmt) REVERT: D 44 HIS cc_start: 0.7555 (m90) cc_final: 0.6983 (m90) outliers start: 33 outliers final: 27 residues processed: 224 average time/residue: 0.2487 time to fit residues: 78.9247 Evaluate side-chains 219 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 628 GLN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 11939 Z= 0.378 Angle : 0.614 8.753 16178 Z= 0.312 Chirality : 0.047 0.323 1826 Planarity : 0.004 0.063 2098 Dihedral : 4.728 26.461 1630 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.42 % Allowed : 24.31 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.21), residues: 1486 helix: -1.15 (0.28), residues: 329 sheet: -2.43 (0.25), residues: 382 loop : -1.67 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS A 808 PHE 0.022 0.002 PHE C 241 TYR 0.016 0.002 TYR A 692 ARG 0.007 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 185 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7978 (p0) cc_final: 0.7690 (p0) REVERT: A 173 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7953 (tppt) REVERT: A 215 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7494 (ttp80) REVERT: A 236 LYS cc_start: 0.8187 (tptt) cc_final: 0.7648 (mttp) REVERT: A 252 GLN cc_start: 0.7999 (mt0) cc_final: 0.7560 (mt0) REVERT: A 374 GLU cc_start: 0.8137 (pm20) cc_final: 0.7566 (pm20) REVERT: A 577 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7348 (mm-30) REVERT: B 45 MET cc_start: 0.7874 (mtm) cc_final: 0.7344 (mtm) REVERT: B 325 MET cc_start: 0.7340 (mmp) cc_final: 0.6633 (mtp) REVERT: G 38 MET cc_start: 0.8088 (mmm) cc_final: 0.7593 (mmm) REVERT: G 44 HIS cc_start: 0.7156 (m-70) cc_final: 0.6897 (m-70) REVERT: C 13 GLN cc_start: 0.8779 (tt0) cc_final: 0.8429 (pt0) REVERT: C 49 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7387 (mtt90) REVERT: C 82 TRP cc_start: 0.8651 (m100) cc_final: 0.8201 (m-10) REVERT: C 188 MET cc_start: 0.8045 (mmm) cc_final: 0.7667 (mmt) REVERT: D 14 LYS cc_start: 0.8487 (tmtt) cc_final: 0.8028 (ttmt) REVERT: D 44 HIS cc_start: 0.7620 (m90) cc_final: 0.7050 (m90) outliers start: 56 outliers final: 42 residues processed: 227 average time/residue: 0.2338 time to fit residues: 75.7520 Evaluate side-chains 219 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 176 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 757 ASP Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11939 Z= 0.183 Angle : 0.548 12.372 16178 Z= 0.275 Chirality : 0.043 0.261 1826 Planarity : 0.004 0.062 2098 Dihedral : 4.435 28.717 1630 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.31 % Allowed : 25.49 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.21), residues: 1486 helix: -0.86 (0.29), residues: 329 sheet: -2.17 (0.26), residues: 362 loop : -1.55 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.003 0.001 HIS B 54 PHE 0.022 0.001 PHE C 241 TYR 0.014 0.001 TYR G 40 ARG 0.008 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7709 (p0) cc_final: 0.7421 (p0) REVERT: A 173 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7864 (tppt) REVERT: A 215 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7402 (ttp80) REVERT: A 252 GLN cc_start: 0.7935 (mt0) cc_final: 0.7518 (mt0) REVERT: A 290 GLN cc_start: 0.7387 (mt0) cc_final: 0.7173 (mt0) REVERT: A 374 GLU cc_start: 0.7995 (pm20) cc_final: 0.7154 (pm20) REVERT: A 577 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 782 ASP cc_start: 0.7713 (p0) cc_final: 0.7421 (p0) REVERT: B 45 MET cc_start: 0.7822 (mtm) cc_final: 0.7378 (mtm) REVERT: B 297 TRP cc_start: 0.8812 (m100) cc_final: 0.8308 (m100) REVERT: B 325 MET cc_start: 0.7284 (mmp) cc_final: 0.6584 (mtp) REVERT: G 38 MET cc_start: 0.8044 (mmm) cc_final: 0.7594 (mmm) REVERT: G 44 HIS cc_start: 0.7101 (m-70) cc_final: 0.6832 (m-70) REVERT: C 49 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7394 (mtt90) REVERT: C 82 TRP cc_start: 0.8565 (m100) cc_final: 0.8168 (m-10) REVERT: C 188 MET cc_start: 0.8020 (mmm) cc_final: 0.7645 (mmt) REVERT: C 209 LYS cc_start: 0.6525 (mttt) cc_final: 0.6137 (mttt) REVERT: C 220 GLN cc_start: 0.7596 (mp10) cc_final: 0.7389 (mp10) REVERT: D 14 LYS cc_start: 0.8471 (tmtt) cc_final: 0.8036 (ttmt) REVERT: D 44 HIS cc_start: 0.7597 (m90) cc_final: 0.7074 (m90) outliers start: 42 outliers final: 36 residues processed: 220 average time/residue: 0.2593 time to fit residues: 80.5382 Evaluate side-chains 214 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 11939 Z= 0.467 Angle : 0.677 10.698 16178 Z= 0.344 Chirality : 0.049 0.310 1826 Planarity : 0.004 0.064 2098 Dihedral : 5.056 29.052 1630 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.87 % Allowed : 25.18 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.20), residues: 1486 helix: -0.96 (0.29), residues: 329 sheet: -2.46 (0.25), residues: 373 loop : -1.75 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.007 0.001 HIS A 808 PHE 0.024 0.002 PHE C 241 TYR 0.019 0.002 TYR A 692 ARG 0.008 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 171 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8124 (p0) cc_final: 0.7817 (p0) REVERT: A 173 LYS cc_start: 0.8392 (ttpt) cc_final: 0.7996 (tppt) REVERT: A 252 GLN cc_start: 0.7983 (mt0) cc_final: 0.7561 (mt0) REVERT: A 374 GLU cc_start: 0.8228 (pm20) cc_final: 0.7320 (pm20) REVERT: A 782 ASP cc_start: 0.7759 (p0) cc_final: 0.7401 (p0) REVERT: B 45 MET cc_start: 0.7903 (mtm) cc_final: 0.7448 (mtm) REVERT: B 325 MET cc_start: 0.7397 (mmp) cc_final: 0.6553 (mtp) REVERT: G 44 HIS cc_start: 0.7103 (m-70) cc_final: 0.6850 (m-70) REVERT: C 17 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7946 (mt0) REVERT: C 49 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7676 (mpt-90) REVERT: C 82 TRP cc_start: 0.8725 (m100) cc_final: 0.8247 (m-10) REVERT: C 188 MET cc_start: 0.8053 (mmm) cc_final: 0.7691 (mmt) REVERT: D 44 HIS cc_start: 0.7641 (m90) cc_final: 0.7122 (m90) outliers start: 49 outliers final: 43 residues processed: 207 average time/residue: 0.2431 time to fit residues: 72.2300 Evaluate side-chains 212 residues out of total 1292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114394 restraints weight = 17339.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118442 restraints weight = 9442.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121135 restraints weight = 6415.848| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11939 Z= 0.181 Angle : 0.558 11.787 16178 Z= 0.279 Chirality : 0.043 0.224 1826 Planarity : 0.004 0.059 2098 Dihedral : 4.501 31.025 1630 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.08 % Allowed : 25.89 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1486 helix: -0.72 (0.30), residues: 329 sheet: -2.22 (0.26), residues: 363 loop : -1.52 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.003 0.001 HIS B 54 PHE 0.021 0.001 PHE C 241 TYR 0.015 0.001 TYR G 40 ARG 0.009 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.08 seconds wall clock time: 47 minutes 17.76 seconds (2837.76 seconds total)