Starting phenix.real_space_refine on Sun Feb 18 05:21:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/02_2024/6o20_0607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/02_2024/6o20_0607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/02_2024/6o20_0607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/02_2024/6o20_0607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/02_2024/6o20_0607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/02_2024/6o20_0607.pdb" } resolution = 3.3 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 149 5.16 5 C 13497 2.51 5 N 3549 2.21 5 O 3751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 34": "OD1" <-> "OD2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A ASP 489": "OD1" <-> "OD2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 700": "NH1" <-> "NH2" Residue "E GLU 703": "OE1" <-> "OE2" Residue "E ARG 706": "NH1" <-> "NH2" Residue "E ARG 707": "NH1" <-> "NH2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 64": "OD1" <-> "OD2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ASP 356": "OD1" <-> "OD2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 382": "OD1" <-> "OD2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ASP 489": "OD1" <-> "OD2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 382": "OD1" <-> "OD2" Residue "C ASP 406": "OD1" <-> "OD2" Residue "C ASP 489": "OD1" <-> "OD2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ASP 356": "OD1" <-> "OD2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 382": "OD1" <-> "OD2" Residue "D ASP 406": "OD1" <-> "OD2" Residue "D ASP 489": "OD1" <-> "OD2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20950 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5009 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 601} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 115 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "F" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1125 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 145} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.43, per 1000 atoms: 0.50 Number of scatterers: 20950 At special positions: 0 Unit cell: (128.139, 128.139, 126.021, 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 4 19.99 S 149 16.00 O 3751 8.00 N 3549 7.00 C 13497 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: 8.29 Conformation dependent library (CDL) restraints added in 3.9 seconds 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4952 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 4 sheets defined 61.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.696A pdb=" N ARG A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.532A pdb=" N ASN A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.610A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 3.602A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.578A pdb=" N LEU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.731A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.688A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.707A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.662A pdb=" N ALA A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.813A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.773A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 261 through 264 removed outlier: 4.028A pdb=" N LYS A 264 " --> pdb=" O GLN A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.881A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.537A pdb=" N PHE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.821A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 403 removed outlier: 3.717A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.532A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.981A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.689A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 removed outlier: 4.073A pdb=" N MET A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.566A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 512 removed outlier: 4.192A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.639A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.718A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 561 " --> pdb=" O ILE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.607A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 removed outlier: 3.710A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 653 removed outlier: 4.342A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR A 647 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 651 " --> pdb=" O TYR A 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 710 removed outlier: 3.737A pdb=" N ILE E 704 " --> pdb=" O ARG E 700 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 705 " --> pdb=" O GLY E 701 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR E 709 " --> pdb=" O LEU E 705 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 710 " --> pdb=" O ARG E 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.739A pdb=" N ALA F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.784A pdb=" N VAL F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 39 " --> pdb=" O VAL F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 53 Processing helix chain 'F' and resid 64 through 75 removed outlier: 3.669A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET F 72 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 removed outlier: 3.913A pdb=" N ARG F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 113 removed outlier: 3.640A pdb=" N MET F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN F 111 " --> pdb=" O HIS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.697A pdb=" N ARG B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.532A pdb=" N ASN B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.611A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.602A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.578A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.730A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.688A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.707A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.662A pdb=" N ALA B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.813A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.774A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 261 through 264 removed outlier: 4.029A pdb=" N LYS B 264 " --> pdb=" O GLN B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.881A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 removed outlier: 3.537A pdb=" N PHE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 349 removed outlier: 3.821A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 403 removed outlier: 3.718A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.533A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 425 through 443 removed outlier: 3.980A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.689A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 removed outlier: 4.073A pdb=" N MET B 466 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.565A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 512 removed outlier: 4.192A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.638A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.718A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 581 removed outlier: 3.608A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 608 removed outlier: 3.709A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.697A pdb=" N ARG C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.532A pdb=" N ASN C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.611A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 removed outlier: 3.602A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.578A pdb=" N LEU C 105 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.730A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.687A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.707A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.662A pdb=" N ALA C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.813A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.773A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 261 through 264 removed outlier: 4.028A pdb=" N LYS C 264 " --> pdb=" O GLN C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.881A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.537A pdb=" N PHE C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 349 removed outlier: 3.821A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 403 removed outlier: 3.718A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.532A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 409' Processing helix chain 'C' and resid 425 through 443 removed outlier: 3.980A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.689A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 removed outlier: 4.073A pdb=" N MET C 466 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.566A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 512 removed outlier: 4.192A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.639A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.718A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 581 removed outlier: 3.607A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 608 removed outlier: 3.710A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.696A pdb=" N ARG D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.532A pdb=" N ASN D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.610A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.602A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.577A pdb=" N LEU D 105 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.730A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.688A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.707A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.662A pdb=" N ALA D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.813A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.773A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 261 through 264 removed outlier: 4.029A pdb=" N LYS D 264 " --> pdb=" O GLN D 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.881A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 323 removed outlier: 3.537A pdb=" N PHE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 349 removed outlier: 3.822A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 403 removed outlier: 3.717A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 398 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 399 " --> pdb=" O GLY D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 4.532A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 409' Processing helix chain 'D' and resid 425 through 443 removed outlier: 3.981A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.689A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 removed outlier: 4.073A pdb=" N MET D 466 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 3.565A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 512 removed outlier: 4.191A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.639A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.718A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 561 " --> pdb=" O ILE D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 581 removed outlier: 3.607A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 608 removed outlier: 3.710A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 278 Processing sheet with id=AA2, first strand: chain 'B' and resid 273 through 278 Processing sheet with id=AA3, first strand: chain 'C' and resid 273 through 278 Processing sheet with id=AA4, first strand: chain 'D' and resid 273 through 278 871 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 9.04 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: 5506 1.33 - 1.45: 4024 1.45 - 1.57: 11643 1.57 - 1.69: 0 1.69 - 1.81: 246 Bond restraints: 21419 Sorted by residual: bond pdb=" CA LYS F 30 " pdb=" C LYS F 30 " ideal model delta sigma weight residual 1.522 1.456 0.065 1.32e-02 5.74e+03 2.45e+01 bond pdb=" C VAL D 452 " pdb=" N PRO D 453 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.06e-02 8.90e+03 5.63e+00 bond pdb=" C VAL B 452 " pdb=" N PRO B 453 " ideal model delta sigma weight residual 1.337 1.361 -0.025 1.06e-02 8.90e+03 5.41e+00 bond pdb=" C VAL C 452 " pdb=" N PRO C 453 " ideal model delta sigma weight residual 1.337 1.361 -0.025 1.06e-02 8.90e+03 5.36e+00 bond pdb=" C VAL A 452 " pdb=" N PRO A 453 " ideal model delta sigma weight residual 1.337 1.361 -0.024 1.06e-02 8.90e+03 5.30e+00 ... (remaining 21414 not shown) Histogram of bond angle deviations from ideal: 94.53 - 102.44: 114 102.44 - 110.34: 5434 110.34 - 118.25: 10701 118.25 - 126.16: 12441 126.16 - 134.07: 383 Bond angle restraints: 29073 Sorted by residual: angle pdb=" N MET F 76 " pdb=" CA MET F 76 " pdb=" C MET F 76 " ideal model delta sigma weight residual 111.24 94.53 16.71 1.38e+00 5.25e-01 1.47e+02 angle pdb=" N ILE A 420 " pdb=" CA ILE A 420 " pdb=" C ILE A 420 " ideal model delta sigma weight residual 111.56 106.01 5.55 8.60e-01 1.35e+00 4.16e+01 angle pdb=" N ILE D 420 " pdb=" CA ILE D 420 " pdb=" C ILE D 420 " ideal model delta sigma weight residual 111.56 106.02 5.54 8.60e-01 1.35e+00 4.15e+01 angle pdb=" N ILE C 420 " pdb=" CA ILE C 420 " pdb=" C ILE C 420 " ideal model delta sigma weight residual 111.56 106.03 5.53 8.60e-01 1.35e+00 4.13e+01 angle pdb=" N ILE B 420 " pdb=" CA ILE B 420 " pdb=" C ILE B 420 " ideal model delta sigma weight residual 111.56 106.04 5.52 8.60e-01 1.35e+00 4.12e+01 ... (remaining 29068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11237 17.97 - 35.94: 1225 35.94 - 53.92: 237 53.92 - 71.89: 31 71.89 - 89.86: 28 Dihedral angle restraints: 12758 sinusoidal: 5097 harmonic: 7661 Sorted by residual: dihedral pdb=" CA ASN F 60 " pdb=" C ASN F 60 " pdb=" N GLY F 61 " pdb=" CA GLY F 61 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR B 623 " pdb=" C TYR B 623 " pdb=" N GLY B 624 " pdb=" CA GLY B 624 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TYR A 623 " pdb=" C TYR A 623 " pdb=" N GLY A 624 " pdb=" CA GLY A 624 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 12755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3054 0.097 - 0.194: 229 0.194 - 0.291: 21 0.291 - 0.388: 1 0.388 - 0.485: 2 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CB VAL F 136 " pdb=" CA VAL F 136 " pdb=" CG1 VAL F 136 " pdb=" CG2 VAL F 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA SER F 101 " pdb=" N SER F 101 " pdb=" C SER F 101 " pdb=" CB SER F 101 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA MET F 76 " pdb=" N MET F 76 " pdb=" C MET F 76 " pdb=" CB MET F 76 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 3304 not shown) Planarity restraints: 3701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 99 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C TYR F 99 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR F 99 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE F 100 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 526 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO D 527 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 526 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 527 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.037 5.00e-02 4.00e+02 ... (remaining 3698 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 186 2.59 - 3.17: 16764 3.17 - 3.75: 32201 3.75 - 4.32: 45455 4.32 - 4.90: 73626 Nonbonded interactions: 168232 Sorted by model distance: nonbonded pdb=" NH1 ARG C 632 " pdb=" OD1 ASP D 34 " model vdw 2.014 2.520 nonbonded pdb=" OE1 GLU C 403 " pdb=" OH TYR C 415 " model vdw 2.021 2.440 nonbonded pdb=" OE1 GLU D 403 " pdb=" OH TYR D 415 " model vdw 2.022 2.440 nonbonded pdb=" OE1 GLU A 403 " pdb=" OH TYR A 415 " model vdw 2.022 2.440 nonbonded pdb=" OE1 GLU B 403 " pdb=" OH TYR B 415 " model vdw 2.022 2.440 ... (remaining 168227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 638) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.000 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 53.700 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.080 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 0.065 21419 Z= 0.524 Angle : 1.090 16.713 29073 Z= 0.603 Chirality : 0.058 0.485 3307 Planarity : 0.007 0.065 3701 Dihedral : 15.646 89.860 7806 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 0.40 % Allowed : 10.93 % Favored : 88.67 % Cbeta Deviations : 0.04 % 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: -5.94 (0.11), residues: 2612 helix: -4.42 (0.06), residues: 1527 sheet: -3.92 (0.42), residues: 76 loop : -2.79 (0.16), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 613 HIS 0.005 0.001 HIS B 122 PHE 0.015 0.002 PHE B 115 TYR 0.014 0.002 TYR D 621 ARG 0.007 0.001 ARG E 700 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 787 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8255 (mmm-85) REVERT: A 99 MET cc_start: 0.7439 (mtp) cc_final: 0.7196 (mtt) REVERT: A 126 MET cc_start: 0.8287 (mmm) cc_final: 0.7917 (mtm) REVERT: A 162 TYR cc_start: 0.8482 (m-10) cc_final: 0.8125 (m-10) REVERT: A 164 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7660 (mt-10) REVERT: A 188 ASP cc_start: 0.7583 (p0) cc_final: 0.7318 (p0) REVERT: A 314 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8218 (tttp) REVERT: A 323 LYS cc_start: 0.8433 (tptp) cc_final: 0.7972 (tptt) REVERT: A 407 ILE cc_start: 0.8446 (mm) cc_final: 0.8162 (mt) REVERT: A 418 GLN cc_start: 0.7012 (tp-100) cc_final: 0.6294 (tp-100) REVERT: A 442 MET cc_start: 0.8450 (mmm) cc_final: 0.8210 (mmt) REVERT: A 485 MET cc_start: 0.7724 (mmt) cc_final: 0.7087 (mmt) REVERT: A 522 GLU cc_start: 0.8538 (mp0) cc_final: 0.8055 (mp0) REVERT: A 553 PHE cc_start: 0.6984 (t80) cc_final: 0.6261 (p90) REVERT: A 637 HIS cc_start: 0.7654 (p-80) cc_final: 0.7267 (p90) REVERT: F 71 MET cc_start: 0.7441 (tpp) cc_final: 0.7188 (tpp) REVERT: F 75 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7278 (mmtp) REVERT: F 86 ARG cc_start: 0.7179 (ttt-90) cc_final: 0.6925 (ttp-170) REVERT: F 118 ASP cc_start: 0.8199 (t0) cc_final: 0.7960 (t0) REVERT: F 123 GLU cc_start: 0.7794 (tp30) cc_final: 0.7589 (tp30) REVERT: F 135 GLN cc_start: 0.8855 (mp10) cc_final: 0.8530 (mp10) REVERT: F 139 GLU cc_start: 0.7937 (tp30) cc_final: 0.7638 (tp30) REVERT: F 144 MET cc_start: 0.8193 (mmm) cc_final: 0.7755 (mpp) REVERT: B 46 ASP cc_start: 0.7511 (t0) cc_final: 0.7105 (t70) REVERT: B 129 ASN cc_start: 0.9009 (t0) cc_final: 0.8578 (t0) REVERT: B 214 GLN cc_start: 0.8249 (tt0) cc_final: 0.7993 (tm-30) REVERT: B 323 LYS cc_start: 0.8357 (tptp) cc_final: 0.8056 (tppt) REVERT: B 330 CYS cc_start: 0.8281 (m) cc_final: 0.8061 (m) REVERT: B 369 GLN cc_start: 0.7562 (pt0) cc_final: 0.7136 (tt0) REVERT: B 389 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6194 (mt-10) REVERT: B 420 ILE cc_start: 0.8281 (mt) cc_final: 0.8039 (tt) REVERT: B 451 VAL cc_start: 0.9156 (p) cc_final: 0.8938 (t) REVERT: B 474 MET cc_start: 0.7971 (ttp) cc_final: 0.7769 (ttm) REVERT: B 522 GLU cc_start: 0.8000 (mp0) cc_final: 0.7315 (mp0) REVERT: B 623 TYR cc_start: 0.7470 (m-80) cc_final: 0.7085 (m-80) REVERT: C 43 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7372 (mmm-85) REVERT: C 97 LEU cc_start: 0.7438 (mm) cc_final: 0.7030 (mm) REVERT: C 126 MET cc_start: 0.7860 (mmm) cc_final: 0.7628 (mtp) REVERT: C 160 ILE cc_start: 0.8860 (pt) cc_final: 0.8363 (pt) REVERT: C 258 HIS cc_start: 0.8314 (t-90) cc_final: 0.7848 (t-170) REVERT: C 323 LYS cc_start: 0.7967 (tptp) cc_final: 0.7545 (mptt) REVERT: C 328 TYR cc_start: 0.8173 (m-10) cc_final: 0.7846 (m-10) REVERT: C 340 MET cc_start: 0.8595 (mmm) cc_final: 0.8204 (tpp) REVERT: C 365 ILE cc_start: 0.7676 (mt) cc_final: 0.7249 (pt) REVERT: C 383 ASN cc_start: 0.8308 (m-40) cc_final: 0.8003 (m-40) REVERT: C 386 LEU cc_start: 0.8554 (tp) cc_final: 0.8298 (tp) REVERT: C 389 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6775 (mt-10) REVERT: C 489 ASP cc_start: 0.7934 (t70) cc_final: 0.7666 (m-30) REVERT: C 515 GLU cc_start: 0.7960 (tp30) cc_final: 0.7589 (tp30) REVERT: C 516 ASP cc_start: 0.8348 (t0) cc_final: 0.8047 (t0) REVERT: C 546 ASN cc_start: 0.7969 (t0) cc_final: 0.7750 (t0) REVERT: C 570 MET cc_start: 0.8773 (tpp) cc_final: 0.8560 (mmm) REVERT: C 603 MET cc_start: 0.7919 (tmm) cc_final: 0.7531 (tmm) REVERT: C 611 PHE cc_start: 0.6660 (m-10) cc_final: 0.6008 (m-10) REVERT: C 612 LEU cc_start: 0.8815 (mp) cc_final: 0.8067 (mt) REVERT: D 61 LEU cc_start: 0.6952 (mt) cc_final: 0.6460 (mt) REVERT: D 100 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7298 (tt0) REVERT: D 216 TYR cc_start: 0.8075 (t80) cc_final: 0.7379 (t80) REVERT: D 255 MET cc_start: 0.7277 (mmm) cc_final: 0.6717 (mmm) REVERT: D 328 TYR cc_start: 0.8537 (m-10) cc_final: 0.8167 (m-10) REVERT: D 381 GLN cc_start: 0.7056 (mt0) cc_final: 0.6628 (tp40) REVERT: D 402 LEU cc_start: 0.8702 (mt) cc_final: 0.8461 (mt) REVERT: D 555 TYR cc_start: 0.8555 (t80) cc_final: 0.8111 (t80) REVERT: D 580 ASP cc_start: 0.8371 (t70) cc_final: 0.7752 (t0) REVERT: D 621 TYR cc_start: 0.5468 (p90) cc_final: 0.5116 (p90) REVERT: D 629 TRP cc_start: 0.8684 (m100) cc_final: 0.8438 (m100) outliers start: 9 outliers final: 3 residues processed: 791 average time/residue: 0.3355 time to fit residues: 396.2618 Evaluate side-chains 522 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 517 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 389 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 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 128 GLN A 158 ASN A 310 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS F 3 GLN F 135 GLN B 27 GLN B 158 ASN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS B 513 GLN B 519 ASN B 582 HIS B 636 HIS C 157 HIS C 158 ASN ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS D 27 GLN D 51 GLN D 128 GLN D 158 ASN D 265 HIS ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21419 Z= 0.191 Angle : 0.671 10.200 29073 Z= 0.336 Chirality : 0.041 0.166 3307 Planarity : 0.005 0.053 3701 Dihedral : 6.048 68.011 2871 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.67 % Allowed : 18.57 % Favored : 78.76 % 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: -3.76 (0.14), residues: 2612 helix: -2.50 (0.10), residues: 1500 sheet: -3.31 (0.46), residues: 76 loop : -2.16 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 29 HIS 0.004 0.001 HIS D 426 PHE 0.021 0.001 PHE D 319 TYR 0.016 0.001 TYR B 623 ARG 0.006 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 590 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8127 (mmm-85) REVERT: A 38 MET cc_start: 0.8896 (mtp) cc_final: 0.8494 (mtp) REVERT: A 126 MET cc_start: 0.8223 (mmm) cc_final: 0.7832 (mtm) REVERT: A 159 LEU cc_start: 0.9159 (mm) cc_final: 0.8933 (mm) REVERT: A 162 TYR cc_start: 0.8424 (m-10) cc_final: 0.8062 (m-10) REVERT: A 164 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7133 (mt-10) REVERT: A 181 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8031 (mp) REVERT: A 230 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: A 288 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 323 LYS cc_start: 0.8420 (tptp) cc_final: 0.7999 (tptt) REVERT: A 359 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6634 (ptt-90) REVERT: A 418 GLN cc_start: 0.7255 (tp-100) cc_final: 0.6239 (tp40) REVERT: A 442 MET cc_start: 0.8457 (mmm) cc_final: 0.8116 (mmt) REVERT: A 485 MET cc_start: 0.7990 (mmt) cc_final: 0.7758 (mmm) REVERT: A 486 ILE cc_start: 0.9223 (tt) cc_final: 0.8950 (tt) REVERT: A 522 GLU cc_start: 0.8530 (mp0) cc_final: 0.8127 (mp0) REVERT: A 553 PHE cc_start: 0.6724 (t80) cc_final: 0.6241 (p90) REVERT: A 637 HIS cc_start: 0.7572 (p-80) cc_final: 0.7246 (p90) REVERT: E 700 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.6857 (ptt90) REVERT: F 2 ASP cc_start: 0.6655 (t0) cc_final: 0.6363 (t0) REVERT: F 3 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6358 (pp30) REVERT: F 74 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6620 (ttt180) REVERT: F 75 LYS cc_start: 0.7461 (mmtt) cc_final: 0.7195 (mmmt) REVERT: F 109 MET cc_start: 0.9214 (mmt) cc_final: 0.8685 (mmt) REVERT: F 114 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7461 (mt-10) REVERT: F 123 GLU cc_start: 0.7307 (tp30) cc_final: 0.7012 (tp30) REVERT: F 135 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8115 (mp-120) REVERT: F 139 GLU cc_start: 0.7884 (tp30) cc_final: 0.7005 (tp30) REVERT: F 144 MET cc_start: 0.8272 (mmm) cc_final: 0.8061 (tpp) REVERT: B 99 MET cc_start: 0.8027 (mtm) cc_final: 0.7684 (mtm) REVERT: B 195 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8201 (tt) REVERT: B 442 MET cc_start: 0.8967 (mmm) cc_final: 0.8709 (mmm) REVERT: C 43 ARG cc_start: 0.8303 (mmt180) cc_final: 0.7810 (mmm-85) REVERT: C 97 LEU cc_start: 0.7419 (mm) cc_final: 0.6924 (mt) REVERT: C 126 MET cc_start: 0.7827 (mmm) cc_final: 0.7441 (mtm) REVERT: C 160 ILE cc_start: 0.8858 (pt) cc_final: 0.8611 (pt) REVERT: C 161 TYR cc_start: 0.8549 (t80) cc_final: 0.7654 (t80) REVERT: C 215 MET cc_start: 0.8154 (tpp) cc_final: 0.7830 (tpp) REVERT: C 242 THR cc_start: 0.8849 (m) cc_final: 0.8621 (t) REVERT: C 380 HIS cc_start: 0.7960 (t70) cc_final: 0.7657 (t70) REVERT: C 386 LEU cc_start: 0.8442 (tp) cc_final: 0.8145 (tp) REVERT: C 389 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: C 497 MET cc_start: 0.8252 (mmp) cc_final: 0.7974 (mmt) REVERT: C 515 GLU cc_start: 0.8032 (tp30) cc_final: 0.7721 (tp30) REVERT: C 516 ASP cc_start: 0.8420 (t0) cc_final: 0.8107 (t0) REVERT: C 525 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6746 (m-30) REVERT: C 546 ASN cc_start: 0.7960 (t0) cc_final: 0.7661 (t0) REVERT: C 611 PHE cc_start: 0.6644 (m-10) cc_final: 0.5993 (m-10) REVERT: C 612 LEU cc_start: 0.8879 (mp) cc_final: 0.8132 (mt) REVERT: D 61 LEU cc_start: 0.6883 (mt) cc_final: 0.6283 (mt) REVERT: D 104 GLU cc_start: 0.7878 (pm20) cc_final: 0.6934 (tp30) REVERT: D 216 TYR cc_start: 0.8084 (t80) cc_final: 0.7379 (t80) REVERT: D 233 GLU cc_start: 0.7228 (tt0) cc_final: 0.6864 (tt0) REVERT: D 255 MET cc_start: 0.7404 (mmm) cc_final: 0.7046 (mmm) REVERT: D 354 LEU cc_start: 0.7679 (tt) cc_final: 0.7270 (mt) REVERT: D 381 GLN cc_start: 0.6856 (mt0) cc_final: 0.6263 (tm-30) REVERT: D 553 PHE cc_start: 0.7376 (t80) cc_final: 0.6358 (p90) REVERT: D 580 ASP cc_start: 0.8199 (t70) cc_final: 0.7831 (t0) REVERT: D 591 GLU cc_start: 0.8185 (pt0) cc_final: 0.7959 (pt0) REVERT: D 618 ILE cc_start: 0.8419 (mp) cc_final: 0.8183 (mm) outliers start: 60 outliers final: 29 residues processed: 626 average time/residue: 0.3195 time to fit residues: 306.7688 Evaluate side-chains 524 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 485 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 451 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 196 optimal weight: 0.0970 chunk 160 optimal weight: 6.9990 chunk 65 optimal weight: 0.0980 chunk 236 optimal weight: 7.9990 chunk 255 optimal weight: 0.3980 chunk 210 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 197 ASN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 60 ASN F 135 GLN B 91 ASN B 118 GLN B 128 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 257 GLN D 265 HIS D 310 GLN D 418 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21419 Z= 0.242 Angle : 0.642 9.711 29073 Z= 0.321 Chirality : 0.042 0.171 3307 Planarity : 0.004 0.055 3701 Dihedral : 5.140 64.844 2863 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 4.40 % Allowed : 19.41 % Favored : 76.19 % 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: -2.40 (0.15), residues: 2612 helix: -1.20 (0.12), residues: 1495 sheet: -3.13 (0.45), residues: 82 loop : -1.89 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 29 HIS 0.012 0.001 HIS D 509 PHE 0.018 0.001 PHE D 319 TYR 0.021 0.002 TYR A 621 ARG 0.006 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 502 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8446 (mtt180) cc_final: 0.8149 (mmm-85) REVERT: A 126 MET cc_start: 0.8323 (mmm) cc_final: 0.7891 (mtm) REVERT: A 159 LEU cc_start: 0.9176 (mm) cc_final: 0.8902 (mm) REVERT: A 162 TYR cc_start: 0.8447 (m-10) cc_final: 0.8181 (m-10) REVERT: A 164 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7514 (mt-10) REVERT: A 181 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 188 ASP cc_start: 0.7476 (p0) cc_final: 0.7231 (p0) REVERT: A 296 VAL cc_start: 0.9007 (p) cc_final: 0.8768 (p) REVERT: A 323 LYS cc_start: 0.8416 (tptp) cc_final: 0.8005 (tptt) REVERT: A 359 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6540 (ptt-90) REVERT: A 382 ASP cc_start: 0.7106 (m-30) cc_final: 0.6694 (m-30) REVERT: A 418 GLN cc_start: 0.7327 (tp-100) cc_final: 0.6769 (tp40) REVERT: A 442 MET cc_start: 0.8495 (mmm) cc_final: 0.8295 (mmt) REVERT: A 486 ILE cc_start: 0.9242 (tt) cc_final: 0.8948 (tt) REVERT: A 497 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: A 522 GLU cc_start: 0.8562 (mp0) cc_final: 0.8137 (mp0) REVERT: A 525 ASP cc_start: 0.7312 (t0) cc_final: 0.7071 (t0) REVERT: A 553 PHE cc_start: 0.6631 (t80) cc_final: 0.6166 (p90) REVERT: A 637 HIS cc_start: 0.7611 (p-80) cc_final: 0.7311 (p90) REVERT: E 703 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6571 (mm-30) REVERT: F 2 ASP cc_start: 0.6992 (t0) cc_final: 0.6544 (t0) REVERT: F 74 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6567 (ttt180) REVERT: F 75 LYS cc_start: 0.7754 (mmtt) cc_final: 0.6999 (mmtp) REVERT: F 76 MET cc_start: 0.6757 (mmp) cc_final: 0.6491 (mmm) REVERT: F 139 GLU cc_start: 0.7950 (tp30) cc_final: 0.7102 (tp30) REVERT: B 126 MET cc_start: 0.7772 (ttm) cc_final: 0.7556 (ttm) REVERT: B 195 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8240 (tt) REVERT: B 214 GLN cc_start: 0.7968 (tp40) cc_final: 0.7730 (tp-100) REVERT: B 216 TYR cc_start: 0.8719 (t80) cc_final: 0.8459 (t80) REVERT: B 250 GLU cc_start: 0.7698 (tp30) cc_final: 0.7294 (tp30) REVERT: B 294 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7470 (tt0) REVERT: B 330 CYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8183 (m) REVERT: B 371 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7483 (ptpp) REVERT: C 43 ARG cc_start: 0.8332 (mmt180) cc_final: 0.7905 (mmm-85) REVERT: C 97 LEU cc_start: 0.7422 (mm) cc_final: 0.7003 (mm) REVERT: C 126 MET cc_start: 0.7974 (mmm) cc_final: 0.7655 (mtp) REVERT: C 181 LEU cc_start: 0.9008 (mm) cc_final: 0.8662 (mt) REVERT: C 328 TYR cc_start: 0.8121 (m-10) cc_final: 0.7530 (m-10) REVERT: C 340 MET cc_start: 0.8585 (mmm) cc_final: 0.7876 (tpp) REVERT: C 386 LEU cc_start: 0.8545 (tp) cc_final: 0.8244 (tp) REVERT: C 481 MET cc_start: 0.8185 (mmm) cc_final: 0.7855 (mmt) REVERT: C 546 ASN cc_start: 0.7987 (t0) cc_final: 0.7689 (t0) REVERT: C 554 MET cc_start: 0.7840 (tpp) cc_final: 0.7556 (tpp) REVERT: C 612 LEU cc_start: 0.8894 (mp) cc_final: 0.8430 (mt) REVERT: D 61 LEU cc_start: 0.6930 (mt) cc_final: 0.6170 (mt) REVERT: D 216 TYR cc_start: 0.8128 (t80) cc_final: 0.7463 (t80) REVERT: D 233 GLU cc_start: 0.7384 (tt0) cc_final: 0.6992 (tt0) REVERT: D 255 MET cc_start: 0.7457 (mmm) cc_final: 0.7122 (mmm) REVERT: D 301 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7261 (ttmm) REVERT: D 328 TYR cc_start: 0.8513 (m-10) cc_final: 0.8064 (m-10) REVERT: D 381 GLN cc_start: 0.6789 (mt0) cc_final: 0.6294 (tm-30) REVERT: D 553 PHE cc_start: 0.7595 (t80) cc_final: 0.6292 (p90) REVERT: D 580 ASP cc_start: 0.8183 (t70) cc_final: 0.7809 (t0) REVERT: D 591 GLU cc_start: 0.8319 (pt0) cc_final: 0.8118 (pt0) REVERT: D 618 ILE cc_start: 0.8532 (mp) cc_final: 0.8228 (mm) outliers start: 99 outliers final: 63 residues processed: 561 average time/residue: 0.3141 time to fit residues: 274.6823 Evaluate side-chains 531 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 461 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 237 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 67 optimal weight: 0.0020 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 265 HIS D 267 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21419 Z= 0.173 Angle : 0.593 9.021 29073 Z= 0.293 Chirality : 0.040 0.166 3307 Planarity : 0.004 0.046 3701 Dihedral : 4.580 31.988 2860 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.36 % Favored : 93.61 % Rotamer: Outliers : 3.55 % Allowed : 21.68 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2612 helix: -0.38 (0.13), residues: 1492 sheet: -3.06 (0.47), residues: 82 loop : -1.66 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 29 HIS 0.012 0.001 HIS C 238 PHE 0.020 0.001 PHE D 319 TYR 0.026 0.001 TYR D 621 ARG 0.006 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 516 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9117 (mm) cc_final: 0.8879 (mm) REVERT: A 162 TYR cc_start: 0.8434 (m-10) cc_final: 0.8059 (m-10) REVERT: A 181 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7968 (mp) REVERT: A 188 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7190 (p0) REVERT: A 323 LYS cc_start: 0.8337 (tptp) cc_final: 0.7974 (tptt) REVERT: A 382 ASP cc_start: 0.7210 (m-30) cc_final: 0.6696 (m-30) REVERT: A 397 VAL cc_start: 0.9098 (p) cc_final: 0.8884 (p) REVERT: A 418 GLN cc_start: 0.7435 (tp40) cc_final: 0.6875 (tp40) REVERT: A 486 ILE cc_start: 0.9197 (tt) cc_final: 0.8891 (tt) REVERT: A 497 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7494 (tmm) REVERT: A 522 GLU cc_start: 0.8517 (mp0) cc_final: 0.8157 (mp0) REVERT: A 525 ASP cc_start: 0.7275 (t0) cc_final: 0.7013 (t0) REVERT: A 534 PHE cc_start: 0.8380 (t80) cc_final: 0.8076 (t80) REVERT: A 553 PHE cc_start: 0.6630 (t80) cc_final: 0.6118 (p90) REVERT: A 637 HIS cc_start: 0.7623 (p-80) cc_final: 0.7305 (p90) REVERT: E 700 ARG cc_start: 0.7550 (ttp-110) cc_final: 0.6713 (ptt90) REVERT: E 703 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6643 (mm-30) REVERT: F 2 ASP cc_start: 0.6913 (t0) cc_final: 0.6517 (t0) REVERT: F 74 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6639 (ttt180) REVERT: F 75 LYS cc_start: 0.7788 (mmtt) cc_final: 0.6885 (mptt) REVERT: F 76 MET cc_start: 0.6645 (mmp) cc_final: 0.6404 (mmm) REVERT: F 126 ARG cc_start: 0.8810 (ttm170) cc_final: 0.8583 (ttm-80) REVERT: F 139 GLU cc_start: 0.7867 (tp30) cc_final: 0.7097 (tp30) REVERT: F 144 MET cc_start: 0.8223 (tpp) cc_final: 0.7975 (tpp) REVERT: B 34 ASP cc_start: 0.7549 (m-30) cc_final: 0.7051 (m-30) REVERT: B 46 ASP cc_start: 0.7757 (m-30) cc_final: 0.7555 (m-30) REVERT: B 195 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8283 (tt) REVERT: B 250 GLU cc_start: 0.7706 (tp30) cc_final: 0.7500 (tp30) REVERT: B 294 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7489 (tt0) REVERT: B 330 CYS cc_start: 0.8509 (m) cc_final: 0.8209 (m) REVERT: B 371 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7307 (ptpp) REVERT: C 43 ARG cc_start: 0.8355 (mmt180) cc_final: 0.7929 (mmm-85) REVERT: C 97 LEU cc_start: 0.7431 (mm) cc_final: 0.7017 (mm) REVERT: C 181 LEU cc_start: 0.8995 (mm) cc_final: 0.8754 (mt) REVERT: C 250 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 311 THR cc_start: 0.8032 (t) cc_final: 0.7690 (t) REVERT: C 328 TYR cc_start: 0.8113 (m-10) cc_final: 0.7738 (m-10) REVERT: C 340 MET cc_start: 0.8479 (mmm) cc_final: 0.7779 (tpp) REVERT: C 386 LEU cc_start: 0.8526 (tp) cc_final: 0.8206 (tp) REVERT: C 485 MET cc_start: 0.7480 (mmm) cc_final: 0.7268 (mtt) REVERT: C 546 ASN cc_start: 0.7914 (t0) cc_final: 0.7606 (t0) REVERT: D 61 LEU cc_start: 0.6793 (mt) cc_final: 0.6048 (mt) REVERT: D 113 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7978 (tp30) REVERT: D 216 TYR cc_start: 0.8101 (t80) cc_final: 0.7544 (t80) REVERT: D 233 GLU cc_start: 0.7366 (tt0) cc_final: 0.7011 (tt0) REVERT: D 234 LEU cc_start: 0.8454 (mp) cc_final: 0.7989 (tt) REVERT: D 301 LYS cc_start: 0.7683 (ttmm) cc_final: 0.7271 (ttmm) REVERT: D 328 TYR cc_start: 0.8592 (m-10) cc_final: 0.8158 (m-80) REVERT: D 381 GLN cc_start: 0.6692 (mt0) cc_final: 0.6180 (tm-30) REVERT: D 553 PHE cc_start: 0.7550 (t80) cc_final: 0.6333 (p90) REVERT: D 580 ASP cc_start: 0.8144 (t70) cc_final: 0.7741 (t0) REVERT: D 591 GLU cc_start: 0.8167 (pt0) cc_final: 0.7964 (pt0) REVERT: D 603 MET cc_start: 0.8093 (tmm) cc_final: 0.7867 (tmm) outliers start: 80 outliers final: 46 residues processed: 568 average time/residue: 0.3116 time to fit residues: 276.2305 Evaluate side-chains 532 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 480 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 187 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 128 optimal weight: 0.0870 chunk 225 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 overall best weight: 3.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 637 HIS F 111 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 267 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21419 Z= 0.324 Angle : 0.679 8.954 29073 Z= 0.337 Chirality : 0.044 0.180 3307 Planarity : 0.004 0.049 3701 Dihedral : 4.797 46.822 2860 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.53 % Allowed : 22.48 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2612 helix: -0.09 (0.13), residues: 1518 sheet: -2.72 (0.53), residues: 77 loop : -1.61 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 29 HIS 0.005 0.001 HIS C 509 PHE 0.024 0.002 PHE D 319 TYR 0.024 0.002 TYR A 621 ARG 0.009 0.001 ARG D 589 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 493 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8795 (mtp) cc_final: 0.8552 (mtp) REVERT: A 126 MET cc_start: 0.8251 (mmm) cc_final: 0.7942 (mtm) REVERT: A 159 LEU cc_start: 0.9139 (mm) cc_final: 0.8835 (mm) REVERT: A 162 TYR cc_start: 0.8624 (m-10) cc_final: 0.8249 (m-10) REVERT: A 181 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8100 (mp) REVERT: A 188 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7087 (p0) REVERT: A 323 LYS cc_start: 0.8437 (tptp) cc_final: 0.7996 (tptt) REVERT: A 355 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5858 (tmm-80) REVERT: A 418 GLN cc_start: 0.7669 (tp40) cc_final: 0.7179 (tp40) REVERT: A 442 MET cc_start: 0.8610 (mmt) cc_final: 0.8110 (mmt) REVERT: A 486 ILE cc_start: 0.9233 (tt) cc_final: 0.8991 (tt) REVERT: A 497 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: A 522 GLU cc_start: 0.8542 (mp0) cc_final: 0.8192 (mp0) REVERT: A 534 PHE cc_start: 0.8431 (t80) cc_final: 0.8097 (t80) REVERT: A 553 PHE cc_start: 0.6779 (t80) cc_final: 0.6378 (p90) REVERT: A 637 HIS cc_start: 0.7587 (p90) cc_final: 0.7254 (p90) REVERT: E 703 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6541 (mm-30) REVERT: F 2 ASP cc_start: 0.7356 (t0) cc_final: 0.6907 (t0) REVERT: F 14 GLU cc_start: 0.7648 (tt0) cc_final: 0.7448 (tt0) REVERT: F 74 ARG cc_start: 0.7094 (mtm110) cc_final: 0.6625 (ttt180) REVERT: F 75 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7008 (mptt) REVERT: F 76 MET cc_start: 0.6678 (mmp) cc_final: 0.6431 (mmm) REVERT: F 139 GLU cc_start: 0.7918 (tp30) cc_final: 0.7008 (tp30) REVERT: F 144 MET cc_start: 0.8622 (tpp) cc_final: 0.8126 (tpp) REVERT: B 99 MET cc_start: 0.8297 (mtm) cc_final: 0.8010 (mtm) REVERT: B 190 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7482 (mtp180) REVERT: B 195 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8245 (tt) REVERT: B 250 GLU cc_start: 0.7902 (tp30) cc_final: 0.7680 (tp30) REVERT: B 294 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7534 (tt0) REVERT: B 330 CYS cc_start: 0.8541 (m) cc_final: 0.8239 (m) REVERT: B 371 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7586 (ptpp) REVERT: B 580 ASP cc_start: 0.8236 (t70) cc_final: 0.8034 (t0) REVERT: B 594 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7249 (mtm-85) REVERT: B 634 GLU cc_start: 0.7374 (pt0) cc_final: 0.7067 (pt0) REVERT: C 43 ARG cc_start: 0.8425 (mmt180) cc_final: 0.7930 (mmm-85) REVERT: C 80 GLU cc_start: 0.7047 (pm20) cc_final: 0.6821 (mt-10) REVERT: C 97 LEU cc_start: 0.7413 (mm) cc_final: 0.7003 (mm) REVERT: C 161 TYR cc_start: 0.8815 (t80) cc_final: 0.8523 (t80) REVERT: C 260 MET cc_start: 0.9038 (mmm) cc_final: 0.8654 (mmm) REVERT: C 328 TYR cc_start: 0.8257 (m-10) cc_final: 0.7886 (m-10) REVERT: C 381 GLN cc_start: 0.6993 (mm-40) cc_final: 0.6536 (mm-40) REVERT: C 386 LEU cc_start: 0.8623 (tp) cc_final: 0.8309 (tp) REVERT: C 537 PHE cc_start: 0.8957 (t80) cc_final: 0.8715 (t80) REVERT: C 546 ASN cc_start: 0.8130 (t0) cc_final: 0.7854 (t0) REVERT: C 570 MET cc_start: 0.9030 (tpp) cc_final: 0.8633 (mmm) REVERT: D 61 LEU cc_start: 0.6806 (mt) cc_final: 0.6007 (mt) REVERT: D 211 PHE cc_start: 0.7752 (m-80) cc_final: 0.7434 (m-80) REVERT: D 216 TYR cc_start: 0.8170 (t80) cc_final: 0.7395 (t80) REVERT: D 233 GLU cc_start: 0.7492 (tt0) cc_final: 0.7139 (tt0) REVERT: D 234 LEU cc_start: 0.8523 (mp) cc_final: 0.8265 (tt) REVERT: D 257 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8070 (tm-30) REVERT: D 301 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7411 (ttmm) REVERT: D 328 TYR cc_start: 0.8782 (m-10) cc_final: 0.8167 (m-80) REVERT: D 381 GLN cc_start: 0.7105 (mt0) cc_final: 0.6605 (tm-30) REVERT: D 415 TYR cc_start: 0.8026 (t80) cc_final: 0.7381 (t80) REVERT: D 591 GLU cc_start: 0.8289 (pt0) cc_final: 0.8033 (tt0) outliers start: 102 outliers final: 71 residues processed: 556 average time/residue: 0.3147 time to fit residues: 273.1306 Evaluate side-chains 544 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 467 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 619 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 8.9990 chunk 226 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN A 546 ASN A 572 ASN F 60 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 122 HIS B 129 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21419 Z= 0.245 Angle : 0.630 9.197 29073 Z= 0.311 Chirality : 0.042 0.172 3307 Planarity : 0.004 0.046 3701 Dihedral : 4.712 53.001 2860 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.66 % Favored : 93.30 % Rotamer: Outliers : 4.18 % Allowed : 23.55 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2612 helix: 0.26 (0.14), residues: 1527 sheet: -2.76 (0.52), residues: 77 loop : -1.46 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 29 HIS 0.011 0.001 HIS C 238 PHE 0.028 0.001 PHE D 319 TYR 0.021 0.002 TYR F 138 ARG 0.005 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 504 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8246 (mmm) cc_final: 0.7924 (mtm) REVERT: A 159 LEU cc_start: 0.9110 (mm) cc_final: 0.8837 (mm) REVERT: A 162 TYR cc_start: 0.8489 (m-10) cc_final: 0.8131 (m-10) REVERT: A 181 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 188 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7080 (p0) REVERT: A 340 MET cc_start: 0.8628 (tpp) cc_final: 0.8236 (tpp) REVERT: A 355 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5891 (tmm-80) REVERT: A 418 GLN cc_start: 0.7674 (tp40) cc_final: 0.7214 (tp40) REVERT: A 442 MET cc_start: 0.8550 (mmt) cc_final: 0.8090 (mmt) REVERT: A 486 ILE cc_start: 0.9193 (tt) cc_final: 0.8907 (tt) REVERT: A 497 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7508 (tmm) REVERT: A 522 GLU cc_start: 0.8452 (mp0) cc_final: 0.8196 (mp0) REVERT: A 534 PHE cc_start: 0.8371 (t80) cc_final: 0.8113 (t80) REVERT: A 553 PHE cc_start: 0.6720 (t80) cc_final: 0.6283 (p90) REVERT: A 637 HIS cc_start: 0.7556 (p90) cc_final: 0.7254 (p90) REVERT: E 703 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6624 (mm-30) REVERT: F 2 ASP cc_start: 0.7320 (t0) cc_final: 0.7089 (t0) REVERT: F 14 GLU cc_start: 0.7636 (tt0) cc_final: 0.7413 (tt0) REVERT: F 74 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6667 (ttt180) REVERT: F 75 LYS cc_start: 0.7803 (mmtt) cc_final: 0.6814 (mptt) REVERT: F 76 MET cc_start: 0.6682 (mmp) cc_final: 0.5471 (tmm) REVERT: F 139 GLU cc_start: 0.7868 (tp30) cc_final: 0.7143 (tp30) REVERT: F 143 GLN cc_start: 0.8569 (mt0) cc_final: 0.8300 (tt0) REVERT: F 144 MET cc_start: 0.8499 (tpp) cc_final: 0.8024 (tpp) REVERT: B 75 ARG cc_start: 0.6408 (mtt180) cc_final: 0.6160 (mmt90) REVERT: B 190 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7482 (mtp180) REVERT: B 195 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8243 (tt) REVERT: B 294 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7541 (tt0) REVERT: B 330 CYS cc_start: 0.8487 (m) cc_final: 0.8183 (m) REVERT: B 634 GLU cc_start: 0.7493 (pt0) cc_final: 0.7268 (pt0) REVERT: C 43 ARG cc_start: 0.8396 (mmt180) cc_final: 0.7921 (mmm-85) REVERT: C 58 LEU cc_start: 0.7973 (mp) cc_final: 0.7451 (pp) REVERT: C 80 GLU cc_start: 0.7068 (pm20) cc_final: 0.6799 (mt-10) REVERT: C 97 LEU cc_start: 0.7407 (mm) cc_final: 0.7014 (mm) REVERT: C 328 TYR cc_start: 0.8223 (m-10) cc_final: 0.8015 (m-10) REVERT: C 381 GLN cc_start: 0.6998 (mm-40) cc_final: 0.6450 (mm110) REVERT: C 386 LEU cc_start: 0.8622 (tp) cc_final: 0.8383 (tp) REVERT: C 537 PHE cc_start: 0.8981 (t80) cc_final: 0.8773 (t80) REVERT: C 546 ASN cc_start: 0.8069 (t0) cc_final: 0.7767 (t0) REVERT: C 570 MET cc_start: 0.8989 (tpp) cc_final: 0.8586 (mmm) REVERT: D 234 LEU cc_start: 0.8444 (mp) cc_final: 0.8198 (tt) REVERT: D 328 TYR cc_start: 0.8804 (m-10) cc_final: 0.8209 (m-80) REVERT: D 381 GLN cc_start: 0.6986 (mt0) cc_final: 0.6683 (pp30) REVERT: D 415 TYR cc_start: 0.8020 (t80) cc_final: 0.7388 (t80) REVERT: D 570 MET cc_start: 0.8491 (mtp) cc_final: 0.8274 (mtp) REVERT: D 591 GLU cc_start: 0.8227 (pt0) cc_final: 0.7913 (tt0) REVERT: D 603 MET cc_start: 0.8119 (tmm) cc_final: 0.7892 (tmm) outliers start: 94 outliers final: 74 residues processed: 556 average time/residue: 0.3151 time to fit residues: 272.5008 Evaluate side-chains 560 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 480 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 250 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 0.0010 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 129 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21419 Z= 0.192 Angle : 0.615 12.775 29073 Z= 0.300 Chirality : 0.041 0.162 3307 Planarity : 0.003 0.041 3701 Dihedral : 4.567 53.697 2860 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 3.78 % Allowed : 24.48 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2612 helix: 0.56 (0.14), residues: 1506 sheet: -2.72 (0.54), residues: 77 loop : -1.42 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 29 HIS 0.003 0.001 HIS B 426 PHE 0.028 0.001 PHE D 319 TYR 0.022 0.001 TYR C 162 ARG 0.006 0.000 ARG E 706 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 502 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8763 (mtp) cc_final: 0.8502 (mtp) REVERT: A 159 LEU cc_start: 0.9034 (mm) cc_final: 0.8783 (mm) REVERT: A 162 TYR cc_start: 0.8384 (m-10) cc_final: 0.7996 (m-10) REVERT: A 181 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8090 (mp) REVERT: A 188 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7030 (p0) REVERT: A 314 LYS cc_start: 0.8535 (ttpt) cc_final: 0.7957 (tttp) REVERT: A 355 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5766 (tmm-80) REVERT: A 442 MET cc_start: 0.8510 (mmt) cc_final: 0.8123 (mmt) REVERT: A 497 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7459 (tmm) REVERT: A 522 GLU cc_start: 0.8485 (mp0) cc_final: 0.8250 (mp0) REVERT: A 534 PHE cc_start: 0.8358 (t80) cc_final: 0.8127 (t80) REVERT: A 553 PHE cc_start: 0.6665 (t80) cc_final: 0.6243 (p90) REVERT: A 637 HIS cc_start: 0.7556 (p90) cc_final: 0.7261 (p90) REVERT: F 2 ASP cc_start: 0.7324 (t0) cc_final: 0.7073 (t0) REVERT: F 14 GLU cc_start: 0.7570 (tt0) cc_final: 0.7344 (tt0) REVERT: F 74 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6667 (ttt180) REVERT: F 75 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7325 (mmmt) REVERT: F 76 MET cc_start: 0.6720 (mmp) cc_final: 0.5537 (tmm) REVERT: F 127 GLU cc_start: 0.8389 (tt0) cc_final: 0.7960 (tt0) REVERT: F 139 GLU cc_start: 0.7830 (tp30) cc_final: 0.7173 (tp30) REVERT: F 143 GLN cc_start: 0.8489 (mt0) cc_final: 0.8247 (tt0) REVERT: B 99 MET cc_start: 0.8133 (mtm) cc_final: 0.7772 (mtm) REVERT: B 190 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7444 (mtp180) REVERT: B 195 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8276 (tt) REVERT: B 294 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7516 (tt0) REVERT: B 330 CYS cc_start: 0.8486 (m) cc_final: 0.8179 (m) REVERT: B 634 GLU cc_start: 0.7490 (pt0) cc_final: 0.7285 (pt0) REVERT: C 43 ARG cc_start: 0.8401 (mmt180) cc_final: 0.7932 (mmm-85) REVERT: C 80 GLU cc_start: 0.7095 (pm20) cc_final: 0.6852 (mt-10) REVERT: C 97 LEU cc_start: 0.7437 (mm) cc_final: 0.7035 (mm) REVERT: C 381 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6626 (mm-40) REVERT: C 386 LEU cc_start: 0.8588 (tp) cc_final: 0.8348 (tp) REVERT: C 442 MET cc_start: 0.7432 (mmt) cc_final: 0.6984 (mtt) REVERT: C 485 MET cc_start: 0.7903 (mtt) cc_final: 0.7474 (mtt) REVERT: C 537 PHE cc_start: 0.9013 (t80) cc_final: 0.8804 (t80) REVERT: C 546 ASN cc_start: 0.7985 (t0) cc_final: 0.7677 (t0) REVERT: C 570 MET cc_start: 0.8955 (tpp) cc_final: 0.8550 (mmm) REVERT: C 608 MET cc_start: 0.8251 (mmm) cc_final: 0.7995 (mmp) REVERT: D 381 GLN cc_start: 0.6997 (mt0) cc_final: 0.6726 (pp30) REVERT: D 415 TYR cc_start: 0.7950 (t80) cc_final: 0.7312 (t80) REVERT: D 591 GLU cc_start: 0.8101 (pt0) cc_final: 0.7776 (tt0) REVERT: D 603 MET cc_start: 0.8090 (tmm) cc_final: 0.7883 (tmm) outliers start: 85 outliers final: 66 residues processed: 549 average time/residue: 0.3002 time to fit residues: 258.3522 Evaluate side-chains 554 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 482 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 149 optimal weight: 0.0060 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 170 optimal weight: 0.0980 chunk 123 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 196 optimal weight: 0.8980 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 129 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21419 Z= 0.217 Angle : 0.630 12.257 29073 Z= 0.307 Chirality : 0.042 0.165 3307 Planarity : 0.004 0.060 3701 Dihedral : 4.536 54.313 2860 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.53 % Allowed : 24.34 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2612 helix: 0.67 (0.14), residues: 1504 sheet: -2.54 (0.58), residues: 71 loop : -1.39 (0.21), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.007 0.001 HIS C 238 PHE 0.029 0.001 PHE D 319 TYR 0.020 0.001 TYR C 328 ARG 0.004 0.000 ARG E 706 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 486 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7503 (tpp80) REVERT: A 159 LEU cc_start: 0.9029 (mm) cc_final: 0.8766 (mm) REVERT: A 162 TYR cc_start: 0.8387 (m-10) cc_final: 0.7993 (m-10) REVERT: A 181 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8081 (mp) REVERT: A 188 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7040 (p0) REVERT: A 219 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8351 (mp) REVERT: A 314 LYS cc_start: 0.8524 (ttpt) cc_final: 0.7963 (tttp) REVERT: A 340 MET cc_start: 0.8627 (tpp) cc_final: 0.8339 (tpp) REVERT: A 355 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5747 (tmm-80) REVERT: A 442 MET cc_start: 0.8518 (mmt) cc_final: 0.8107 (mmt) REVERT: A 486 ILE cc_start: 0.9153 (tt) cc_final: 0.8811 (tt) REVERT: A 497 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7455 (tmm) REVERT: A 522 GLU cc_start: 0.8428 (mp0) cc_final: 0.8198 (mp0) REVERT: A 534 PHE cc_start: 0.8393 (t80) cc_final: 0.8156 (t80) REVERT: A 553 PHE cc_start: 0.6678 (t80) cc_final: 0.6256 (p90) REVERT: A 637 HIS cc_start: 0.7569 (p90) cc_final: 0.7265 (p90) REVERT: F 2 ASP cc_start: 0.7353 (t0) cc_final: 0.7101 (t0) REVERT: F 7 GLU cc_start: 0.8514 (pm20) cc_final: 0.8154 (mp0) REVERT: F 14 GLU cc_start: 0.7623 (tt0) cc_final: 0.7399 (tt0) REVERT: F 74 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6693 (ttt180) REVERT: F 75 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7314 (mmmt) REVERT: F 76 MET cc_start: 0.6713 (mmp) cc_final: 0.5514 (tmm) REVERT: F 109 MET cc_start: 0.9133 (mmt) cc_final: 0.8826 (mmt) REVERT: F 127 GLU cc_start: 0.8287 (tt0) cc_final: 0.7989 (tt0) REVERT: F 139 GLU cc_start: 0.7824 (tp30) cc_final: 0.7081 (tp30) REVERT: F 144 MET cc_start: 0.8172 (tpp) cc_final: 0.7880 (tpp) REVERT: B 99 MET cc_start: 0.8192 (mtm) cc_final: 0.7788 (mtm) REVERT: B 190 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7457 (mtp180) REVERT: B 195 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8296 (tt) REVERT: B 282 GLU cc_start: 0.7338 (mp0) cc_final: 0.6918 (mp0) REVERT: B 294 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7542 (tt0) REVERT: B 330 CYS cc_start: 0.8495 (m) cc_final: 0.8185 (m) REVERT: B 481 MET cc_start: 0.8430 (tpp) cc_final: 0.8147 (tpp) REVERT: C 43 ARG cc_start: 0.8433 (mmt180) cc_final: 0.8029 (mmm-85) REVERT: C 58 LEU cc_start: 0.7929 (mp) cc_final: 0.7375 (pp) REVERT: C 233 GLU cc_start: 0.8165 (tt0) cc_final: 0.7895 (tt0) REVERT: C 328 TYR cc_start: 0.8215 (m-10) cc_final: 0.7926 (m-10) REVERT: C 381 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6636 (mm110) REVERT: C 386 LEU cc_start: 0.8583 (tp) cc_final: 0.8353 (tp) REVERT: C 442 MET cc_start: 0.7304 (mmt) cc_final: 0.6879 (mtt) REVERT: C 485 MET cc_start: 0.7946 (mtt) cc_final: 0.7551 (mtt) REVERT: C 537 PHE cc_start: 0.9032 (t80) cc_final: 0.8768 (t80) REVERT: C 546 ASN cc_start: 0.7970 (t0) cc_final: 0.7659 (t0) REVERT: C 608 MET cc_start: 0.8349 (mmm) cc_final: 0.8126 (mmp) REVERT: D 415 TYR cc_start: 0.7956 (t80) cc_final: 0.7322 (t80) REVERT: D 497 MET cc_start: 0.7254 (tpt) cc_final: 0.7021 (tpt) REVERT: D 591 GLU cc_start: 0.8112 (pt0) cc_final: 0.7820 (tt0) REVERT: D 603 MET cc_start: 0.8099 (tmm) cc_final: 0.7888 (tmm) outliers start: 102 outliers final: 78 residues processed: 546 average time/residue: 0.3030 time to fit residues: 260.5674 Evaluate side-chains 561 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 476 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 556 CYS Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 219 optimal weight: 0.0040 chunk 233 optimal weight: 2.9990 chunk 140 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 220 optimal weight: 0.5980 chunk 232 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 129 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS C 258 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 546 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21419 Z= 0.161 Angle : 0.611 10.762 29073 Z= 0.296 Chirality : 0.041 0.162 3307 Planarity : 0.003 0.052 3701 Dihedral : 4.459 55.774 2860 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.13 % Favored : 93.84 % Rotamer: Outliers : 3.60 % Allowed : 25.06 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2612 helix: 0.76 (0.14), residues: 1523 sheet: -2.52 (0.58), residues: 71 loop : -1.23 (0.22), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.014 0.001 HIS C 238 PHE 0.029 0.001 PHE D 319 TYR 0.024 0.001 TYR C 162 ARG 0.004 0.000 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 504 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7300 (tpp80) REVERT: A 46 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7531 (t0) REVERT: A 159 LEU cc_start: 0.8959 (mm) cc_final: 0.8747 (mm) REVERT: A 162 TYR cc_start: 0.8322 (m-10) cc_final: 0.7899 (m-10) REVERT: A 181 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 188 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7014 (p0) REVERT: A 340 MET cc_start: 0.8585 (tpp) cc_final: 0.8219 (tpp) REVERT: A 355 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.5727 (tmm-80) REVERT: A 397 VAL cc_start: 0.9054 (p) cc_final: 0.8832 (p) REVERT: A 442 MET cc_start: 0.8460 (mmt) cc_final: 0.8100 (mmt) REVERT: A 486 ILE cc_start: 0.9120 (tt) cc_final: 0.8767 (tt) REVERT: A 522 GLU cc_start: 0.8361 (mp0) cc_final: 0.8158 (mp0) REVERT: A 534 PHE cc_start: 0.8345 (t80) cc_final: 0.8130 (t80) REVERT: A 553 PHE cc_start: 0.6596 (t80) cc_final: 0.6146 (p90) REVERT: A 592 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 622 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 637 HIS cc_start: 0.7606 (p90) cc_final: 0.7304 (p90) REVERT: F 2 ASP cc_start: 0.7297 (t0) cc_final: 0.7011 (t0) REVERT: F 7 GLU cc_start: 0.8435 (pm20) cc_final: 0.8155 (mp0) REVERT: F 75 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7277 (mmmt) REVERT: F 76 MET cc_start: 0.6672 (mmp) cc_final: 0.5494 (tmm) REVERT: F 127 GLU cc_start: 0.8321 (tt0) cc_final: 0.8010 (tt0) REVERT: F 139 GLU cc_start: 0.7790 (tp30) cc_final: 0.7316 (tp30) REVERT: B 99 MET cc_start: 0.8104 (mtm) cc_final: 0.7696 (mtm) REVERT: B 190 ARG cc_start: 0.7682 (mtp85) cc_final: 0.7449 (mtp180) REVERT: B 195 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8325 (tt) REVERT: B 294 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7518 (tt0) REVERT: B 330 CYS cc_start: 0.8473 (m) cc_final: 0.8138 (m) REVERT: C 43 ARG cc_start: 0.8456 (mmt180) cc_final: 0.8042 (mmm-85) REVERT: C 58 LEU cc_start: 0.7864 (mp) cc_final: 0.7297 (pp) REVERT: C 97 LEU cc_start: 0.7366 (mm) cc_final: 0.6968 (mm) REVERT: C 328 TYR cc_start: 0.8239 (m-10) cc_final: 0.7876 (m-10) REVERT: C 381 GLN cc_start: 0.7151 (mm-40) cc_final: 0.6672 (mm110) REVERT: C 382 ASP cc_start: 0.8380 (m-30) cc_final: 0.7931 (t0) REVERT: C 386 LEU cc_start: 0.8558 (tp) cc_final: 0.8334 (tp) REVERT: C 409 ARG cc_start: 0.8947 (ptm-80) cc_final: 0.8426 (ttt-90) REVERT: C 442 MET cc_start: 0.7425 (mmt) cc_final: 0.6978 (mtt) REVERT: C 485 MET cc_start: 0.7957 (mtt) cc_final: 0.7563 (mtt) REVERT: C 519 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8031 (m110) REVERT: C 608 MET cc_start: 0.8469 (mmm) cc_final: 0.8266 (mmp) REVERT: D 211 PHE cc_start: 0.7694 (m-80) cc_final: 0.7390 (m-80) REVERT: D 591 GLU cc_start: 0.7971 (pt0) cc_final: 0.7659 (tt0) REVERT: D 634 GLU cc_start: 0.8381 (tt0) cc_final: 0.7950 (tt0) outliers start: 81 outliers final: 61 residues processed: 550 average time/residue: 0.3115 time to fit residues: 267.5221 Evaluate side-chains 550 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 482 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 556 CYS Chi-restraints excluded: chain D residue 557 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.2980 chunk 246 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 129 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21419 Z= 0.170 Angle : 0.617 10.611 29073 Z= 0.298 Chirality : 0.041 0.172 3307 Planarity : 0.003 0.077 3701 Dihedral : 4.425 56.331 2860 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.80 % Rotamer: Outliers : 3.29 % Allowed : 25.41 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2612 helix: 0.81 (0.14), residues: 1527 sheet: -2.44 (0.59), residues: 71 loop : -1.19 (0.22), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 29 HIS 0.006 0.001 HIS C 238 PHE 0.028 0.001 PHE D 319 TYR 0.016 0.001 TYR A 415 ARG 0.004 0.000 ARG D 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 493 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7328 (tpp80) REVERT: A 46 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7431 (t0) REVERT: A 159 LEU cc_start: 0.8931 (mm) cc_final: 0.8719 (mm) REVERT: A 162 TYR cc_start: 0.8353 (m-10) cc_final: 0.7890 (m-10) REVERT: A 181 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7946 (mp) REVERT: A 188 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.7000 (p0) REVERT: A 340 MET cc_start: 0.8598 (tpp) cc_final: 0.8209 (tpp) REVERT: A 355 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5725 (tmm-80) REVERT: A 442 MET cc_start: 0.8452 (mmt) cc_final: 0.8135 (mmt) REVERT: A 486 ILE cc_start: 0.9154 (tt) cc_final: 0.8796 (tt) REVERT: A 522 GLU cc_start: 0.8322 (mp0) cc_final: 0.8103 (mp0) REVERT: A 534 PHE cc_start: 0.8351 (t80) cc_final: 0.8108 (t80) REVERT: A 553 PHE cc_start: 0.6602 (t80) cc_final: 0.6143 (p90) REVERT: A 592 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8814 (mp) REVERT: A 622 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 637 HIS cc_start: 0.7618 (p90) cc_final: 0.7287 (p90) REVERT: F 2 ASP cc_start: 0.7278 (t0) cc_final: 0.7019 (t0) REVERT: F 75 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7289 (mmmt) REVERT: F 76 MET cc_start: 0.6646 (mmp) cc_final: 0.5484 (tmm) REVERT: F 127 GLU cc_start: 0.8088 (tt0) cc_final: 0.7540 (tt0) REVERT: F 139 GLU cc_start: 0.7800 (tp30) cc_final: 0.7574 (tp30) REVERT: B 99 MET cc_start: 0.8108 (mtm) cc_final: 0.7721 (mtm) REVERT: B 190 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7432 (mtp180) REVERT: B 195 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (tt) REVERT: B 294 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7519 (tt0) REVERT: B 309 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7216 (tt0) REVERT: B 330 CYS cc_start: 0.8475 (m) cc_final: 0.8137 (m) REVERT: C 43 ARG cc_start: 0.8463 (mmt180) cc_final: 0.8051 (mmm-85) REVERT: C 97 LEU cc_start: 0.7366 (mm) cc_final: 0.6962 (mm) REVERT: C 328 TYR cc_start: 0.8196 (m-10) cc_final: 0.7837 (m-10) REVERT: C 340 MET cc_start: 0.8878 (mmm) cc_final: 0.7838 (tpp) REVERT: C 381 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6750 (mm110) REVERT: C 382 ASP cc_start: 0.8429 (m-30) cc_final: 0.8003 (t0) REVERT: C 386 LEU cc_start: 0.8559 (tp) cc_final: 0.8338 (tp) REVERT: C 409 ARG cc_start: 0.8920 (ptm-80) cc_final: 0.8422 (ttt-90) REVERT: C 442 MET cc_start: 0.7386 (mmt) cc_final: 0.6963 (mtt) REVERT: C 485 MET cc_start: 0.7963 (mtt) cc_final: 0.7553 (mtt) REVERT: D 591 GLU cc_start: 0.7926 (pt0) cc_final: 0.7661 (tt0) REVERT: D 634 GLU cc_start: 0.8382 (tt0) cc_final: 0.7972 (tt0) outliers start: 74 outliers final: 64 residues processed: 539 average time/residue: 0.2970 time to fit residues: 250.7230 Evaluate side-chains 553 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 483 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 556 CYS Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 567 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 30 optimal weight: 0.0000 chunk 57 optimal weight: 0.9980 chunk 206 optimal weight: 0.3980 chunk 86 optimal weight: 0.0970 chunk 212 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 60 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 129 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS C 446 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.158490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132994 restraints weight = 31817.455| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.98 r_work: 0.3488 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21419 Z= 0.147 Angle : 0.610 10.983 29073 Z= 0.294 Chirality : 0.040 0.172 3307 Planarity : 0.003 0.051 3701 Dihedral : 4.362 58.094 2860 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.80 % Allowed : 26.39 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2612 helix: 0.93 (0.14), residues: 1525 sheet: -2.34 (0.59), residues: 71 loop : -1.17 (0.22), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.018 0.001 HIS C 238 PHE 0.029 0.001 PHE D 319 TYR 0.016 0.001 TYR A 415 ARG 0.004 0.000 ARG E 706 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5523.07 seconds wall clock time: 99 minutes 47.51 seconds (5987.51 seconds total)