Starting phenix.real_space_refine on Tue Dec 12 10:10:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/12_2023/6o20_0607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/12_2023/6o20_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_0607/12_2023/6o20_0607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/12_2023/6o20_0607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/12_2023/6o20_0607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o20_0607/12_2023/6o20_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.57, 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: 8.21 Conformation dependent library (CDL) restraints added in 4.1 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: 5.64 Time building geometry restraints manager: 8.36 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: 0.850 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: 4.920 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 53.110 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.470 ------------------------------------------------------------------------------- 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 : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 791 average time/residue: 0.3447 time to fit residues: 406.8220 Evaluate side-chains 511 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 508 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1992 time to fit residues: 4.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.0470 chunk 197 optimal weight: 0.0970 chunk 109 optimal weight: 0.0030 chunk 67 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 151 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 overall best weight: 0.3888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN 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 128 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 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 446 ASN C 582 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21419 Z= 0.170 Angle : 0.674 10.365 29073 Z= 0.335 Chirality : 0.041 0.175 3307 Planarity : 0.005 0.052 3701 Dihedral : 5.198 30.712 2859 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.40 % Allowed : 18.48 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.71 (0.14), residues: 2612 helix: -2.46 (0.11), residues: 1486 sheet: -3.35 (0.46), residues: 76 loop : -2.15 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 29 HIS 0.005 0.001 HIS D 509 PHE 0.020 0.001 PHE D 319 TYR 0.025 0.002 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 647 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 593 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 23 residues processed: 629 average time/residue: 0.3253 time to fit residues: 315.6916 Evaluate side-chains 501 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 478 time to evaluate : 2.406 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1985 time to fit residues: 11.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 234 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 418 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN B 91 ASN B 118 GLN C 51 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS D 265 HIS ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN D 582 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21419 Z= 0.167 Angle : 0.617 9.064 29073 Z= 0.306 Chirality : 0.041 0.161 3307 Planarity : 0.004 0.057 3701 Dihedral : 4.742 28.054 2859 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.43 % Favored : 93.53 % Rotamer: Outliers : 2.44 % Allowed : 20.21 % Favored : 77.34 % 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: -2.46 (0.15), residues: 2612 helix: -1.26 (0.12), residues: 1487 sheet: -3.15 (0.48), residues: 76 loop : -1.89 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 29 HIS 0.004 0.001 HIS D 509 PHE 0.016 0.001 PHE D 319 TYR 0.017 0.001 TYR B 328 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 564 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 509 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 28 residues processed: 536 average time/residue: 0.3198 time to fit residues: 267.9146 Evaluate side-chains 486 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 458 time to evaluate : 2.446 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1899 time to fit residues: 13.3257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 158 optimal weight: 0.3980 chunk 237 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3982 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= 0.184 Angle : 0.612 9.030 29073 Z= 0.300 Chirality : 0.041 0.168 3307 Planarity : 0.004 0.050 3701 Dihedral : 4.535 25.457 2859 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.68 % Rotamer: Outliers : 1.60 % Allowed : 22.88 % Favored : 75.52 % 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: -1.60 (0.16), residues: 2612 helix: -0.41 (0.13), residues: 1484 sheet: -3.11 (0.49), residues: 71 loop : -1.77 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 29 HIS 0.004 0.001 HIS C 426 PHE 0.027 0.001 PHE D 574 TYR 0.021 0.001 TYR B 328 ARG 0.007 0.000 ARG E 706 *********************** 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 537 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 501 time to evaluate : 2.283 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 520 average time/residue: 0.3138 time to fit residues: 256.0445 Evaluate side-chains 478 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 459 time to evaluate : 2.392 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1971 time to fit residues: 10.2499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 3 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 214 optimal weight: 0.0170 chunk 173 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 225 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 overall best weight: 2.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** 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** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 208 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** D 267 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21419 Z= 0.273 Angle : 0.651 8.405 29073 Z= 0.324 Chirality : 0.043 0.172 3307 Planarity : 0.004 0.052 3701 Dihedral : 4.608 24.881 2859 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.09 % Allowed : 23.28 % Favored : 74.63 % 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: -1.12 (0.17), residues: 2612 helix: -0.07 (0.13), residues: 1516 sheet: -2.68 (0.54), residues: 77 loop : -1.51 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 29 HIS 0.007 0.001 HIS D 426 PHE 0.030 0.001 PHE C 537 TYR 0.023 0.002 TYR B 328 ARG 0.008 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 542 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 495 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 523 average time/residue: 0.3084 time to fit residues: 252.8849 Evaluate side-chains 488 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 466 time to evaluate : 2.210 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1837 time to fit residues: 10.8840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS B 129 ASN B 358 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** 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: 0.7755 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21419 Z= 0.301 Angle : 0.667 10.063 29073 Z= 0.330 Chirality : 0.044 0.178 3307 Planarity : 0.004 0.050 3701 Dihedral : 4.669 24.041 2859 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.51 % Favored : 93.45 % Rotamer: Outliers : 2.09 % Allowed : 23.99 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2612 helix: 0.11 (0.13), residues: 1531 sheet: -2.64 (0.54), residues: 77 loop : -1.48 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 29 HIS 0.007 0.001 HIS D 426 PHE 0.025 0.001 PHE D 319 TYR 0.028 0.002 TYR B 328 ARG 0.010 0.000 ARG B 594 *********************** 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 539 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 492 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 26 residues processed: 516 average time/residue: 0.3132 time to fit residues: 254.8116 Evaluate side-chains 483 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 457 time to evaluate : 3.147 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1945 time to fit residues: 12.8516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 140 optimal weight: 0.3980 chunk 250 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 152 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN B 128 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21419 Z= 0.163 Angle : 0.613 11.518 29073 Z= 0.299 Chirality : 0.041 0.165 3307 Planarity : 0.003 0.053 3701 Dihedral : 4.425 22.439 2859 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 0.84 % Allowed : 24.88 % Favored : 74.28 % 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: -0.49 (0.17), residues: 2612 helix: 0.51 (0.14), residues: 1522 sheet: -2.68 (0.54), residues: 77 loop : -1.36 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 29 HIS 0.008 0.001 HIS D 426 PHE 0.026 0.001 PHE D 319 TYR 0.021 0.001 TYR B 328 ARG 0.005 0.000 ARG B 594 *********************** 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 529 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 510 time to evaluate : 2.352 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 521 average time/residue: 0.3149 time to fit residues: 257.7063 Evaluate side-chains 479 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 469 time to evaluate : 2.344 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2001 time to fit residues: 6.9066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 129 ASN B 369 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21419 Z= 0.231 Angle : 0.642 9.926 29073 Z= 0.315 Chirality : 0.043 0.192 3307 Planarity : 0.004 0.072 3701 Dihedral : 4.453 24.141 2859 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 1.02 % Allowed : 26.03 % Favored : 72.95 % 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: -0.39 (0.17), residues: 2612 helix: 0.57 (0.14), residues: 1526 sheet: -2.62 (0.53), residues: 77 loop : -1.30 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 613 HIS 0.009 0.001 HIS D 426 PHE 0.025 0.001 PHE D 319 TYR 0.019 0.002 TYR B 328 ARG 0.006 0.000 ARG B 594 *********************** 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 492 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 469 time to evaluate : 2.248 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 481 average time/residue: 0.3245 time to fit residues: 244.9126 Evaluate side-chains 471 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 458 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2147 time to fit residues: 8.0499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 0.5980 chunk 220 optimal weight: 0.9990 chunk 232 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** 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 ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 21419 Z= 0.155 Angle : 0.619 9.504 29073 Z= 0.300 Chirality : 0.041 0.191 3307 Planarity : 0.004 0.067 3701 Dihedral : 4.337 21.026 2859 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 0.31 % Allowed : 27.10 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2612 helix: 0.77 (0.14), residues: 1513 sheet: -2.56 (0.54), residues: 77 loop : -1.23 (0.21), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 613 HIS 0.006 0.001 HIS D 426 PHE 0.030 0.001 PHE C 537 TYR 0.020 0.001 TYR C 336 ARG 0.013 0.000 ARG B 594 *********************** 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 497 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 490 time to evaluate : 2.518 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 493 average time/residue: 0.3179 time to fit residues: 247.4356 Evaluate side-chains 466 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 463 time to evaluate : 2.423 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2573 time to fit residues: 4.6838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 7.9990 chunk 246 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 259 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 126 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5125 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= 0.175 Angle : 0.629 9.836 29073 Z= 0.307 Chirality : 0.042 0.194 3307 Planarity : 0.003 0.053 3701 Dihedral : 4.336 24.816 2859 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 0.40 % Allowed : 27.28 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2612 helix: 0.82 (0.14), residues: 1514 sheet: -2.61 (0.54), residues: 77 loop : -1.19 (0.21), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 29 HIS 0.007 0.001 HIS D 426 PHE 0.029 0.001 PHE D 319 TYR 0.021 0.001 TYR C 336 ARG 0.013 0.000 ARG B 594 ********************** 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 482 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 473 time to evaluate : 2.608 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 477 average time/residue: 0.3089 time to fit residues: 233.9030 Evaluate side-chains 460 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 456 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1976 time to fit residues: 4.6742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 190 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131336 restraints weight = 32254.034| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.87 r_work: 0.3384 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5156 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= 0.195 Angle : 0.631 10.282 29073 Z= 0.307 Chirality : 0.042 0.193 3307 Planarity : 0.004 0.049 3701 Dihedral : 4.311 20.085 2859 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 0.40 % Allowed : 27.54 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2612 helix: 0.87 (0.14), residues: 1517 sheet: -2.48 (0.55), residues: 77 loop : -1.14 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP C 29 HIS 0.003 0.001 HIS B 426 PHE 0.029 0.001 PHE D 319 TYR 0.019 0.001 TYR C 336 ARG 0.013 0.000 ARG B 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5314.96 seconds wall clock time: 96 minutes 46.59 seconds (5806.59 seconds total)