Starting phenix.real_space_refine on Tue Dec 31 15:02:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpg_34192/12_2024/8gpg_34192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpg_34192/12_2024/8gpg_34192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gpg_34192/12_2024/8gpg_34192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpg_34192/12_2024/8gpg_34192.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpg_34192/12_2024/8gpg_34192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpg_34192/12_2024/8gpg_34192.cif" } resolution = 4.1 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9981 2.51 5 N 2661 2.21 5 O 3123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15864 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "D" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "X" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3214 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 8 Chain: "Y" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3214 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 8 Chain: "Z" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3214 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 8 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Z" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 10.08, per 1000 atoms: 0.64 Number of scatterers: 15864 At special positions: 0 Unit cell: (130.38, 138.86, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3123 8.00 N 2661 7.00 C 9981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.04 Simple disulfide: pdb=" SG CYS X 54 " - pdb=" SG CYS X 74 " distance=2.03 Simple disulfide: pdb=" SG CYS X 228 " - pdb=" SG CYS X 257 " distance=2.03 Simple disulfide: pdb=" SG CYS X 238 " - pdb=" SG CYS X 249 " distance=2.03 Simple disulfide: pdb=" SG CYS X 306 " - pdb=" SG CYS X 331 " distance=2.03 Simple disulfide: pdb=" SG CYS X 378 " - pdb=" SG CYS X 445 " distance=2.03 Simple disulfide: pdb=" SG CYS X 385 " - pdb=" SG CYS X 418 " distance=2.03 Simple disulfide: pdb=" SG CYS X 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 228 " - pdb=" SG CYS Y 257 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 238 " - pdb=" SG CYS Y 249 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 306 " - pdb=" SG CYS Y 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 378 " - pdb=" SG CYS Y 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 385 " - pdb=" SG CYS Y 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 54 " - pdb=" SG CYS Z 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 228 " - pdb=" SG CYS Z 257 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 238 " - pdb=" SG CYS Z 249 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 306 " - pdb=" SG CYS Z 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 378 " - pdb=" SG CYS Z 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 385 " - pdb=" SG CYS Z 418 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA M 3 " - " MAN M 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG G 1 " - " ASN X 88 " " NAG H 1 " - " ASN X 272 " " NAG I 1 " - " ASN X 625 " " NAG J 1 " - " ASN Y 88 " " NAG K 1 " - " ASN Y 272 " " NAG L 1 " - " ASN Y 625 " " NAG M 1 " - " ASN Z 88 " " NAG N 1 " - " ASN Z 625 " " NAG O 1 " - " ASN Z 272 " " NAG X 701 " - " ASN X 244 " " NAG X 702 " - " ASN X 251 " " NAG X 703 " - " ASN X 386 " " NAG X 704 " - " ASN X 444 " " NAG X 705 " - " ASN X 448 " " NAG X 706 " - " ASN X 611 " " NAG X 707 " - " ASN X 339 " " NAG Y 701 " - " ASN Y 244 " " NAG Y 702 " - " ASN Y 251 " " NAG Y 703 " - " ASN Y 386 " " NAG Y 704 " - " ASN Y 444 " " NAG Y 705 " - " ASN Y 448 " " NAG Y 706 " - " ASN Y 611 " " NAG Y 707 " - " ASN Y 339 " " NAG Z 701 " - " ASN Z 244 " " NAG Z 702 " - " ASN Z 251 " " NAG Z 703 " - " ASN Z 386 " " NAG Z 704 " - " ASN Z 444 " " NAG Z 705 " - " ASN Z 448 " " NAG Z 706 " - " ASN Z 611 " " NAG Z 707 " - " ASN Z 339 " Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 2.0 seconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 38 sheets defined 19.5% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.520A pdb=" N ASP A 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.746A pdb=" N VAL B 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.548A pdb=" N MET C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.759A pdb=" N VAL D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 105 Processing helix chain 'X' and resid 106 through 115 removed outlier: 3.694A pdb=" N SER X 115 " --> pdb=" O LEU X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 351 removed outlier: 3.742A pdb=" N GLU X 351 " --> pdb=" O GLU X 347 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 373 removed outlier: 3.505A pdb=" N MET X 373 " --> pdb=" O LEU X 369 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 481 Processing helix chain 'X' and resid 529 through 537 Processing helix chain 'X' and resid 571 through 595 removed outlier: 4.355A pdb=" N GLN X 575 " --> pdb=" O TRP X 571 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 625 removed outlier: 3.554A pdb=" N ASN X 625 " --> pdb=" O GLU X 621 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 636 removed outlier: 3.511A pdb=" N LYS X 633 " --> pdb=" O ILE X 629 " (cutoff:3.500A) Processing helix chain 'X' and resid 638 through 652 removed outlier: 3.627A pdb=" N GLN X 652 " --> pdb=" O GLU X 648 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 116 removed outlier: 3.800A pdb=" N LEU Y 116 " --> pdb=" O TRP Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 335 through 356 removed outlier: 4.042A pdb=" N ASN Y 339 " --> pdb=" O GLY Y 335 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU Y 347 " --> pdb=" O ASN Y 343 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU Y 351 " --> pdb=" O GLU Y 347 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS Y 352 " --> pdb=" O LYS Y 348 " (cutoff:3.500A) Processing helix chain 'Y' and resid 368 through 373 removed outlier: 3.732A pdb=" N MET Y 373 " --> pdb=" O LEU Y 369 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 392 removed outlier: 3.596A pdb=" N PHE Y 391 " --> pdb=" O THR Y 388 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN Y 392 " --> pdb=" O LYS Y 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 388 through 392' Processing helix chain 'Y' and resid 474 through 483 removed outlier: 3.597A pdb=" N ASN Y 478 " --> pdb=" O ASN Y 474 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 537 Processing helix chain 'Y' and resid 571 through 596 removed outlier: 4.306A pdb=" N GLN Y 575 " --> pdb=" O TRP Y 571 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP Y 596 " --> pdb=" O PHE Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 624 removed outlier: 4.035A pdb=" N TRP Y 623 " --> pdb=" O TYR Y 619 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 636 Processing helix chain 'Y' and resid 638 through 652 Processing helix chain 'Z' and resid 99 through 116 removed outlier: 3.862A pdb=" N GLN Z 103 " --> pdb=" O ASN Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 335 through 353 removed outlier: 3.966A pdb=" N GLU Z 340 " --> pdb=" O THR Z 336 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU Z 351 " --> pdb=" O GLU Z 347 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS Z 352 " --> pdb=" O LYS Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 387 through 391 removed outlier: 3.607A pdb=" N LEU Z 390 " --> pdb=" O THR Z 387 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE Z 391 " --> pdb=" O THR Z 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 387 through 391' Processing helix chain 'Z' and resid 475 through 481 removed outlier: 4.060A pdb=" N TRP Z 479 " --> pdb=" O ILE Z 475 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 537 Processing helix chain 'Z' and resid 572 through 595 Processing helix chain 'Z' and resid 618 through 623 removed outlier: 3.591A pdb=" N ILE Z 622 " --> pdb=" O SER Z 618 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP Z 623 " --> pdb=" O TYR Z 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 618 through 623' Processing helix chain 'Z' and resid 627 through 636 Processing helix chain 'Z' and resid 638 through 653 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.770A pdb=" N LEU A 12 " --> pdb=" O THR A 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.515A pdb=" N ARG A 38 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP A 34 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 113 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG A 99 " --> pdb=" O MET A 111 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET A 111 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N MET A 101 " --> pdb=" O HIS A 109 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS A 109 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.162A pdb=" N LEU B 11 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 58 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.879A pdb=" N LEU C 45 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N SER C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N CYS C 95 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 113 " --> pdb=" O CYS C 95 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG C 97 " --> pdb=" O MET C 111 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET C 111 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG C 99 " --> pdb=" O HIS C 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.715A pdb=" N LEU D 11 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 110 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 13 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU D 38 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR D 54 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 42 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 54 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU D 58 " --> pdb=" O TYR D 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.407A pdb=" N THR E 21 " --> pdb=" O TRP E 7 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU E 16 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.007A pdb=" N LEU E 45 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N SER E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N CYS E 95 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL E 113 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG E 97 " --> pdb=" O MET E 111 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N MET E 111 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG E 99 " --> pdb=" O HIS E 109 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.007A pdb=" N LEU E 45 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N SER E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.516A pdb=" N LEU F 11 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL F 13 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 494 through 499 removed outlier: 4.834A pdb=" N VAL X 36 " --> pdb=" O THR X 606 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR X 606 " --> pdb=" O VAL X 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 45 through 47 removed outlier: 3.644A pdb=" N ILE X 235 " --> pdb=" O VAL X 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'X' and resid 269 through 271 removed outlier: 3.755A pdb=" N GLY X 451 " --> pdb=" O LEU X 270 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N THR X 446 " --> pdb=" O VAL X 302 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N VAL X 302 " --> pdb=" O THR X 446 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N ASN X 448 " --> pdb=" O LYS X 300 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N LYS X 300 " --> pdb=" O ASN X 448 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR X 450 " --> pdb=" O LEU X 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 269 through 271 removed outlier: 3.755A pdb=" N GLY X 451 " --> pdb=" O LEU X 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'X' and resid 358 through 359 removed outlier: 6.596A pdb=" N THR X 358 " --> pdb=" O GLU X 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'X' and resid 374 through 378 Processing sheet with id=AC5, first strand: chain 'Y' and resid 494 through 499 removed outlier: 4.721A pdb=" N VAL Y 36 " --> pdb=" O THR Y 606 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Y 606 " --> pdb=" O VAL Y 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'Y' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'Y' and resid 91 through 93 Processing sheet with id=AC9, first strand: chain 'Y' and resid 269 through 271 removed outlier: 3.556A pdb=" N GLY Y 451 " --> pdb=" O LEU Y 270 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY Y 451 " --> pdb=" O LYS Y 300 " (cutoff:3.500A) removed outlier: 10.701A pdb=" N LYS Y 300 " --> pdb=" O GLY Y 451 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N ILE Y 453 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N LEU Y 298 " --> pdb=" O ILE Y 453 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N THR Y 455 " --> pdb=" O VAL Y 296 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N VAL Y 296 " --> pdb=" O THR Y 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 269 through 271 removed outlier: 3.556A pdb=" N GLY Y 451 " --> pdb=" O LEU Y 270 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 332 through 333 Processing sheet with id=AD3, first strand: chain 'Y' and resid 374 through 378 Processing sheet with id=AD4, first strand: chain 'Z' and resid 495 through 499 removed outlier: 4.583A pdb=" N VAL Z 36 " --> pdb=" O THR Z 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 45 through 47 removed outlier: 3.671A pdb=" N ILE Z 235 " --> pdb=" O VAL Z 255 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Z' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'Z' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'Z' and resid 270 through 271 removed outlier: 6.852A pdb=" N LEU Z 270 " --> pdb=" O THR Z 450 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N ASN Z 448 " --> pdb=" O LYS Z 300 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N LYS Z 300 " --> pdb=" O ASN Z 448 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR Z 450 " --> pdb=" O LEU Z 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 270 through 271 removed outlier: 6.852A pdb=" N LEU Z 270 " --> pdb=" O THR Z 450 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 332 through 334 Processing sheet with id=AE2, first strand: chain 'Z' and resid 374 through 378 560 hydrogen bonds defined for protein. 1503 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: 5.55 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4961 1.34 - 1.46: 3920 1.46 - 1.58: 7157 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 16176 Sorted by residual: bond pdb=" C3 BMA M 3 " pdb=" O3 BMA M 3 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG Z 707 " pdb=" O5 NAG Z 707 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sigma weight residual 1.410 1.458 -0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" C1 MAN J 5 " pdb=" C2 MAN J 5 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 16171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 21575 2.53 - 5.05: 305 5.05 - 7.58: 37 7.58 - 10.11: 4 10.11 - 12.64: 3 Bond angle restraints: 21924 Sorted by residual: angle pdb=" C PHE X 243 " pdb=" N ASN X 244 " pdb=" CA ASN X 244 " ideal model delta sigma weight residual 122.61 130.10 -7.49 1.56e+00 4.11e-01 2.31e+01 angle pdb=" CB MET Y 104 " pdb=" CG MET Y 104 " pdb=" SD MET Y 104 " ideal model delta sigma weight residual 112.70 100.06 12.64 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C ILE Z 443 " pdb=" N ASN Z 444 " pdb=" CA ASN Z 444 " ideal model delta sigma weight residual 122.74 115.46 7.28 1.82e+00 3.02e-01 1.60e+01 angle pdb=" CA LEU A 80 " pdb=" CB LEU A 80 " pdb=" CG LEU A 80 " ideal model delta sigma weight residual 116.30 128.81 -12.51 3.50e+00 8.16e-02 1.28e+01 angle pdb=" CA CYS F 23 " pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " ideal model delta sigma weight residual 114.40 121.86 -7.46 2.30e+00 1.89e-01 1.05e+01 ... (remaining 21919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 9606 24.93 - 49.87: 554 49.87 - 74.80: 81 74.80 - 99.74: 38 99.74 - 124.67: 14 Dihedral angle restraints: 10293 sinusoidal: 4782 harmonic: 5511 Sorted by residual: dihedral pdb=" CB CYS Y 598 " pdb=" SG CYS Y 598 " pdb=" SG CYS Y 604 " pdb=" CB CYS Y 604 " ideal model delta sinusoidal sigma weight residual 93.00 164.51 -71.51 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 93 " pdb=" CB CYS B 93 " ideal model delta sinusoidal sigma weight residual 93.00 157.77 -64.77 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS Y 378 " pdb=" SG CYS Y 378 " pdb=" SG CYS Y 445 " pdb=" CB CYS Y 445 " ideal model delta sinusoidal sigma weight residual 93.00 45.90 47.10 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 10290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2313 0.082 - 0.164: 261 0.164 - 0.246: 10 0.246 - 0.328: 4 0.328 - 0.410: 4 Chirality restraints: 2592 Sorted by residual: chirality pdb=" C1 NAG Y 701 " pdb=" ND2 ASN Y 244 " pdb=" C2 NAG Y 701 " pdb=" O5 NAG Y 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C1 NAG Z 704 " pdb=" ND2 ASN Z 444 " pdb=" C2 NAG Z 704 " pdb=" O5 NAG Z 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C1 NAG Y 706 " pdb=" ND2 ASN Y 611 " pdb=" C2 NAG Y 706 " pdb=" O5 NAG Y 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2589 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN Z 444 " 0.002 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" CG ASN Z 444 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN Z 444 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN Z 444 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG Z 704 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 479 " 0.010 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP Y 479 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 479 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 479 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 479 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 479 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 479 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 479 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 479 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 479 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU X 106 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLU X 106 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU X 106 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP X 107 " -0.020 2.00e-02 2.50e+03 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 425 2.68 - 3.24: 15197 3.24 - 3.79: 23596 3.79 - 4.35: 29143 4.35 - 4.90: 47940 Nonbonded interactions: 116301 Sorted by model distance: nonbonded pdb=" OD2 ASP D 87 " pdb=" OH TYR D 91 " model vdw 2.130 3.040 nonbonded pdb=" OD2 ASP B 87 " pdb=" OH TYR B 91 " model vdw 2.131 3.040 nonbonded pdb=" ND2 ASN X 293 " pdb=" OD2 ASP X 477 " model vdw 2.145 3.120 nonbonded pdb=" O TYR D 37 " pdb=" OG1 THR D 96 " model vdw 2.157 3.040 nonbonded pdb=" OE2 GLU C 105 " pdb=" OH TYR D 37 " model vdw 2.169 3.040 ... (remaining 116296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 38.140 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.005 0.069 16176 Z= 0.311 Angle : 0.762 12.635 21924 Z= 0.376 Chirality : 0.051 0.410 2592 Planarity : 0.005 0.062 2700 Dihedral : 16.308 124.670 6651 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.43 (0.19), residues: 1854 helix: 1.16 (0.30), residues: 312 sheet: -0.44 (0.24), residues: 456 loop : -1.91 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP Y 479 HIS 0.005 0.002 HIS Y 352 PHE 0.020 0.002 PHE Y 53 TYR 0.021 0.002 TYR Z 227 ARG 0.008 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.7656 (tpp) cc_final: 0.7096 (tpp) REVERT: B 65 ASP cc_start: 0.7399 (t0) cc_final: 0.6980 (t0) REVERT: C 47 TRP cc_start: 0.8541 (t60) cc_final: 0.7498 (t60) REVERT: C 75 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7959 (mtmm) REVERT: D 35 ASP cc_start: 0.8692 (m-30) cc_final: 0.8339 (m-30) REVERT: D 97 ARG cc_start: 0.7939 (tmt-80) cc_final: 0.7594 (tpt-90) REVERT: E 47 TRP cc_start: 0.8707 (t60) cc_final: 0.8458 (t60) REVERT: E 77 GLN cc_start: 0.6851 (pt0) cc_final: 0.6634 (pm20) REVERT: F 35 ASP cc_start: 0.8366 (m-30) cc_final: 0.8165 (m-30) REVERT: F 57 SER cc_start: 0.8827 (m) cc_final: 0.8572 (m) REVERT: F 58 GLU cc_start: 0.7243 (mp0) cc_final: 0.6971 (mp0) REVERT: X 104 MET cc_start: 0.8561 (tmm) cc_final: 0.7967 (tmm) REVERT: X 492 GLU cc_start: 0.8619 (tt0) cc_final: 0.8328 (tt0) REVERT: X 588 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8876 (tptt) REVERT: Y 479 TRP cc_start: 0.7413 (m100) cc_final: 0.6916 (m100) REVERT: Z 484 TYR cc_start: 0.8764 (p90) cc_final: 0.8088 (p90) REVERT: Z 486 TYR cc_start: 0.8929 (m-10) cc_final: 0.8452 (m-10) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2644 time to fit residues: 123.4510 Evaluate side-chains 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN F 6 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 259 HIS ** X 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 374 HIS X 478 ASN ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Z 268 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16176 Z= 0.187 Angle : 0.628 10.978 21924 Z= 0.314 Chirality : 0.047 0.494 2592 Planarity : 0.004 0.063 2700 Dihedral : 12.159 117.891 3039 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.20 (0.19), residues: 1854 helix: 1.51 (0.29), residues: 315 sheet: -0.26 (0.24), residues: 450 loop : -1.83 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 36 HIS 0.009 0.001 HIS Y 375 PHE 0.015 0.001 PHE X 53 TYR 0.018 0.001 TYR Z 227 ARG 0.005 0.000 ARG Y 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 ASP cc_start: 0.8661 (m-30) cc_final: 0.8260 (m-30) REVERT: D 43 ARG cc_start: 0.7522 (ttp-110) cc_final: 0.7217 (ttp-110) REVERT: D 58 GLU cc_start: 0.6039 (mp0) cc_final: 0.5814 (mp0) REVERT: D 97 ARG cc_start: 0.8004 (tmt-80) cc_final: 0.7625 (tpt-90) REVERT: E 90 MET cc_start: 0.6252 (mmt) cc_final: 0.5971 (mmt) REVERT: F 35 ASP cc_start: 0.8569 (m-30) cc_final: 0.8280 (m-30) REVERT: F 57 SER cc_start: 0.8862 (m) cc_final: 0.8596 (m) REVERT: F 58 GLU cc_start: 0.7117 (mp0) cc_final: 0.6808 (mp0) REVERT: F 92 TYR cc_start: 0.8494 (m-10) cc_final: 0.8274 (m-10) REVERT: X 54 CYS cc_start: 0.6932 (t) cc_final: 0.6700 (t) REVERT: X 374 HIS cc_start: 0.8039 (t70) cc_final: 0.7764 (t-170) REVERT: X 484 TYR cc_start: 0.8488 (p90) cc_final: 0.7820 (p90) REVERT: X 492 GLU cc_start: 0.8616 (tt0) cc_final: 0.8328 (tt0) REVERT: X 588 LYS cc_start: 0.9254 (tmtt) cc_final: 0.8880 (tptt) REVERT: Y 97 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8260 (tmtt) REVERT: Y 353 PHE cc_start: 0.5352 (m-10) cc_final: 0.5055 (m-10) REVERT: Y 479 TRP cc_start: 0.7096 (m100) cc_final: 0.6475 (m100) REVERT: Y 484 TYR cc_start: 0.8184 (p90) cc_final: 0.7920 (p90) REVERT: Z 484 TYR cc_start: 0.8746 (p90) cc_final: 0.8169 (p90) REVERT: Z 486 TYR cc_start: 0.8891 (m-10) cc_final: 0.8502 (m-10) outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.2620 time to fit residues: 127.5914 Evaluate side-chains 244 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 259 HIS ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 268 GLN ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Z 268 GLN ** Z 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 653 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 16176 Z= 0.452 Angle : 0.780 10.511 21924 Z= 0.393 Chirality : 0.050 0.471 2592 Planarity : 0.005 0.052 2700 Dihedral : 11.414 117.507 3039 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.06 % Allowed : 5.60 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.52 (0.19), residues: 1854 helix: 1.34 (0.29), residues: 309 sheet: -0.52 (0.23), residues: 468 loop : -2.05 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 36 HIS 0.009 0.003 HIS Y 374 PHE 0.019 0.002 PHE Z 376 TYR 0.030 0.003 TYR Z 227 ARG 0.006 0.001 ARG Z 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 ASP cc_start: 0.7254 (t0) cc_final: 0.6920 (t0) REVERT: C 38 ARG cc_start: 0.8216 (ptt180) cc_final: 0.7903 (ptt180) REVERT: D 35 ASP cc_start: 0.8643 (m-30) cc_final: 0.8291 (m-30) REVERT: D 58 GLU cc_start: 0.6268 (mp0) cc_final: 0.5851 (mp0) REVERT: D 97 ARG cc_start: 0.8168 (tmt-80) cc_final: 0.7724 (tpt-90) REVERT: E 46 GLU cc_start: 0.8022 (mp0) cc_final: 0.7582 (mp0) REVERT: E 47 TRP cc_start: 0.8851 (t60) cc_final: 0.8076 (t60) REVERT: E 50 GLU cc_start: 0.8038 (tt0) cc_final: 0.7769 (tt0) REVERT: E 77 GLN cc_start: 0.7091 (pt0) cc_final: 0.6812 (pm20) REVERT: F 35 ASP cc_start: 0.8554 (m-30) cc_final: 0.8234 (m-30) REVERT: F 58 GLU cc_start: 0.7428 (mp0) cc_final: 0.7002 (mp0) REVERT: F 110 GLU cc_start: 0.8404 (pp20) cc_final: 0.8134 (pp20) REVERT: X 292 LYS cc_start: 0.8115 (tptp) cc_final: 0.7801 (mmmt) REVERT: X 362 GLN cc_start: 0.4443 (mp10) cc_final: 0.3858 (mp10) REVERT: X 492 GLU cc_start: 0.8486 (tt0) cc_final: 0.8202 (tt0) REVERT: X 530 MET cc_start: 0.9078 (mmm) cc_final: 0.8862 (mmm) REVERT: X 588 LYS cc_start: 0.9292 (tmtt) cc_final: 0.8933 (tptt) REVERT: Y 103 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8101 (tm-30) REVERT: Y 104 MET cc_start: 0.8809 (tmm) cc_final: 0.8369 (tmm) REVERT: Z 484 TYR cc_start: 0.8755 (p90) cc_final: 0.8404 (p90) REVERT: Z 486 TYR cc_start: 0.9131 (m-10) cc_final: 0.8831 (m-10) REVERT: Z 584 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8209 (tm-30) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.2724 time to fit residues: 113.2077 Evaluate side-chains 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16176 Z= 0.257 Angle : 0.673 11.385 21924 Z= 0.339 Chirality : 0.048 0.488 2592 Planarity : 0.004 0.045 2700 Dihedral : 10.671 118.096 3039 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.36 (0.19), residues: 1854 helix: 1.51 (0.30), residues: 309 sheet: -0.48 (0.24), residues: 456 loop : -1.91 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 98 HIS 0.009 0.002 HIS Y 375 PHE 0.016 0.002 PHE Z 376 TYR 0.024 0.002 TYR X 619 ARG 0.004 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.8267 (ptt180) cc_final: 0.7910 (ptt180) REVERT: D 35 ASP cc_start: 0.8675 (m-30) cc_final: 0.8296 (m-30) REVERT: D 58 GLU cc_start: 0.6161 (mp0) cc_final: 0.5813 (mp0) REVERT: D 97 ARG cc_start: 0.8146 (tmt-80) cc_final: 0.7778 (tpt-90) REVERT: E 36 TRP cc_start: 0.9085 (m-10) cc_final: 0.8536 (m-10) REVERT: E 46 GLU cc_start: 0.7918 (mp0) cc_final: 0.7404 (mp0) REVERT: E 47 TRP cc_start: 0.8886 (t60) cc_final: 0.8132 (t60) REVERT: E 77 GLN cc_start: 0.7160 (pt0) cc_final: 0.6830 (pm20) REVERT: E 90 MET cc_start: 0.6588 (mmt) cc_final: 0.6343 (mmt) REVERT: F 35 ASP cc_start: 0.8557 (m-30) cc_final: 0.8302 (m-30) REVERT: F 58 GLU cc_start: 0.7164 (mp0) cc_final: 0.6844 (mp0) REVERT: F 92 TYR cc_start: 0.8487 (m-10) cc_final: 0.8203 (m-10) REVERT: F 97 ARG cc_start: 0.8452 (tpt90) cc_final: 0.8041 (tpt-90) REVERT: F 110 GLU cc_start: 0.8396 (pp20) cc_final: 0.8108 (pp20) REVERT: X 54 CYS cc_start: 0.7084 (t) cc_final: 0.6841 (t) REVERT: X 100 MET cc_start: 0.7407 (ttp) cc_final: 0.6845 (ttp) REVERT: X 484 TYR cc_start: 0.8566 (p90) cc_final: 0.7952 (p90) REVERT: X 492 GLU cc_start: 0.8443 (tt0) cc_final: 0.8155 (tt0) REVERT: X 588 LYS cc_start: 0.9294 (tmtt) cc_final: 0.8958 (tptt) REVERT: Y 97 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8330 (tmtt) REVERT: Y 103 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7853 (tm-30) REVERT: Y 353 PHE cc_start: 0.5872 (m-10) cc_final: 0.5636 (m-10) REVERT: Y 383 PHE cc_start: 0.8005 (m-80) cc_final: 0.7781 (m-80) REVERT: Z 97 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8305 (tmmt) REVERT: Z 104 MET cc_start: 0.9310 (mmm) cc_final: 0.9068 (tpp) REVERT: Z 383 PHE cc_start: 0.8052 (m-80) cc_final: 0.7653 (m-80) REVERT: Z 484 TYR cc_start: 0.8688 (p90) cc_final: 0.8304 (p90) REVERT: Z 486 TYR cc_start: 0.9107 (m-10) cc_final: 0.8678 (m-10) REVERT: Z 530 MET cc_start: 0.8744 (tpt) cc_final: 0.8357 (tpt) REVERT: Z 584 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8464 (tm-30) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2623 time to fit residues: 122.2053 Evaluate side-chains 235 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 155 optimal weight: 0.0170 chunk 126 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 268 GLN ** Z 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 490 GLN Z 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16176 Z= 0.226 Angle : 0.657 10.748 21924 Z= 0.330 Chirality : 0.048 0.491 2592 Planarity : 0.004 0.043 2700 Dihedral : 10.201 118.820 3039 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.35 (0.19), residues: 1854 helix: 1.64 (0.30), residues: 309 sheet: -0.48 (0.24), residues: 453 loop : -1.94 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP X 479 HIS 0.007 0.001 HIS Y 375 PHE 0.014 0.002 PHE X 53 TYR 0.020 0.002 TYR X 619 ARG 0.004 0.000 ARG Z 469 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8474 (pttm) cc_final: 0.8133 (mttp) REVERT: C 6 GLN cc_start: 0.6261 (mt0) cc_final: 0.5949 (mt0) REVERT: C 38 ARG cc_start: 0.8297 (ptt180) cc_final: 0.7922 (ptt180) REVERT: C 90 MET cc_start: 0.6377 (mmp) cc_final: 0.6048 (mmp) REVERT: C 101 MET cc_start: 0.7062 (ttp) cc_final: 0.6819 (ttp) REVERT: D 35 ASP cc_start: 0.8585 (m-30) cc_final: 0.8224 (m-30) REVERT: D 58 GLU cc_start: 0.6104 (mp0) cc_final: 0.5703 (mp0) REVERT: E 36 TRP cc_start: 0.9076 (m-10) cc_final: 0.8579 (m-10) REVERT: E 47 TRP cc_start: 0.8858 (t60) cc_final: 0.8255 (t60) REVERT: E 72 ASP cc_start: 0.7486 (t70) cc_final: 0.7206 (t0) REVERT: E 77 GLN cc_start: 0.7126 (pt0) cc_final: 0.6658 (pm20) REVERT: E 90 MET cc_start: 0.6477 (mmt) cc_final: 0.6175 (mmt) REVERT: F 35 ASP cc_start: 0.8540 (m-30) cc_final: 0.8268 (m-30) REVERT: F 58 GLU cc_start: 0.7280 (mp0) cc_final: 0.7022 (mp0) REVERT: F 92 TYR cc_start: 0.8482 (m-10) cc_final: 0.8240 (m-10) REVERT: F 110 GLU cc_start: 0.8380 (pp20) cc_final: 0.8039 (pp20) REVERT: X 54 CYS cc_start: 0.6946 (t) cc_final: 0.6643 (t) REVERT: X 100 MET cc_start: 0.7388 (ttp) cc_final: 0.6835 (ttp) REVERT: X 484 TYR cc_start: 0.8508 (p90) cc_final: 0.7990 (p90) REVERT: X 492 GLU cc_start: 0.8417 (tt0) cc_final: 0.8108 (tt0) REVERT: X 588 LYS cc_start: 0.9300 (tmtt) cc_final: 0.8986 (tptt) REVERT: Y 103 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7923 (tm-30) REVERT: Y 374 HIS cc_start: 0.7898 (t70) cc_final: 0.7686 (t-170) REVERT: Z 97 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8298 (tmmt) REVERT: Z 104 MET cc_start: 0.9188 (mmm) cc_final: 0.8988 (tpp) REVERT: Z 484 TYR cc_start: 0.8677 (p90) cc_final: 0.8351 (p90) REVERT: Z 486 TYR cc_start: 0.9119 (m-10) cc_final: 0.8691 (m-10) outliers start: 2 outliers final: 0 residues processed: 306 average time/residue: 0.2770 time to fit residues: 128.9458 Evaluate side-chains 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 36 optimal weight: 0.0170 chunk 107 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16176 Z= 0.223 Angle : 0.648 11.420 21924 Z= 0.326 Chirality : 0.047 0.485 2592 Planarity : 0.004 0.056 2700 Dihedral : 9.849 118.813 3039 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.27 (0.19), residues: 1854 helix: 1.69 (0.30), residues: 309 sheet: -0.43 (0.24), residues: 483 loop : -1.92 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP X 479 HIS 0.009 0.002 HIS Y 375 PHE 0.015 0.002 PHE X 53 TYR 0.025 0.002 TYR Z 233 ARG 0.003 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6571 (mp10) cc_final: 0.6354 (mp10) REVERT: C 6 GLN cc_start: 0.6471 (mt0) cc_final: 0.6036 (mt0) REVERT: C 38 ARG cc_start: 0.8338 (ptt180) cc_final: 0.7974 (ptt180) REVERT: C 47 TRP cc_start: 0.8394 (t60) cc_final: 0.8167 (t60) REVERT: C 90 MET cc_start: 0.6337 (mmp) cc_final: 0.5986 (mmp) REVERT: D 35 ASP cc_start: 0.8648 (m-30) cc_final: 0.8268 (m-30) REVERT: D 58 GLU cc_start: 0.6128 (mp0) cc_final: 0.5711 (mp0) REVERT: E 36 TRP cc_start: 0.9070 (m-10) cc_final: 0.8586 (m-10) REVERT: E 47 TRP cc_start: 0.8865 (t60) cc_final: 0.8159 (t60) REVERT: E 77 GLN cc_start: 0.7122 (pt0) cc_final: 0.6782 (pm20) REVERT: E 90 MET cc_start: 0.6590 (mmt) cc_final: 0.6203 (mmt) REVERT: F 35 ASP cc_start: 0.8549 (m-30) cc_final: 0.8310 (m-30) REVERT: F 58 GLU cc_start: 0.7278 (mp0) cc_final: 0.7037 (mp0) REVERT: F 92 TYR cc_start: 0.8526 (m-10) cc_final: 0.8314 (m-10) REVERT: F 97 ARG cc_start: 0.8421 (tpt90) cc_final: 0.8013 (tpt-90) REVERT: X 100 MET cc_start: 0.7903 (ttp) cc_final: 0.7168 (ttp) REVERT: X 484 TYR cc_start: 0.8511 (p90) cc_final: 0.8011 (p90) REVERT: X 492 GLU cc_start: 0.8391 (tt0) cc_final: 0.8092 (tt0) REVERT: X 588 LYS cc_start: 0.9308 (tmtt) cc_final: 0.8971 (tptt) REVERT: Y 103 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7881 (tm-30) REVERT: Z 97 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8252 (tmmt) REVERT: Z 104 MET cc_start: 0.9221 (mmm) cc_final: 0.9009 (tpp) REVERT: Z 383 PHE cc_start: 0.7985 (m-80) cc_final: 0.7521 (m-80) REVERT: Z 484 TYR cc_start: 0.8661 (p90) cc_final: 0.8381 (p90) REVERT: Z 486 TYR cc_start: 0.9124 (m-10) cc_final: 0.8680 (m-10) REVERT: Z 584 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8407 (tm-30) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.2902 time to fit residues: 131.0885 Evaluate side-chains 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16176 Z= 0.193 Angle : 0.640 11.020 21924 Z= 0.322 Chirality : 0.047 0.490 2592 Planarity : 0.004 0.055 2700 Dihedral : 9.513 119.180 3039 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.17 (0.19), residues: 1854 helix: 1.85 (0.30), residues: 309 sheet: -0.30 (0.24), residues: 474 loop : -1.90 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 114 HIS 0.006 0.001 HIS Y 375 PHE 0.016 0.001 PHE X 53 TYR 0.030 0.002 TYR Z 233 ARG 0.004 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6739 (mp10) cc_final: 0.6472 (mp10) REVERT: C 6 GLN cc_start: 0.6300 (mt0) cc_final: 0.5762 (mt0) REVERT: C 38 ARG cc_start: 0.8346 (ptt180) cc_final: 0.8044 (ptt180) REVERT: C 90 MET cc_start: 0.6242 (mmp) cc_final: 0.5866 (mmp) REVERT: D 35 ASP cc_start: 0.8598 (m-30) cc_final: 0.8262 (m-30) REVERT: E 36 TRP cc_start: 0.9029 (m-10) cc_final: 0.8548 (m-10) REVERT: E 47 TRP cc_start: 0.8832 (t60) cc_final: 0.8172 (t60) REVERT: E 50 GLU cc_start: 0.7199 (tt0) cc_final: 0.6740 (tt0) REVERT: E 77 GLN cc_start: 0.7115 (pt0) cc_final: 0.6886 (pm20) REVERT: E 90 MET cc_start: 0.6438 (mmt) cc_final: 0.6046 (mmt) REVERT: F 35 ASP cc_start: 0.8489 (m-30) cc_final: 0.8186 (m-30) REVERT: F 58 GLU cc_start: 0.7126 (mp0) cc_final: 0.6787 (mp0) REVERT: F 92 TYR cc_start: 0.8439 (m-10) cc_final: 0.8146 (m-10) REVERT: X 100 MET cc_start: 0.7869 (ttp) cc_final: 0.7109 (ttp) REVERT: X 484 TYR cc_start: 0.8499 (p90) cc_final: 0.8012 (p90) REVERT: X 492 GLU cc_start: 0.8402 (tt0) cc_final: 0.8106 (tt0) REVERT: X 588 LYS cc_start: 0.9299 (tmtt) cc_final: 0.8955 (tptt) REVERT: Y 103 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7930 (tm-30) REVERT: Y 353 PHE cc_start: 0.5723 (m-10) cc_final: 0.5446 (m-10) REVERT: Y 530 MET cc_start: 0.7839 (ttt) cc_final: 0.7543 (mtp) REVERT: Y 622 ILE cc_start: 0.9404 (mt) cc_final: 0.9136 (mt) REVERT: Z 97 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8214 (tmmt) REVERT: Z 104 MET cc_start: 0.9258 (mmm) cc_final: 0.9047 (tpp) REVERT: Z 383 PHE cc_start: 0.7945 (m-80) cc_final: 0.7432 (m-80) REVERT: Z 484 TYR cc_start: 0.8620 (p90) cc_final: 0.8374 (p90) REVERT: Z 486 TYR cc_start: 0.9045 (m-10) cc_final: 0.8500 (m-10) REVERT: Z 584 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8133 (tm-30) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2793 time to fit residues: 128.3688 Evaluate side-chains 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16176 Z= 0.270 Angle : 0.676 13.080 21924 Z= 0.341 Chirality : 0.048 0.492 2592 Planarity : 0.004 0.057 2700 Dihedral : 9.378 119.112 3039 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.32 (0.19), residues: 1854 helix: 1.76 (0.30), residues: 309 sheet: -0.50 (0.24), residues: 486 loop : -1.96 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 114 HIS 0.009 0.002 HIS Z 374 PHE 0.020 0.002 PHE D 101 TYR 0.031 0.002 TYR Z 233 ARG 0.006 0.000 ARG Y 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6809 (mp10) cc_final: 0.6507 (mp10) REVERT: B 59 ARG cc_start: 0.7623 (ptp90) cc_final: 0.7348 (ptp-170) REVERT: C 6 GLN cc_start: 0.6513 (mt0) cc_final: 0.5976 (mt0) REVERT: C 38 ARG cc_start: 0.8347 (ptt180) cc_final: 0.8044 (ptt180) REVERT: C 90 MET cc_start: 0.6210 (mmp) cc_final: 0.5894 (mmp) REVERT: D 35 ASP cc_start: 0.8630 (m-30) cc_final: 0.8294 (m-30) REVERT: E 36 TRP cc_start: 0.9117 (m100) cc_final: 0.8566 (m-10) REVERT: E 47 TRP cc_start: 0.8884 (t60) cc_final: 0.8187 (t60) REVERT: E 77 GLN cc_start: 0.7094 (pt0) cc_final: 0.6837 (pm20) REVERT: E 90 MET cc_start: 0.6525 (mmt) cc_final: 0.6147 (mmt) REVERT: F 35 ASP cc_start: 0.8507 (m-30) cc_final: 0.8238 (m-30) REVERT: F 58 GLU cc_start: 0.7186 (mp0) cc_final: 0.6862 (mp0) REVERT: F 92 TYR cc_start: 0.8474 (m-10) cc_final: 0.8227 (m-10) REVERT: F 97 ARG cc_start: 0.8397 (tpt90) cc_final: 0.8142 (tpt-90) REVERT: X 100 MET cc_start: 0.7937 (ttp) cc_final: 0.7204 (ttp) REVERT: X 484 TYR cc_start: 0.8518 (p90) cc_final: 0.7969 (p90) REVERT: X 492 GLU cc_start: 0.8412 (tt0) cc_final: 0.8111 (tt0) REVERT: X 588 LYS cc_start: 0.9312 (tmtt) cc_final: 0.8980 (tptt) REVERT: Y 103 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7920 (tm-30) REVERT: Y 353 PHE cc_start: 0.5831 (m-10) cc_final: 0.5551 (m-10) REVERT: Y 530 MET cc_start: 0.7960 (ttt) cc_final: 0.7628 (mtp) REVERT: Y 622 ILE cc_start: 0.9428 (mt) cc_final: 0.9180 (mt) REVERT: Z 104 MET cc_start: 0.9283 (mmm) cc_final: 0.9026 (tpp) REVERT: Z 269 LEU cc_start: 0.8463 (mt) cc_final: 0.8233 (mp) REVERT: Z 484 TYR cc_start: 0.8643 (p90) cc_final: 0.8431 (p90) REVERT: Z 486 TYR cc_start: 0.9118 (m-10) cc_final: 0.8623 (m-10) REVERT: Z 584 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8471 (tm-30) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2758 time to fit residues: 117.2282 Evaluate side-chains 226 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16176 Z= 0.197 Angle : 0.660 12.016 21924 Z= 0.331 Chirality : 0.047 0.492 2592 Planarity : 0.004 0.055 2700 Dihedral : 9.125 119.099 3039 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.25 (0.19), residues: 1854 helix: 1.72 (0.30), residues: 312 sheet: -0.35 (0.24), residues: 480 loop : -1.96 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP X 479 HIS 0.005 0.001 HIS Y 375 PHE 0.017 0.001 PHE X 53 TYR 0.034 0.002 TYR X 227 ARG 0.004 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6650 (mp10) cc_final: 0.6349 (mp10) REVERT: A 93 TYR cc_start: 0.8385 (m-10) cc_final: 0.8163 (m-10) REVERT: B 59 ARG cc_start: 0.7547 (ptp90) cc_final: 0.7294 (ptp-170) REVERT: B 97 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7838 (ttp80) REVERT: C 6 GLN cc_start: 0.6496 (mt0) cc_final: 0.5964 (mt0) REVERT: C 38 ARG cc_start: 0.8385 (ptt180) cc_final: 0.8048 (ptt180) REVERT: C 90 MET cc_start: 0.6407 (mmp) cc_final: 0.6078 (mmp) REVERT: D 35 ASP cc_start: 0.8641 (m-30) cc_final: 0.8250 (m-30) REVERT: E 47 TRP cc_start: 0.8877 (t60) cc_final: 0.8145 (t60) REVERT: E 77 GLN cc_start: 0.7029 (pt0) cc_final: 0.6811 (pm20) REVERT: E 90 MET cc_start: 0.6510 (mmt) cc_final: 0.6112 (mmt) REVERT: F 35 ASP cc_start: 0.8468 (m-30) cc_final: 0.8162 (m-30) REVERT: F 92 TYR cc_start: 0.8447 (m-10) cc_final: 0.8217 (m-10) REVERT: X 100 MET cc_start: 0.7877 (ttp) cc_final: 0.7067 (ttp) REVERT: X 292 LYS cc_start: 0.8279 (tptp) cc_final: 0.7646 (mmmt) REVERT: X 484 TYR cc_start: 0.8497 (p90) cc_final: 0.8023 (p90) REVERT: X 492 GLU cc_start: 0.8397 (tt0) cc_final: 0.8077 (tt0) REVERT: X 588 LYS cc_start: 0.9307 (tmtt) cc_final: 0.8988 (tptt) REVERT: Y 97 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8343 (mttt) REVERT: Y 103 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7951 (tm-30) REVERT: Z 97 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8862 (tmtt) REVERT: Z 104 MET cc_start: 0.9242 (mmm) cc_final: 0.8349 (tpp) REVERT: Z 227 TYR cc_start: 0.7410 (m-80) cc_final: 0.7072 (m-80) REVERT: Z 383 PHE cc_start: 0.7944 (m-80) cc_final: 0.7447 (m-80) REVERT: Z 484 TYR cc_start: 0.8637 (p90) cc_final: 0.8421 (p90) REVERT: Z 486 TYR cc_start: 0.9046 (m-10) cc_final: 0.8480 (m-10) REVERT: Z 584 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8141 (tm-30) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2692 time to fit residues: 116.4581 Evaluate side-chains 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN ** X 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16176 Z= 0.385 Angle : 0.769 12.330 21924 Z= 0.389 Chirality : 0.050 0.489 2592 Planarity : 0.005 0.062 2700 Dihedral : 9.319 118.797 3039 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.67 (0.19), residues: 1854 helix: 1.37 (0.29), residues: 312 sheet: -0.75 (0.22), residues: 534 loop : -2.21 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP X 479 HIS 0.008 0.002 HIS Z 374 PHE 0.020 0.002 PHE C 78 TYR 0.034 0.003 TYR X 227 ARG 0.007 0.001 ARG E 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6663 (mp10) cc_final: 0.6383 (mp10) REVERT: B 97 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7876 (ttp80) REVERT: C 6 GLN cc_start: 0.6659 (mt0) cc_final: 0.6066 (mt0) REVERT: C 38 ARG cc_start: 0.8356 (ptt180) cc_final: 0.8094 (ptt180) REVERT: C 47 TRP cc_start: 0.8631 (t60) cc_final: 0.8223 (t60) REVERT: C 90 MET cc_start: 0.6601 (mmp) cc_final: 0.6308 (mmp) REVERT: C 102 MET cc_start: 0.7940 (tpp) cc_final: 0.7607 (tpt) REVERT: C 122 VAL cc_start: 0.5924 (t) cc_final: 0.5637 (t) REVERT: D 35 ASP cc_start: 0.8690 (m-30) cc_final: 0.8273 (m-30) REVERT: E 36 TRP cc_start: 0.9159 (m-10) cc_final: 0.8741 (m-10) REVERT: E 47 TRP cc_start: 0.8874 (t60) cc_final: 0.8055 (t60) REVERT: E 77 GLN cc_start: 0.7001 (pt0) cc_final: 0.6731 (pm20) REVERT: E 90 MET cc_start: 0.6767 (mmt) cc_final: 0.6367 (mmt) REVERT: F 35 ASP cc_start: 0.8531 (m-30) cc_final: 0.8252 (m-30) REVERT: F 92 TYR cc_start: 0.8558 (m-10) cc_final: 0.8334 (m-10) REVERT: F 97 ARG cc_start: 0.8404 (tpt90) cc_final: 0.8201 (tpt-90) REVERT: X 100 MET cc_start: 0.8024 (ttp) cc_final: 0.7357 (ttp) REVERT: X 484 TYR cc_start: 0.8535 (p90) cc_final: 0.7995 (p90) REVERT: X 492 GLU cc_start: 0.8430 (tt0) cc_final: 0.8109 (tt0) REVERT: X 588 LYS cc_start: 0.9326 (tmtt) cc_final: 0.8986 (tptt) REVERT: X 635 ILE cc_start: 0.8918 (mm) cc_final: 0.8677 (tt) REVERT: Y 103 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7969 (tm-30) REVERT: Z 104 MET cc_start: 0.9262 (mmm) cc_final: 0.9037 (tpp) REVERT: Z 112 TRP cc_start: 0.8050 (m100) cc_final: 0.7817 (m100) REVERT: Z 486 TYR cc_start: 0.9172 (m-10) cc_final: 0.8730 (m-10) REVERT: Z 584 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8163 (tm-30) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2702 time to fit residues: 109.7519 Evaluate side-chains 217 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN ** Z 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109740 restraints weight = 33457.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112786 restraints weight = 21687.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114899 restraints weight = 16132.842| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16176 Z= 0.203 Angle : 0.677 11.777 21924 Z= 0.341 Chirality : 0.048 0.495 2592 Planarity : 0.004 0.059 2700 Dihedral : 8.917 118.206 3039 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.35 (0.19), residues: 1854 helix: 1.66 (0.29), residues: 312 sheet: -0.45 (0.24), residues: 483 loop : -2.01 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP X 479 HIS 0.008 0.001 HIS Y 375 PHE 0.018 0.002 PHE X 53 TYR 0.021 0.002 TYR X 227 ARG 0.004 0.000 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3144.42 seconds wall clock time: 58 minutes 45.78 seconds (3525.78 seconds total)