Starting phenix.real_space_refine on Sat May 17 18:46:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpg_34192/05_2025/8gpg_34192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpg_34192/05_2025/8gpg_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_34192/05_2025/8gpg_34192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpg_34192/05_2025/8gpg_34192.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpg_34192/05_2025/8gpg_34192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpg_34192/05_2025/8gpg_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.38, per 1000 atoms: 0.59 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: 5.33 Conformation dependent library (CDL) restraints added in 2.1 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: 2.12 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: 5.36 Time building geometry restraints manager: 5.07 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: 0.03 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: 1.380 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.220 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.180 ------------------------------------------------------------------------------- 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 16252 Z= 0.224 Angle : 0.800 12.635 22124 Z= 0.384 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 30) link_NAG-ASN : angle 3.23805 ( 90) link_ALPHA1-6 : bond 0.00582 ( 3) link_ALPHA1-6 : angle 1.64784 ( 9) link_BETA1-4 : bond 0.00662 ( 12) link_BETA1-4 : angle 2.18505 ( 36) link_ALPHA1-3 : bond 0.01161 ( 3) link_ALPHA1-3 : angle 4.52553 ( 9) hydrogen bonds : bond 0.11970 ( 544) hydrogen bonds : angle 6.37796 ( 1503) SS BOND : bond 0.00455 ( 28) SS BOND : angle 1.44282 ( 56) covalent geometry : bond 0.00487 (16176) covalent geometry : angle 0.76174 (21924) *********************** 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 : 1.606 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: 0.2436 time to fit residues: 114.0762 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 : 1.856 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7980 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 478 ASN ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Z 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116905 restraints weight = 33094.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119976 restraints weight = 21259.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122118 restraints weight = 15698.733| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 16252 Z= 0.133 Angle : 0.673 13.815 22124 Z= 0.326 Chirality : 0.047 0.496 2592 Planarity : 0.004 0.066 2700 Dihedral : 12.517 118.493 3039 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.99 % 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: -1.21 (0.19), residues: 1854 helix: 1.52 (0.29), residues: 315 sheet: -0.28 (0.24), residues: 450 loop : -1.84 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 36 HIS 0.008 0.001 HIS Y 375 PHE 0.014 0.001 PHE X 53 TYR 0.018 0.001 TYR Z 227 ARG 0.004 0.000 ARG Y 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 30) link_NAG-ASN : angle 2.95226 ( 90) link_ALPHA1-6 : bond 0.00959 ( 3) link_ALPHA1-6 : angle 1.65824 ( 9) link_BETA1-4 : bond 0.00436 ( 12) link_BETA1-4 : angle 1.92518 ( 36) link_ALPHA1-3 : bond 0.01797 ( 3) link_ALPHA1-3 : angle 5.10278 ( 9) hydrogen bonds : bond 0.04287 ( 544) hydrogen bonds : angle 5.60494 ( 1503) SS BOND : bond 0.00449 ( 28) SS BOND : angle 1.68057 ( 56) covalent geometry : bond 0.00305 (16176) covalent geometry : angle 0.62926 (21924) *********************** 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 315 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 1.664 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: D 35 ASP cc_start: 0.8518 (m-30) cc_final: 0.8206 (m-30) REVERT: D 97 ARG cc_start: 0.7921 (tmt-80) cc_final: 0.7642 (tpt-90) REVERT: E 90 MET cc_start: 0.6342 (mmt) cc_final: 0.6083 (mmt) REVERT: F 35 ASP cc_start: 0.8411 (m-30) cc_final: 0.8202 (m-30) REVERT: F 57 SER cc_start: 0.8816 (m) cc_final: 0.8473 (m) REVERT: F 58 GLU cc_start: 0.7040 (mp0) cc_final: 0.6836 (mp0) REVERT: X 54 CYS cc_start: 0.6927 (t) cc_final: 0.6713 (t) REVERT: X 484 TYR cc_start: 0.8440 (p90) cc_final: 0.7785 (p90) REVERT: X 492 GLU cc_start: 0.8542 (tt0) cc_final: 0.8272 (tt0) REVERT: X 588 LYS cc_start: 0.9313 (tmtt) cc_final: 0.8941 (tptt) REVERT: Y 353 PHE cc_start: 0.5407 (m-10) cc_final: 0.5167 (m-10) REVERT: Y 484 TYR cc_start: 0.8212 (p90) cc_final: 0.7945 (p90) REVERT: Y 576 LEU cc_start: 0.9108 (tp) cc_final: 0.8904 (tt) REVERT: Z 484 TYR cc_start: 0.8715 (p90) cc_final: 0.8135 (p90) REVERT: Z 486 TYR cc_start: 0.8909 (m-10) cc_final: 0.8496 (m-10) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.2639 time to fit residues: 127.2157 Evaluate side-chains 243 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 30 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN 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 374 HIS ** 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 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110174 restraints weight = 33452.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112921 restraints weight = 22275.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114877 restraints weight = 16992.776| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16252 Z= 0.270 Angle : 0.799 14.251 22124 Z= 0.390 Chirality : 0.050 0.476 2592 Planarity : 0.005 0.050 2700 Dihedral : 11.423 117.493 3039 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % 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: -1.49 (0.19), residues: 1854 helix: 1.42 (0.29), residues: 309 sheet: -0.47 (0.24), residues: 453 loop : -2.05 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 36 HIS 0.009 0.003 HIS X 374 PHE 0.018 0.002 PHE A 78 TYR 0.031 0.003 TYR Z 227 ARG 0.006 0.001 ARG Z 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 30) link_NAG-ASN : angle 3.18780 ( 90) link_ALPHA1-6 : bond 0.00795 ( 3) link_ALPHA1-6 : angle 2.02632 ( 9) link_BETA1-4 : bond 0.00413 ( 12) link_BETA1-4 : angle 2.10188 ( 36) link_ALPHA1-3 : bond 0.01537 ( 3) link_ALPHA1-3 : angle 5.21196 ( 9) hydrogen bonds : bond 0.04859 ( 544) hydrogen bonds : angle 5.71447 ( 1503) SS BOND : bond 0.00609 ( 28) SS BOND : angle 1.75908 ( 56) covalent geometry : bond 0.00623 (16176) covalent geometry : angle 0.75815 (21924) *********************** 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 292 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 GLN cc_start: 0.6143 (mt0) cc_final: 0.5794 (mt0) REVERT: C 38 ARG cc_start: 0.8092 (ptt180) cc_final: 0.7837 (ptt180) REVERT: D 35 ASP cc_start: 0.8520 (m-30) cc_final: 0.8221 (m-30) REVERT: D 58 GLU cc_start: 0.6402 (mp0) cc_final: 0.5974 (mp0) REVERT: D 97 ARG cc_start: 0.8126 (tmt-80) cc_final: 0.7789 (tpt-90) REVERT: E 46 GLU cc_start: 0.8124 (mp0) cc_final: 0.7746 (mp0) REVERT: E 47 TRP cc_start: 0.8824 (t60) cc_final: 0.8039 (t60) REVERT: E 50 GLU cc_start: 0.7867 (tt0) cc_final: 0.7594 (tt0) REVERT: F 35 ASP cc_start: 0.8410 (m-30) cc_final: 0.8134 (m-30) REVERT: F 58 GLU cc_start: 0.7278 (mp0) cc_final: 0.6981 (mp0) REVERT: F 92 TYR cc_start: 0.8499 (m-10) cc_final: 0.8249 (m-10) REVERT: X 492 GLU cc_start: 0.8398 (tt0) cc_final: 0.8124 (tt0) REVERT: X 588 LYS cc_start: 0.9366 (tmtt) cc_final: 0.9010 (tptt) REVERT: X 635 ILE cc_start: 0.8975 (mm) cc_final: 0.8602 (tt) REVERT: Y 97 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8375 (tmtt) REVERT: Y 103 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8161 (tm-30) REVERT: Y 104 MET cc_start: 0.8662 (tmm) cc_final: 0.8442 (tmm) REVERT: Z 227 TYR cc_start: 0.7560 (m-80) cc_final: 0.7248 (m-80) REVERT: Z 484 TYR cc_start: 0.8719 (p90) cc_final: 0.8296 (p90) REVERT: Z 486 TYR cc_start: 0.9090 (m-10) cc_final: 0.8841 (m-10) REVERT: Z 584 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8121 (tm-30) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.2582 time to fit residues: 113.1842 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 132 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 130 optimal weight: 0.0870 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.138073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115345 restraints weight = 33044.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118421 restraints weight = 21223.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120582 restraints weight = 15705.575| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16252 Z= 0.134 Angle : 0.690 13.672 22124 Z= 0.333 Chirality : 0.047 0.491 2592 Planarity : 0.004 0.043 2700 Dihedral : 10.545 118.407 3039 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.12 % Allowed : 3.78 % Favored : 96.11 % 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: -1.23 (0.19), residues: 1854 helix: 1.62 (0.30), residues: 309 sheet: -0.32 (0.24), residues: 447 loop : -1.86 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 98 HIS 0.010 0.002 HIS Z 374 PHE 0.013 0.001 PHE A 78 TYR 0.021 0.002 TYR X 619 ARG 0.006 0.000 ARG E 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 30) link_NAG-ASN : angle 2.94858 ( 90) link_ALPHA1-6 : bond 0.01040 ( 3) link_ALPHA1-6 : angle 2.02829 ( 9) link_BETA1-4 : bond 0.00329 ( 12) link_BETA1-4 : angle 2.06334 ( 36) link_ALPHA1-3 : bond 0.01857 ( 3) link_ALPHA1-3 : angle 5.34439 ( 9) hydrogen bonds : bond 0.03881 ( 544) hydrogen bonds : angle 5.30495 ( 1503) SS BOND : bond 0.00550 ( 28) SS BOND : angle 1.46316 ( 56) covalent geometry : bond 0.00308 (16176) covalent geometry : angle 0.64734 (21924) *********************** 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 324 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 1.957 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: 0.6879 (mp10) cc_final: 0.6639 (mp10) REVERT: C 6 GLN cc_start: 0.6115 (mt0) cc_final: 0.5847 (mt0) REVERT: C 38 ARG cc_start: 0.8099 (ptt180) cc_final: 0.7820 (ptt180) REVERT: D 35 ASP cc_start: 0.8504 (m-30) cc_final: 0.8175 (m-30) REVERT: D 58 GLU cc_start: 0.6292 (mp0) cc_final: 0.5943 (mp0) REVERT: D 97 ARG cc_start: 0.8074 (tmt-80) cc_final: 0.7816 (tpt-90) REVERT: E 36 TRP cc_start: 0.9007 (m-10) cc_final: 0.8533 (m-10) REVERT: E 47 TRP cc_start: 0.8834 (t60) cc_final: 0.8102 (t60) REVERT: E 90 MET cc_start: 0.6407 (mmt) cc_final: 0.6121 (mmt) REVERT: F 92 TYR cc_start: 0.8369 (m-10) cc_final: 0.8146 (m-10) REVERT: F 97 ARG cc_start: 0.8299 (tpt90) cc_final: 0.7962 (tpt-90) REVERT: X 54 CYS cc_start: 0.7211 (t) cc_final: 0.6919 (t) REVERT: X 100 MET cc_start: 0.7223 (ttp) cc_final: 0.6768 (ttp) REVERT: X 484 TYR cc_start: 0.8486 (p90) cc_final: 0.7899 (p90) REVERT: X 492 GLU cc_start: 0.8346 (tt0) cc_final: 0.8043 (tt0) REVERT: X 588 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9008 (tptt) REVERT: X 620 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7390 (tm-30) REVERT: Y 103 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7953 (tm-30) REVERT: Y 353 PHE cc_start: 0.5708 (m-10) cc_final: 0.5444 (m-10) REVERT: Y 383 PHE cc_start: 0.7928 (m-80) cc_final: 0.7689 (m-80) REVERT: Y 576 LEU cc_start: 0.9111 (tp) cc_final: 0.8896 (tp) REVERT: Z 97 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8246 (tmmt) REVERT: Z 104 MET cc_start: 0.9171 (mmm) cc_final: 0.8944 (tpp) REVERT: Z 469 ARG cc_start: 0.8240 (tpp80) cc_final: 0.7897 (tpt-90) REVERT: Z 484 TYR cc_start: 0.8686 (p90) cc_final: 0.8291 (p90) REVERT: Z 486 TYR cc_start: 0.9037 (m-10) cc_final: 0.8613 (m-10) REVERT: Z 584 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8395 (tm-30) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.2512 time to fit residues: 122.6404 Evaluate side-chains 242 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 375 HIS ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 297 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109820 restraints weight = 33762.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112560 restraints weight = 22437.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114569 restraints weight = 17104.746| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16252 Z= 0.267 Angle : 0.788 13.473 22124 Z= 0.387 Chirality : 0.050 0.473 2592 Planarity : 0.005 0.057 2700 Dihedral : 10.442 118.099 3039 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -1.55 (0.19), residues: 1854 helix: 1.41 (0.30), residues: 309 sheet: -0.66 (0.23), residues: 483 loop : -2.05 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 479 HIS 0.010 0.003 HIS Z 374 PHE 0.026 0.002 PHE B 101 TYR 0.029 0.003 TYR D 91 ARG 0.006 0.001 ARG E 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 30) link_NAG-ASN : angle 3.19595 ( 90) link_ALPHA1-6 : bond 0.00846 ( 3) link_ALPHA1-6 : angle 2.00967 ( 9) link_BETA1-4 : bond 0.00437 ( 12) link_BETA1-4 : angle 2.10033 ( 36) link_ALPHA1-3 : bond 0.01542 ( 3) link_ALPHA1-3 : angle 5.25652 ( 9) hydrogen bonds : bond 0.04759 ( 544) hydrogen bonds : angle 5.59215 ( 1503) SS BOND : bond 0.00673 ( 28) SS BOND : angle 1.77506 ( 56) covalent geometry : bond 0.00614 (16176) covalent geometry : angle 0.74599 (21924) *********************** 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 288 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 ASP cc_start: 0.7043 (t0) cc_final: 0.6777 (t0) REVERT: B 110 GLU cc_start: 0.8423 (pp20) cc_final: 0.8121 (pp20) REVERT: C 6 GLN cc_start: 0.6565 (mt0) cc_final: 0.6084 (mt0) REVERT: C 38 ARG cc_start: 0.8148 (ptt180) cc_final: 0.7913 (ptt180) REVERT: C 90 MET cc_start: 0.6511 (mmp) cc_final: 0.6233 (mmp) REVERT: D 35 ASP cc_start: 0.8518 (m-30) cc_final: 0.8190 (m-30) REVERT: D 58 GLU cc_start: 0.6381 (mp0) cc_final: 0.5856 (mp0) REVERT: E 36 TRP cc_start: 0.9159 (m-10) cc_final: 0.8704 (m-10) REVERT: E 47 TRP cc_start: 0.8904 (t60) cc_final: 0.8341 (t60) REVERT: E 77 GLN cc_start: 0.6619 (pm20) cc_final: 0.6311 (pm20) REVERT: F 35 ASP cc_start: 0.8486 (m-30) cc_final: 0.8233 (m-30) REVERT: F 97 ARG cc_start: 0.8396 (tpt90) cc_final: 0.8121 (tpt-90) REVERT: X 54 CYS cc_start: 0.6835 (t) cc_final: 0.6626 (t) REVERT: X 484 TYR cc_start: 0.8505 (p90) cc_final: 0.7867 (p90) REVERT: X 492 GLU cc_start: 0.8367 (tt0) cc_final: 0.8112 (tt0) REVERT: X 588 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9067 (tptt) REVERT: X 635 ILE cc_start: 0.8977 (mm) cc_final: 0.8710 (tt) REVERT: Y 103 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8041 (tm-30) REVERT: Z 97 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8337 (tmmt) REVERT: Z 469 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8072 (tpp80) REVERT: Z 484 TYR cc_start: 0.8689 (p90) cc_final: 0.8350 (p90) REVERT: Z 486 TYR cc_start: 0.9159 (m-10) cc_final: 0.8867 (m-10) REVERT: Z 584 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8150 (tm-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2523 time to fit residues: 109.3811 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 : 1.598 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** 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 374 HIS ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN Z 103 GLN Z 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114937 restraints weight = 33073.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117968 restraints weight = 21330.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120084 restraints weight = 15783.264| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16252 Z= 0.136 Angle : 0.695 13.550 22124 Z= 0.339 Chirality : 0.048 0.493 2592 Planarity : 0.004 0.058 2700 Dihedral : 9.863 118.369 3039 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % 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: -1.28 (0.19), residues: 1854 helix: 1.70 (0.30), residues: 309 sheet: -0.50 (0.24), residues: 486 loop : -1.89 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 479 HIS 0.008 0.001 HIS X 374 PHE 0.016 0.001 PHE X 53 TYR 0.020 0.002 TYR X 227 ARG 0.003 0.000 ARG E 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 30) link_NAG-ASN : angle 2.97532 ( 90) link_ALPHA1-6 : bond 0.01035 ( 3) link_ALPHA1-6 : angle 2.04564 ( 9) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 2.05649 ( 36) link_ALPHA1-3 : bond 0.01672 ( 3) link_ALPHA1-3 : angle 5.09629 ( 9) hydrogen bonds : bond 0.03854 ( 544) hydrogen bonds : angle 5.26807 ( 1503) SS BOND : bond 0.00511 ( 28) SS BOND : angle 1.42712 ( 56) covalent geometry : bond 0.00308 (16176) covalent geometry : angle 0.65279 (21924) *********************** 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 311 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6782 (mt0) cc_final: 0.5836 (mt0) REVERT: A 77 GLN cc_start: 0.6796 (mp10) cc_final: 0.6562 (mp10) REVERT: B 110 GLU cc_start: 0.8428 (pp20) cc_final: 0.7953 (pp20) REVERT: C 6 GLN cc_start: 0.6441 (mt0) cc_final: 0.5869 (mt0) REVERT: C 38 ARG cc_start: 0.8211 (ptt180) cc_final: 0.7999 (ptt180) REVERT: C 90 MET cc_start: 0.6389 (mmp) cc_final: 0.6105 (mmp) REVERT: D 35 ASP cc_start: 0.8550 (m-30) cc_final: 0.8186 (m-30) REVERT: D 68 SER cc_start: 0.8313 (t) cc_final: 0.7960 (p) REVERT: E 36 TRP cc_start: 0.9036 (m-10) cc_final: 0.8613 (m-10) REVERT: E 47 TRP cc_start: 0.8819 (t60) cc_final: 0.8210 (t60) REVERT: E 50 GLU cc_start: 0.6920 (tt0) cc_final: 0.6490 (tt0) REVERT: E 90 MET cc_start: 0.6546 (mmt) cc_final: 0.6250 (mmt) REVERT: F 35 ASP cc_start: 0.8460 (m-30) cc_final: 0.8186 (m-30) REVERT: F 97 ARG cc_start: 0.8330 (tpt90) cc_final: 0.8093 (tpt-90) REVERT: F 105 GLN cc_start: 0.8520 (mm110) cc_final: 0.8270 (mp10) REVERT: X 100 MET cc_start: 0.7921 (ttp) cc_final: 0.7167 (ttp) REVERT: X 484 TYR cc_start: 0.8430 (p90) cc_final: 0.7959 (p90) REVERT: X 492 GLU cc_start: 0.8348 (tt0) cc_final: 0.8068 (tt0) REVERT: X 588 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9024 (tptt) REVERT: X 620 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7358 (tm-30) REVERT: Y 54 CYS cc_start: 0.6654 (t) cc_final: 0.6443 (t) REVERT: Y 103 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7897 (tm-30) REVERT: Y 530 MET cc_start: 0.7809 (ttt) cc_final: 0.7482 (mtp) REVERT: Y 622 ILE cc_start: 0.9425 (mt) cc_final: 0.9177 (mt) REVERT: Z 97 LYS cc_start: 0.8829 (tmtt) cc_final: 0.8275 (tmmt) REVERT: Z 233 TYR cc_start: 0.8939 (m-80) cc_final: 0.8552 (m-80) REVERT: Z 469 ARG cc_start: 0.8215 (tpp80) cc_final: 0.7928 (mmt90) REVERT: Z 484 TYR cc_start: 0.8593 (p90) cc_final: 0.8333 (p90) REVERT: Z 486 TYR cc_start: 0.9120 (m-10) cc_final: 0.8646 (m-10) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.2513 time to fit residues: 118.4366 Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 ** 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 = 0.3880 r_free = 0.3880 target = 0.140681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119207 restraints weight = 33108.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122205 restraints weight = 21453.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124342 restraints weight = 15899.986| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16252 Z= 0.131 Angle : 0.692 13.578 22124 Z= 0.334 Chirality : 0.047 0.490 2592 Planarity : 0.004 0.057 2700 Dihedral : 9.508 118.939 3039 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.31 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: -1.18 (0.19), residues: 1854 helix: 1.79 (0.30), residues: 309 sheet: -0.34 (0.24), residues: 474 loop : -1.87 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP X 479 HIS 0.009 0.001 HIS X 374 PHE 0.014 0.001 PHE X 53 TYR 0.022 0.002 TYR Y 486 ARG 0.003 0.000 ARG X 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 30) link_NAG-ASN : angle 3.10247 ( 90) link_ALPHA1-6 : bond 0.01038 ( 3) link_ALPHA1-6 : angle 2.08367 ( 9) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 1.97421 ( 36) link_ALPHA1-3 : bond 0.01675 ( 3) link_ALPHA1-3 : angle 5.01761 ( 9) hydrogen bonds : bond 0.03711 ( 544) hydrogen bonds : angle 5.12598 ( 1503) SS BOND : bond 0.00586 ( 28) SS BOND : angle 1.45514 ( 56) covalent geometry : bond 0.00297 (16176) covalent geometry : angle 0.64788 (21924) *********************** 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 308 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.710 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: 0.6749 (mp10) cc_final: 0.6451 (mp10) REVERT: B 110 GLU cc_start: 0.8327 (pp20) cc_final: 0.7823 (pp20) REVERT: C 6 GLN cc_start: 0.6178 (mt0) cc_final: 0.5739 (mt0) REVERT: C 38 ARG cc_start: 0.8166 (ptt180) cc_final: 0.7939 (ptt180) REVERT: C 90 MET cc_start: 0.6357 (mmp) cc_final: 0.5951 (mmp) REVERT: C 102 MET cc_start: 0.7789 (tpp) cc_final: 0.7580 (tpt) REVERT: D 35 ASP cc_start: 0.8414 (m-30) cc_final: 0.8088 (m-30) REVERT: E 47 TRP cc_start: 0.8800 (t60) cc_final: 0.8176 (t60) REVERT: E 50 GLU cc_start: 0.7051 (tt0) cc_final: 0.6673 (tt0) REVERT: E 77 GLN cc_start: 0.6765 (pm20) cc_final: 0.6502 (pm20) REVERT: E 90 MET cc_start: 0.6377 (mmt) cc_final: 0.6089 (mmt) REVERT: F 35 ASP cc_start: 0.8383 (m-30) cc_final: 0.8113 (m-30) REVERT: F 92 TYR cc_start: 0.8433 (m-10) cc_final: 0.8207 (m-10) REVERT: X 54 CYS cc_start: 0.7006 (t) cc_final: 0.6731 (t) REVERT: X 100 MET cc_start: 0.7956 (ttp) cc_final: 0.7278 (ttp) REVERT: X 484 TYR cc_start: 0.8441 (p90) cc_final: 0.7972 (p90) REVERT: X 492 GLU cc_start: 0.8261 (tt0) cc_final: 0.8009 (tt0) REVERT: X 588 LYS cc_start: 0.9354 (tmtt) cc_final: 0.9026 (tptt) REVERT: X 620 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7308 (tm-30) REVERT: Y 103 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7848 (tm-30) REVERT: Y 530 MET cc_start: 0.7672 (ttt) cc_final: 0.7343 (mtp) REVERT: Y 622 ILE cc_start: 0.9382 (mt) cc_final: 0.9167 (mt) REVERT: Z 97 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8224 (tmmt) REVERT: Z 469 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7909 (mmt90) REVERT: Z 484 TYR cc_start: 0.8550 (p90) cc_final: 0.8281 (p90) REVERT: Z 486 TYR cc_start: 0.9045 (m-10) cc_final: 0.8560 (m-10) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2477 time to fit residues: 116.5157 Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 10 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN Z 103 GLN Z 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117347 restraints weight = 31950.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120346 restraints weight = 20010.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122357 restraints weight = 14562.112| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16252 Z= 0.148 Angle : 0.696 13.406 22124 Z= 0.338 Chirality : 0.047 0.486 2592 Planarity : 0.004 0.055 2700 Dihedral : 9.256 118.732 3039 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.06 % Allowed : 1.42 % Favored : 98.53 % 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: -1.24 (0.19), residues: 1854 helix: 1.79 (0.30), residues: 309 sheet: -0.47 (0.24), residues: 486 loop : -1.89 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 36 HIS 0.008 0.001 HIS Z 374 PHE 0.015 0.001 PHE X 53 TYR 0.018 0.002 TYR D 91 ARG 0.003 0.000 ARG F 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 30) link_NAG-ASN : angle 3.05351 ( 90) link_ALPHA1-6 : bond 0.01128 ( 3) link_ALPHA1-6 : angle 2.16982 ( 9) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.95534 ( 36) link_ALPHA1-3 : bond 0.01439 ( 3) link_ALPHA1-3 : angle 4.94818 ( 9) hydrogen bonds : bond 0.03737 ( 544) hydrogen bonds : angle 5.07650 ( 1503) SS BOND : bond 0.00514 ( 28) SS BOND : angle 1.28742 ( 56) covalent geometry : bond 0.00342 (16176) covalent geometry : angle 0.65447 (21924) *********************** 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 294 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7547 (ptp90) cc_final: 0.7331 (ptp-170) REVERT: B 110 GLU cc_start: 0.8408 (pp20) cc_final: 0.7819 (pp20) REVERT: C 6 GLN cc_start: 0.6538 (mt0) cc_final: 0.6082 (mt0) REVERT: C 38 ARG cc_start: 0.8178 (ptt180) cc_final: 0.7960 (ptt180) REVERT: C 90 MET cc_start: 0.6406 (mmp) cc_final: 0.6036 (mmp) REVERT: C 102 MET cc_start: 0.7753 (tpp) cc_final: 0.7551 (tpt) REVERT: D 35 ASP cc_start: 0.8444 (m-30) cc_final: 0.8121 (m-30) REVERT: E 36 TRP cc_start: 0.8992 (m-10) cc_final: 0.8623 (m-10) REVERT: E 47 TRP cc_start: 0.8793 (t60) cc_final: 0.8209 (t60) REVERT: E 90 MET cc_start: 0.6483 (mmt) cc_final: 0.6143 (mmt) REVERT: F 35 ASP cc_start: 0.8461 (m-30) cc_final: 0.8111 (m-30) REVERT: F 54 TYR cc_start: 0.8577 (p90) cc_final: 0.8307 (p90) REVERT: F 110 GLU cc_start: 0.8195 (pp20) cc_final: 0.7980 (pp20) REVERT: X 100 MET cc_start: 0.7991 (ttp) cc_final: 0.7236 (ttp) REVERT: X 484 TYR cc_start: 0.8459 (p90) cc_final: 0.7999 (p90) REVERT: X 492 GLU cc_start: 0.8324 (tt0) cc_final: 0.8021 (tt0) REVERT: X 588 LYS cc_start: 0.9362 (tmtt) cc_final: 0.9027 (tptt) REVERT: Y 103 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7904 (tm-30) REVERT: Y 374 HIS cc_start: 0.7750 (t70) cc_final: 0.7487 (t-170) REVERT: Z 104 MET cc_start: 0.9095 (tpt) cc_final: 0.8314 (tpp) REVERT: Z 227 TYR cc_start: 0.7412 (m-80) cc_final: 0.6931 (m-80) REVERT: Z 486 TYR cc_start: 0.9071 (m-10) cc_final: 0.8566 (m-10) REVERT: Z 584 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8342 (tm-30) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.2618 time to fit residues: 116.2226 Evaluate side-chains 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 57 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** 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 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN Z 103 GLN ** Z 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.142424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120914 restraints weight = 33024.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123952 restraints weight = 21481.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126083 restraints weight = 15914.820| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16252 Z= 0.123 Angle : 0.700 13.547 22124 Z= 0.338 Chirality : 0.047 0.493 2592 Planarity : 0.004 0.052 2700 Dihedral : 9.033 119.196 3039 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -1.18 (0.19), residues: 1854 helix: 1.76 (0.30), residues: 312 sheet: -0.28 (0.24), residues: 474 loop : -1.90 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP X 479 HIS 0.009 0.001 HIS Y 375 PHE 0.017 0.001 PHE X 53 TYR 0.018 0.002 TYR Z 233 ARG 0.004 0.000 ARG F 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 30) link_NAG-ASN : angle 3.18141 ( 90) link_ALPHA1-6 : bond 0.01098 ( 3) link_ALPHA1-6 : angle 2.18137 ( 9) link_BETA1-4 : bond 0.00377 ( 12) link_BETA1-4 : angle 1.93140 ( 36) link_ALPHA1-3 : bond 0.01687 ( 3) link_ALPHA1-3 : angle 4.96871 ( 9) hydrogen bonds : bond 0.03521 ( 544) hydrogen bonds : angle 5.01774 ( 1503) SS BOND : bond 0.00471 ( 28) SS BOND : angle 1.21936 ( 56) covalent geometry : bond 0.00278 (16176) covalent geometry : angle 0.65677 (21924) *********************** 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 299 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7500 (ptp90) cc_final: 0.7271 (ptp-170) REVERT: B 110 GLU cc_start: 0.8330 (pp20) cc_final: 0.7724 (pp20) REVERT: C 6 GLN cc_start: 0.6535 (mt0) cc_final: 0.6080 (mt0) REVERT: C 38 ARG cc_start: 0.8147 (ptt180) cc_final: 0.7936 (ptt180) REVERT: C 90 MET cc_start: 0.6308 (mmp) cc_final: 0.5944 (mmp) REVERT: D 35 ASP cc_start: 0.8291 (m-30) cc_final: 0.7945 (m-30) REVERT: E 36 TRP cc_start: 0.8942 (m-10) cc_final: 0.8543 (m-10) REVERT: E 47 TRP cc_start: 0.8737 (t60) cc_final: 0.8207 (t60) REVERT: E 90 MET cc_start: 0.6310 (mmt) cc_final: 0.5884 (mmt) REVERT: F 35 ASP cc_start: 0.8394 (m-30) cc_final: 0.8072 (m-30) REVERT: F 54 TYR cc_start: 0.8526 (p90) cc_final: 0.8198 (p90) REVERT: F 110 GLU cc_start: 0.8075 (pp20) cc_final: 0.7870 (pp20) REVERT: X 95 MET cc_start: 0.8609 (ppp) cc_final: 0.8319 (ppp) REVERT: X 100 MET cc_start: 0.7956 (ttp) cc_final: 0.7345 (ttp) REVERT: X 484 TYR cc_start: 0.8435 (p90) cc_final: 0.8100 (p90) REVERT: X 588 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9031 (tptt) REVERT: Y 103 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8016 (tm-30) REVERT: Y 353 PHE cc_start: 0.5648 (m-10) cc_final: 0.5343 (m-80) REVERT: Y 530 MET cc_start: 0.7666 (ttt) cc_final: 0.7348 (mtp) REVERT: Y 622 ILE cc_start: 0.9367 (mt) cc_final: 0.9094 (mt) REVERT: Z 227 TYR cc_start: 0.7337 (m-80) cc_final: 0.6963 (m-80) REVERT: Z 486 TYR cc_start: 0.9010 (m-10) cc_final: 0.8485 (m-10) REVERT: Z 584 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8066 (tm-30) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2656 time to fit residues: 119.5844 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 80 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 ASN ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 374 HIS ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN ** Z 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 478 ASN Z 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113657 restraints weight = 33289.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116878 restraints weight = 21206.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119109 restraints weight = 15627.833| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16252 Z= 0.179 Angle : 0.736 13.421 22124 Z= 0.359 Chirality : 0.048 0.491 2592 Planarity : 0.004 0.053 2700 Dihedral : 8.961 119.140 3039 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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: -1.32 (0.19), residues: 1854 helix: 1.65 (0.30), residues: 312 sheet: -0.50 (0.23), residues: 489 loop : -1.94 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP X 479 HIS 0.013 0.002 HIS Y 374 PHE 0.018 0.002 PHE X 53 TYR 0.024 0.002 TYR X 227 ARG 0.010 0.001 ARG Y 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 30) link_NAG-ASN : angle 3.18573 ( 90) link_ALPHA1-6 : bond 0.00977 ( 3) link_ALPHA1-6 : angle 2.23105 ( 9) link_BETA1-4 : bond 0.00387 ( 12) link_BETA1-4 : angle 1.91535 ( 36) link_ALPHA1-3 : bond 0.01506 ( 3) link_ALPHA1-3 : angle 4.95583 ( 9) hydrogen bonds : bond 0.03905 ( 544) hydrogen bonds : angle 5.11917 ( 1503) SS BOND : bond 0.00503 ( 28) SS BOND : angle 1.49008 ( 56) covalent geometry : bond 0.00419 (16176) covalent geometry : angle 0.69410 (21924) ********************** 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 292 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.8403 (m-10) cc_final: 0.8200 (m-10) REVERT: B 110 GLU cc_start: 0.8370 (pp20) cc_final: 0.7728 (pp20) REVERT: C 6 GLN cc_start: 0.6468 (mt0) cc_final: 0.6008 (mt0) REVERT: C 90 MET cc_start: 0.6494 (mmp) cc_final: 0.6128 (mmp) REVERT: C 101 MET cc_start: 0.7229 (mtp) cc_final: 0.6808 (mtp) REVERT: D 35 ASP cc_start: 0.8405 (m-30) cc_final: 0.8066 (m-30) REVERT: E 36 TRP cc_start: 0.9025 (m-10) cc_final: 0.8620 (m-10) REVERT: E 47 TRP cc_start: 0.8772 (t60) cc_final: 0.8181 (t60) REVERT: E 90 MET cc_start: 0.6535 (mmt) cc_final: 0.6123 (mmt) REVERT: F 35 ASP cc_start: 0.8450 (m-30) cc_final: 0.8167 (m-30) REVERT: F 54 TYR cc_start: 0.8661 (p90) cc_final: 0.8403 (p90) REVERT: F 110 GLU cc_start: 0.8203 (pp20) cc_final: 0.7910 (pp20) REVERT: X 100 MET cc_start: 0.8036 (ttp) cc_final: 0.7367 (ttp) REVERT: X 484 TYR cc_start: 0.8417 (p90) cc_final: 0.8066 (p90) REVERT: X 584 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8303 (tm-30) REVERT: X 588 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9063 (tptt) REVERT: Y 97 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8358 (mttt) REVERT: Y 103 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8045 (tm-30) REVERT: Y 530 MET cc_start: 0.7762 (ttt) cc_final: 0.7354 (mtp) REVERT: Y 622 ILE cc_start: 0.9431 (mt) cc_final: 0.9215 (mt) REVERT: Z 50 THR cc_start: 0.8997 (t) cc_final: 0.8796 (t) REVERT: Z 104 MET cc_start: 0.9132 (tpp) cc_final: 0.7846 (tpp) REVERT: Z 112 TRP cc_start: 0.7945 (m100) cc_final: 0.7739 (m100) REVERT: Z 227 TYR cc_start: 0.7473 (m-80) cc_final: 0.6718 (m-80) REVERT: Z 486 TYR cc_start: 0.9107 (m-10) cc_final: 0.8562 (m-10) REVERT: Z 584 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8392 (tm-30) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2437 time to fit residues: 108.1020 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 : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN Z 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113736 restraints weight = 33297.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116756 restraints weight = 21578.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.118891 restraints weight = 16021.042| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16252 Z= 0.158 Angle : 0.717 13.391 22124 Z= 0.348 Chirality : 0.048 0.490 2592 Planarity : 0.004 0.054 2700 Dihedral : 8.794 118.577 3039 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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: -1.33 (0.19), residues: 1854 helix: 1.63 (0.30), residues: 312 sheet: -0.37 (0.23), residues: 471 loop : -2.00 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP X 479 HIS 0.012 0.002 HIS Y 374 PHE 0.017 0.002 PHE X 53 TYR 0.021 0.002 TYR Z 233 ARG 0.006 0.000 ARG F 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 30) link_NAG-ASN : angle 3.12343 ( 90) link_ALPHA1-6 : bond 0.01047 ( 3) link_ALPHA1-6 : angle 2.23255 ( 9) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 1.90119 ( 36) link_ALPHA1-3 : bond 0.01498 ( 3) link_ALPHA1-3 : angle 4.94095 ( 9) hydrogen bonds : bond 0.03806 ( 544) hydrogen bonds : angle 5.12136 ( 1503) SS BOND : bond 0.00531 ( 28) SS BOND : angle 1.23373 ( 56) covalent geometry : bond 0.00367 (16176) covalent geometry : angle 0.67540 (21924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4454.01 seconds wall clock time: 79 minutes 21.66 seconds (4761.66 seconds total)