Starting phenix.real_space_refine on Sun Aug 24 01:27:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpg_34192/08_2025/8gpg_34192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpg_34192/08_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_34192/08_2025/8gpg_34192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpg_34192/08_2025/8gpg_34192.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpg_34192/08_2025/8gpg_34192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpg_34192/08_2025/8gpg_34192.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.48, per 1000 atoms: 0.22 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: 1.22 Conformation dependent library (CDL) restraints added in 359.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.39 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: 3.06 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4961 1.34 - 1.46: 3920 1.46 - 1.58: 7157 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 16176 Sorted by residual: bond pdb=" C3 BMA M 3 " pdb=" O3 BMA M 3 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG Z 707 " pdb=" O5 NAG Z 707 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sigma weight residual 1.410 1.458 -0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" C1 MAN J 5 " pdb=" C2 MAN J 5 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 16171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 21575 2.53 - 5.05: 305 5.05 - 7.58: 37 7.58 - 10.11: 4 10.11 - 12.64: 3 Bond angle restraints: 21924 Sorted by residual: angle pdb=" C PHE X 243 " pdb=" N ASN X 244 " pdb=" CA ASN X 244 " ideal model delta sigma weight residual 122.61 130.10 -7.49 1.56e+00 4.11e-01 2.31e+01 angle pdb=" CB MET Y 104 " pdb=" CG MET Y 104 " pdb=" SD MET Y 104 " ideal model delta sigma weight residual 112.70 100.06 12.64 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C ILE Z 443 " pdb=" N ASN Z 444 " pdb=" CA ASN Z 444 " ideal model delta sigma weight residual 122.74 115.46 7.28 1.82e+00 3.02e-01 1.60e+01 angle pdb=" CA LEU A 80 " pdb=" CB LEU A 80 " pdb=" CG LEU A 80 " ideal model delta sigma weight residual 116.30 128.81 -12.51 3.50e+00 8.16e-02 1.28e+01 angle pdb=" CA CYS F 23 " pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " ideal model delta sigma weight residual 114.40 121.86 -7.46 2.30e+00 1.89e-01 1.05e+01 ... (remaining 21919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 9606 24.93 - 49.87: 554 49.87 - 74.80: 81 74.80 - 99.74: 38 99.74 - 124.67: 14 Dihedral angle restraints: 10293 sinusoidal: 4782 harmonic: 5511 Sorted by residual: dihedral pdb=" CB CYS Y 598 " pdb=" SG CYS Y 598 " pdb=" SG CYS Y 604 " pdb=" CB CYS Y 604 " ideal model delta sinusoidal sigma weight residual 93.00 164.51 -71.51 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 93 " pdb=" CB CYS B 93 " ideal model delta sinusoidal sigma weight residual 93.00 157.77 -64.77 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS Y 378 " pdb=" SG CYS Y 378 " pdb=" SG CYS Y 445 " pdb=" CB CYS Y 445 " ideal model delta sinusoidal sigma weight residual 93.00 45.90 47.10 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 10290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2313 0.082 - 0.164: 261 0.164 - 0.246: 10 0.246 - 0.328: 4 0.328 - 0.410: 4 Chirality restraints: 2592 Sorted by residual: chirality pdb=" C1 NAG Y 701 " pdb=" ND2 ASN Y 244 " pdb=" C2 NAG Y 701 " pdb=" O5 NAG Y 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C1 NAG Z 704 " pdb=" ND2 ASN Z 444 " pdb=" C2 NAG Z 704 " pdb=" O5 NAG Z 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C1 NAG Y 706 " pdb=" ND2 ASN Y 611 " pdb=" C2 NAG Y 706 " pdb=" O5 NAG Y 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2589 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN Z 444 " 0.002 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" CG ASN Z 444 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN Z 444 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN Z 444 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG Z 704 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 479 " 0.010 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP Y 479 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 479 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 479 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 479 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 479 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 479 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 479 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 479 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 479 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU X 106 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLU X 106 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU X 106 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP X 107 " -0.020 2.00e-02 2.50e+03 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 425 2.68 - 3.24: 15197 3.24 - 3.79: 23596 3.79 - 4.35: 29143 4.35 - 4.90: 47940 Nonbonded interactions: 116301 Sorted by model distance: nonbonded pdb=" OD2 ASP D 87 " pdb=" OH TYR D 91 " model vdw 2.130 3.040 nonbonded pdb=" OD2 ASP B 87 " pdb=" OH TYR B 91 " model vdw 2.131 3.040 nonbonded pdb=" ND2 ASN X 293 " pdb=" OD2 ASP X 477 " model vdw 2.145 3.120 nonbonded pdb=" O TYR D 37 " pdb=" OG1 THR D 96 " model vdw 2.157 3.040 nonbonded pdb=" OE2 GLU C 105 " pdb=" OH TYR D 37 " model vdw 2.169 3.040 ... (remaining 116296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- 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 : 13.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG C 38 TYR 0.021 0.002 TYR Z 227 PHE 0.020 0.002 PHE Y 53 TRP 0.065 0.003 TRP Y 479 HIS 0.005 0.002 HIS Y 352 Details of bonding type rmsd covalent geometry : bond 0.00487 (16176) covalent geometry : angle 0.76174 (21924) SS BOND : bond 0.00455 ( 28) SS BOND : angle 1.44282 ( 56) hydrogen bonds : bond 0.11970 ( 544) hydrogen bonds : angle 6.37796 ( 1503) link_ALPHA1-3 : bond 0.01161 ( 3) link_ALPHA1-3 : angle 4.52553 ( 9) 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_NAG-ASN : bond 0.00581 ( 30) link_NAG-ASN : angle 3.23805 ( 90) *********************** 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 : 0.696 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: 0.8459 (t60) REVERT: F 35 ASP cc_start: 0.8366 (m-30) cc_final: 0.8118 (m-30) REVERT: F 57 SER cc_start: 0.8827 (m) cc_final: 0.8542 (m) REVERT: F 58 GLU cc_start: 0.7243 (mp0) cc_final: 0.6970 (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: 0.1221 time to fit residues: 57.8922 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 : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 259 HIS ** X 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 478 ASN Y 268 GLN ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Z 653 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111225 restraints weight = 33723.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114105 restraints weight = 22235.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116120 restraints weight = 16711.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117195 restraints weight = 13699.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118391 restraints weight = 12083.236| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16252 Z= 0.253 Angle : 0.767 14.356 22124 Z= 0.376 Chirality : 0.049 0.479 2592 Planarity : 0.005 0.066 2700 Dihedral : 12.284 116.514 3039 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.06 % Allowed : 7.08 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.19), residues: 1854 helix: 1.30 (0.29), residues: 315 sheet: -0.51 (0.24), residues: 441 loop : -1.98 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 99 TYR 0.024 0.002 TYR Z 227 PHE 0.017 0.002 PHE Z 376 TRP 0.040 0.002 TRP E 36 HIS 0.008 0.003 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00581 (16176) covalent geometry : angle 0.72772 (21924) SS BOND : bond 0.00602 ( 28) SS BOND : angle 1.58865 ( 56) hydrogen bonds : bond 0.04696 ( 544) hydrogen bonds : angle 5.75668 ( 1503) link_ALPHA1-3 : bond 0.01728 ( 3) link_ALPHA1-3 : angle 5.35239 ( 9) link_ALPHA1-6 : bond 0.00776 ( 3) link_ALPHA1-6 : angle 1.74214 ( 9) link_BETA1-4 : bond 0.00443 ( 12) link_BETA1-4 : angle 2.09305 ( 36) link_NAG-ASN : bond 0.00670 ( 30) link_NAG-ASN : angle 3.02702 ( 90) *********************** 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 284 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 ASP cc_start: 0.7101 (t0) cc_final: 0.6819 (t0) REVERT: D 35 ASP cc_start: 0.8518 (m-30) cc_final: 0.8205 (m-30) REVERT: D 58 GLU cc_start: 0.6117 (mp0) cc_final: 0.5908 (mp0) REVERT: D 97 ARG cc_start: 0.8061 (tmt-80) cc_final: 0.7693 (tpt-90) REVERT: E 47 TRP cc_start: 0.8773 (t60) cc_final: 0.8195 (t60) REVERT: E 50 GLU cc_start: 0.7701 (tt0) cc_final: 0.7423 (tt0) REVERT: F 35 ASP cc_start: 0.8319 (m-30) cc_final: 0.8117 (m-30) REVERT: F 58 GLU cc_start: 0.7200 (mp0) cc_final: 0.6936 (mp0) REVERT: X 292 LYS cc_start: 0.8069 (tptt) cc_final: 0.7641 (mmmt) REVERT: X 492 GLU cc_start: 0.8437 (tt0) cc_final: 0.8147 (tt0) REVERT: X 588 LYS cc_start: 0.9341 (tmtt) cc_final: 0.8967 (tptt) REVERT: Y 353 PHE cc_start: 0.5726 (m-10) cc_final: 0.5504 (m-10) REVERT: Y 479 TRP cc_start: 0.7100 (m100) cc_final: 0.6447 (m100) REVERT: Z 484 TYR cc_start: 0.8720 (p90) cc_final: 0.8183 (p90) REVERT: Z 486 TYR cc_start: 0.9059 (m-10) cc_final: 0.8769 (m-10) REVERT: Z 584 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8129 (tm-30) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.1187 time to fit residues: 51.5289 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 : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 25 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 184 optimal weight: 0.0570 chunk 138 optimal weight: 6.9990 chunk 104 optimal weight: 0.0070 chunk 120 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.9916 ------------------------------------------------------------------------------- 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 374 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 Z 268 GLN Z 577 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115849 restraints weight = 33615.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118945 restraints weight = 21581.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121072 restraints weight = 15914.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122372 restraints weight = 12879.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123485 restraints weight = 11179.741| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16252 Z= 0.136 Angle : 0.696 13.647 22124 Z= 0.335 Chirality : 0.047 0.490 2592 Planarity : 0.004 0.044 2700 Dihedral : 11.008 118.281 3039 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.12 % Allowed : 4.48 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.19), residues: 1854 helix: 1.65 (0.30), residues: 309 sheet: -0.35 (0.24), residues: 447 loop : -1.88 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 469 TYR 0.020 0.002 TYR Z 227 PHE 0.014 0.001 PHE Y 53 TRP 0.025 0.002 TRP E 36 HIS 0.008 0.001 HIS X 374 Details of bonding type rmsd covalent geometry : bond 0.00311 (16176) covalent geometry : angle 0.65253 (21924) SS BOND : bond 0.00519 ( 28) SS BOND : angle 1.58991 ( 56) hydrogen bonds : bond 0.03862 ( 544) hydrogen bonds : angle 5.35938 ( 1503) link_ALPHA1-3 : bond 0.01775 ( 3) link_ALPHA1-3 : angle 5.20994 ( 9) link_ALPHA1-6 : bond 0.01062 ( 3) link_ALPHA1-6 : angle 2.40424 ( 9) link_BETA1-4 : bond 0.00438 ( 12) link_BETA1-4 : angle 2.09456 ( 36) link_NAG-ASN : bond 0.00608 ( 30) link_NAG-ASN : angle 2.93039 ( 90) *********************** 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 330 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 328 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 ASP cc_start: 0.8460 (m-30) cc_final: 0.8149 (m-30) REVERT: D 43 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7286 (ttp-110) REVERT: D 97 ARG cc_start: 0.8016 (tmt-80) cc_final: 0.7761 (tpt-90) REVERT: E 47 TRP cc_start: 0.8767 (t60) cc_final: 0.7938 (t60) REVERT: E 90 MET cc_start: 0.6410 (mmt) cc_final: 0.6124 (mmt) REVERT: F 58 GLU cc_start: 0.6996 (mp0) cc_final: 0.6741 (mp0) REVERT: F 92 TYR cc_start: 0.8402 (m-10) cc_final: 0.8100 (m-10) REVERT: F 97 ARG cc_start: 0.8318 (tpt90) cc_final: 0.7999 (tpt-90) REVERT: X 54 CYS cc_start: 0.7047 (t) cc_final: 0.6764 (t) REVERT: X 100 MET cc_start: 0.8052 (ttp) cc_final: 0.7349 (ttp) REVERT: X 374 HIS cc_start: 0.8152 (t70) cc_final: 0.7721 (t-170) REVERT: X 484 TYR cc_start: 0.8500 (p90) cc_final: 0.7976 (p90) REVERT: X 492 GLU cc_start: 0.8443 (tt0) cc_final: 0.8155 (tt0) REVERT: X 588 LYS cc_start: 0.9328 (tmtt) cc_final: 0.8980 (tptt) REVERT: X 620 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7365 (tm-30) REVERT: Y 103 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8077 (tm-30) REVERT: Y 353 PHE cc_start: 0.5712 (m-10) cc_final: 0.5407 (m-10) REVERT: Y 479 TRP cc_start: 0.7059 (m100) cc_final: 0.6852 (m100) REVERT: Y 484 TYR cc_start: 0.8179 (p90) cc_final: 0.7863 (p90) REVERT: Z 484 TYR cc_start: 0.8723 (p90) cc_final: 0.8260 (p90) REVERT: Z 486 TYR cc_start: 0.8999 (m-10) cc_final: 0.8565 (m-10) outliers start: 2 outliers final: 0 residues processed: 330 average time/residue: 0.1135 time to fit residues: 57.0477 Evaluate side-chains 237 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 103 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN X 478 ASN ** Y 374 HIS ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115317 restraints weight = 33263.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118247 restraints weight = 21510.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120363 restraints weight = 16047.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121845 restraints weight = 13008.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122823 restraints weight = 11194.673| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 0.047 16252 Z= 0.148 Angle : 0.690 13.769 22124 Z= 0.333 Chirality : 0.047 0.488 2592 Planarity : 0.004 0.042 2700 Dihedral : 10.440 118.970 3039 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.19), residues: 1854 helix: 1.61 (0.30), residues: 309 sheet: -0.32 (0.24), residues: 438 loop : -1.88 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 108 TYR 0.020 0.002 TYR X 619 PHE 0.018 0.001 PHE X 53 TRP 0.021 0.002 TRP E 36 HIS 0.011 0.001 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00346 (16176) covalent geometry : angle 0.64848 (21924) SS BOND : bond 0.00546 ( 28) SS BOND : angle 1.46762 ( 56) hydrogen bonds : bond 0.03792 ( 544) hydrogen bonds : angle 5.23823 ( 1503) link_ALPHA1-3 : bond 0.01856 ( 3) link_ALPHA1-3 : angle 5.30679 ( 9) link_ALPHA1-6 : bond 0.00981 ( 3) link_ALPHA1-6 : angle 2.02901 ( 9) link_BETA1-4 : bond 0.00350 ( 12) link_BETA1-4 : angle 2.03288 ( 36) link_NAG-ASN : bond 0.00591 ( 30) link_NAG-ASN : angle 2.89175 ( 90) *********************** 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 310 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6900 (mp10) cc_final: 0.6637 (mp10) REVERT: C 38 ARG cc_start: 0.7976 (ptt180) cc_final: 0.7761 (ptt180) REVERT: C 90 MET cc_start: 0.6138 (mmp) cc_final: 0.5789 (mmp) REVERT: D 35 ASP cc_start: 0.8481 (m-30) cc_final: 0.8187 (m-30) REVERT: D 58 GLU cc_start: 0.6164 (mp0) cc_final: 0.5778 (mp0) REVERT: E 47 TRP cc_start: 0.8810 (t60) cc_final: 0.7836 (t60) REVERT: E 50 GLU cc_start: 0.6905 (tt0) cc_final: 0.6220 (tt0) REVERT: E 77 GLN cc_start: 0.6655 (pm20) cc_final: 0.6422 (pm20) REVERT: E 90 MET cc_start: 0.6437 (mmt) cc_final: 0.6118 (mmt) REVERT: F 79 LYS cc_start: 0.7594 (tttm) cc_final: 0.7368 (tttp) REVERT: X 100 MET cc_start: 0.7985 (ttp) cc_final: 0.7270 (ttp) REVERT: X 484 TYR cc_start: 0.8461 (p90) cc_final: 0.7834 (p90) REVERT: X 492 GLU cc_start: 0.8317 (tt0) cc_final: 0.8022 (tt0) REVERT: X 588 LYS cc_start: 0.9338 (tmtt) cc_final: 0.8989 (tptt) REVERT: X 620 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7329 (tm-30) REVERT: Y 103 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8101 (tm-30) REVERT: Y 104 MET cc_start: 0.8646 (tmm) cc_final: 0.8266 (tmm) REVERT: Y 353 PHE cc_start: 0.5748 (m-10) cc_final: 0.5458 (m-10) REVERT: Y 484 TYR cc_start: 0.8273 (p90) cc_final: 0.8051 (p90) REVERT: Y 576 LEU cc_start: 0.9195 (tp) cc_final: 0.8949 (tp) REVERT: Z 97 LYS cc_start: 0.8765 (tmtt) cc_final: 0.8163 (tmmt) REVERT: Z 104 MET cc_start: 0.8893 (tpt) cc_final: 0.8687 (tpp) REVERT: Z 484 TYR cc_start: 0.8705 (p90) cc_final: 0.8339 (p90) REVERT: Z 486 TYR cc_start: 0.9023 (m-10) cc_final: 0.8574 (m-10) REVERT: Z 584 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8053 (tm-30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.0904 time to fit residues: 43.6522 Evaluate side-chains 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 111 optimal weight: 0.0050 chunk 5 optimal weight: 3.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN X 374 HIS ** 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 490 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.142799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121206 restraints weight = 33006.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124127 restraints weight = 21244.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126295 restraints weight = 15828.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127657 restraints weight = 12746.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.128833 restraints weight = 10992.992| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16252 Z= 0.125 Angle : 0.678 13.611 22124 Z= 0.326 Chirality : 0.047 0.496 2592 Planarity : 0.004 0.042 2700 Dihedral : 9.960 119.134 3039 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.19), residues: 1854 helix: 1.72 (0.30), residues: 309 sheet: -0.32 (0.23), residues: 486 loop : -1.85 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 97 TYR 0.015 0.002 TYR X 619 PHE 0.017 0.001 PHE X 53 TRP 0.031 0.002 TRP E 36 HIS 0.009 0.002 HIS Y 375 Details of bonding type rmsd covalent geometry : bond 0.00282 (16176) covalent geometry : angle 0.63718 (21924) SS BOND : bond 0.00522 ( 28) SS BOND : angle 1.34770 ( 56) hydrogen bonds : bond 0.03663 ( 544) hydrogen bonds : angle 5.12730 ( 1503) link_ALPHA1-3 : bond 0.01832 ( 3) link_ALPHA1-3 : angle 5.16918 ( 9) link_ALPHA1-6 : bond 0.01013 ( 3) link_ALPHA1-6 : angle 2.03333 ( 9) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 2.00495 ( 36) link_NAG-ASN : bond 0.00585 ( 30) link_NAG-ASN : angle 2.85570 ( 90) *********************** 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 332 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6874 (mp10) cc_final: 0.6656 (mp10) REVERT: C 47 TRP cc_start: 0.8387 (t60) cc_final: 0.8062 (t60) REVERT: C 90 MET cc_start: 0.6137 (mmp) cc_final: 0.5728 (mmp) REVERT: D 31 ASN cc_start: 0.8947 (t0) cc_final: 0.8512 (t0) REVERT: D 35 ASP cc_start: 0.8380 (m-30) cc_final: 0.8100 (m-30) REVERT: D 58 GLU cc_start: 0.6171 (mp0) cc_final: 0.5921 (mp0) REVERT: E 47 TRP cc_start: 0.8802 (t60) cc_final: 0.8168 (t60) REVERT: E 50 GLU cc_start: 0.6684 (tt0) cc_final: 0.5962 (tt0) REVERT: E 90 MET cc_start: 0.6328 (mmt) cc_final: 0.5888 (mmt) REVERT: F 92 TYR cc_start: 0.8349 (m-10) cc_final: 0.7938 (m-10) REVERT: X 100 MET cc_start: 0.7889 (ttp) cc_final: 0.7245 (ttp) REVERT: X 484 TYR cc_start: 0.8441 (p90) cc_final: 0.7953 (p90) REVERT: X 492 GLU cc_start: 0.8247 (tt0) cc_final: 0.7971 (tt0) REVERT: X 588 LYS cc_start: 0.9328 (tmtt) cc_final: 0.8984 (tptt) REVERT: X 620 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7357 (tm-30) REVERT: Y 103 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8054 (tm-30) REVERT: Y 353 PHE cc_start: 0.5673 (m-10) cc_final: 0.5343 (m-80) REVERT: Y 484 TYR cc_start: 0.8304 (p90) cc_final: 0.8084 (p90) REVERT: Y 576 LEU cc_start: 0.9194 (tp) cc_final: 0.8929 (tp) REVERT: Z 97 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8121 (tmmt) REVERT: Z 104 MET cc_start: 0.8962 (tpt) cc_final: 0.8708 (tpt) REVERT: Z 484 TYR cc_start: 0.8686 (p90) cc_final: 0.8363 (p90) REVERT: Z 486 TYR cc_start: 0.9014 (m-10) cc_final: 0.8466 (m-10) outliers start: 1 outliers final: 1 residues processed: 331 average time/residue: 0.0969 time to fit residues: 49.0102 Evaluate side-chains 240 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 165 optimal weight: 7.9990 chunk 13 optimal weight: 0.0000 chunk 56 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 478 ASN ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112565 restraints weight = 33339.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115435 restraints weight = 22021.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117480 restraints weight = 16562.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118892 restraints weight = 13555.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119776 restraints weight = 11755.255| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16252 Z= 0.197 Angle : 0.722 13.551 22124 Z= 0.353 Chirality : 0.048 0.486 2592 Planarity : 0.004 0.047 2700 Dihedral : 9.803 119.045 3039 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.19), residues: 1854 helix: 1.63 (0.30), residues: 309 sheet: -0.46 (0.23), residues: 480 loop : -1.91 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 99 TYR 0.019 0.002 TYR X 619 PHE 0.021 0.002 PHE B 101 TRP 0.029 0.002 TRP X 479 HIS 0.010 0.002 HIS Y 375 Details of bonding type rmsd covalent geometry : bond 0.00457 (16176) covalent geometry : angle 0.68583 (21924) SS BOND : bond 0.00531 ( 28) SS BOND : angle 1.45558 ( 56) hydrogen bonds : bond 0.04172 ( 544) hydrogen bonds : angle 5.24626 ( 1503) link_ALPHA1-3 : bond 0.01636 ( 3) link_ALPHA1-3 : angle 5.08301 ( 9) link_ALPHA1-6 : bond 0.00920 ( 3) link_ALPHA1-6 : angle 2.07009 ( 9) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.99861 ( 36) link_NAG-ASN : bond 0.00564 ( 30) link_NAG-ASN : angle 2.78489 ( 90) *********************** 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 294 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6736 (mp10) cc_final: 0.6519 (mp10) REVERT: C 90 MET cc_start: 0.6318 (mmp) cc_final: 0.5952 (mmp) REVERT: D 35 ASP cc_start: 0.8496 (m-30) cc_final: 0.8211 (m-30) REVERT: D 58 GLU cc_start: 0.6355 (mp0) cc_final: 0.5881 (mp0) REVERT: E 36 TRP cc_start: 0.9113 (m100) cc_final: 0.8702 (m-10) REVERT: E 47 TRP cc_start: 0.8823 (t60) cc_final: 0.8193 (t60) REVERT: E 50 GLU cc_start: 0.7025 (tt0) cc_final: 0.6236 (tt0) REVERT: E 72 ASP cc_start: 0.7317 (t70) cc_final: 0.6593 (p0) REVERT: E 90 MET cc_start: 0.6553 (mmt) cc_final: 0.6185 (mmt) REVERT: F 35 ASP cc_start: 0.8355 (m-30) cc_final: 0.8088 (m-30) REVERT: F 92 TYR cc_start: 0.8380 (m-10) cc_final: 0.8011 (m-10) REVERT: X 100 MET cc_start: 0.7868 (ttp) cc_final: 0.7167 (ttp) REVERT: X 484 TYR cc_start: 0.8472 (p90) cc_final: 0.7858 (p90) REVERT: X 492 GLU cc_start: 0.8312 (tt0) cc_final: 0.8039 (tt0) REVERT: X 588 LYS cc_start: 0.9357 (tmtt) cc_final: 0.9026 (tptt) REVERT: Y 103 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8131 (tm-30) REVERT: Y 353 PHE cc_start: 0.5812 (m-10) cc_final: 0.5533 (m-10) REVERT: Z 97 LYS cc_start: 0.8750 (tmtt) cc_final: 0.8156 (tmmt) REVERT: Z 104 MET cc_start: 0.9102 (tpt) cc_final: 0.8664 (tpp) REVERT: Z 484 TYR cc_start: 0.8667 (p90) cc_final: 0.8372 (p90) REVERT: Z 486 TYR cc_start: 0.9115 (m-10) cc_final: 0.8670 (m-10) REVERT: Z 584 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8376 (tm-30) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.0947 time to fit residues: 42.8927 Evaluate side-chains 225 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 490 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116665 restraints weight = 33041.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119600 restraints weight = 21706.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121659 restraints weight = 16208.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123094 restraints weight = 13220.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124119 restraints weight = 11394.194| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16252 Z= 0.180 Angle : 0.719 13.499 22124 Z= 0.350 Chirality : 0.048 0.490 2592 Planarity : 0.004 0.056 2700 Dihedral : 9.603 118.917 3039 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.19), residues: 1854 helix: 1.69 (0.30), residues: 309 sheet: -0.50 (0.23), residues: 483 loop : -1.91 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.022 0.002 TYR X 227 PHE 0.018 0.002 PHE X 53 TRP 0.022 0.002 TRP X 479 HIS 0.007 0.002 HIS Y 375 Details of bonding type rmsd covalent geometry : bond 0.00417 (16176) covalent geometry : angle 0.67634 (21924) SS BOND : bond 0.00536 ( 28) SS BOND : angle 1.41950 ( 56) hydrogen bonds : bond 0.03995 ( 544) hydrogen bonds : angle 5.22105 ( 1503) link_ALPHA1-3 : bond 0.01541 ( 3) link_ALPHA1-3 : angle 5.03048 ( 9) link_ALPHA1-6 : bond 0.00949 ( 3) link_ALPHA1-6 : angle 2.09790 ( 9) link_BETA1-4 : bond 0.00423 ( 12) link_BETA1-4 : angle 2.01024 ( 36) link_NAG-ASN : bond 0.00612 ( 30) link_NAG-ASN : angle 3.13813 ( 90) *********************** 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 296 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 MET cc_start: 0.6261 (mmp) cc_final: 0.5867 (mmp) REVERT: C 101 MET cc_start: 0.6820 (ttm) cc_final: 0.6579 (mtp) REVERT: C 102 MET cc_start: 0.7326 (tpt) cc_final: 0.7018 (tpp) REVERT: D 35 ASP cc_start: 0.8458 (m-30) cc_final: 0.8138 (m-30) REVERT: D 68 SER cc_start: 0.8298 (t) cc_final: 0.7956 (p) REVERT: E 47 TRP cc_start: 0.8744 (t60) cc_final: 0.8014 (t60) REVERT: E 50 GLU cc_start: 0.7400 (tt0) cc_final: 0.6979 (tt0) REVERT: E 90 MET cc_start: 0.6647 (mmt) cc_final: 0.6224 (mmt) REVERT: F 35 ASP cc_start: 0.8374 (m-30) cc_final: 0.8098 (m-30) REVERT: F 92 TYR cc_start: 0.8355 (m-10) cc_final: 0.8085 (m-10) REVERT: X 100 MET cc_start: 0.7849 (ttp) cc_final: 0.7110 (ttp) REVERT: X 104 MET cc_start: 0.8913 (tmm) cc_final: 0.8673 (tmm) REVERT: X 484 TYR cc_start: 0.8459 (p90) cc_final: 0.7982 (p90) REVERT: X 492 GLU cc_start: 0.8309 (tt0) cc_final: 0.8002 (tt0) REVERT: X 588 LYS cc_start: 0.9357 (tmtt) cc_final: 0.9149 (tptt) REVERT: Y 97 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8337 (mttt) REVERT: Y 103 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8071 (tm-30) REVERT: Y 576 LEU cc_start: 0.9229 (tp) cc_final: 0.8905 (tp) REVERT: Z 97 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8099 (tmmt) REVERT: Z 104 MET cc_start: 0.9118 (tpt) cc_final: 0.8814 (tpt) REVERT: Z 486 TYR cc_start: 0.9109 (m-10) cc_final: 0.8625 (m-10) REVERT: Z 584 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8105 (tm-30) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1012 time to fit residues: 46.3405 Evaluate side-chains 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 158 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 134 optimal weight: 0.0010 chunk 183 optimal weight: 4.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN X 99 ASN X 374 HIS ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.140114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117430 restraints weight = 32099.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120680 restraints weight = 19689.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122977 restraints weight = 14182.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124572 restraints weight = 11288.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125620 restraints weight = 9577.997| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2050 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= 0.185 Angle : 0.726 13.522 22124 Z= 0.355 Chirality : 0.048 0.493 2592 Planarity : 0.004 0.058 2700 Dihedral : 9.421 119.088 3039 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.19), residues: 1854 helix: 1.59 (0.30), residues: 312 sheet: -0.56 (0.23), residues: 483 loop : -2.01 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 480 TYR 0.019 0.002 TYR X 619 PHE 0.017 0.002 PHE X 53 TRP 0.033 0.002 TRP X 479 HIS 0.009 0.002 HIS Z 374 Details of bonding type rmsd covalent geometry : bond 0.00431 (16176) covalent geometry : angle 0.68421 (21924) SS BOND : bond 0.00498 ( 28) SS BOND : angle 1.43316 ( 56) hydrogen bonds : bond 0.04109 ( 544) hydrogen bonds : angle 5.21174 ( 1503) link_ALPHA1-3 : bond 0.01597 ( 3) link_ALPHA1-3 : angle 5.03068 ( 9) link_ALPHA1-6 : bond 0.00926 ( 3) link_ALPHA1-6 : angle 2.12325 ( 9) link_BETA1-4 : bond 0.00376 ( 12) link_BETA1-4 : angle 1.97938 ( 36) link_NAG-ASN : bond 0.00640 ( 30) link_NAG-ASN : angle 3.09379 ( 90) *********************** 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 292 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 MET cc_start: 0.6232 (mmp) cc_final: 0.5858 (mmp) REVERT: D 35 ASP cc_start: 0.8486 (m-30) cc_final: 0.8146 (m-30) REVERT: D 68 SER cc_start: 0.8267 (t) cc_final: 0.7899 (p) REVERT: E 47 TRP cc_start: 0.8760 (t60) cc_final: 0.8019 (t60) REVERT: E 50 GLU cc_start: 0.7326 (tt0) cc_final: 0.6896 (tt0) REVERT: E 90 MET cc_start: 0.6695 (mmt) cc_final: 0.6279 (mmt) REVERT: F 35 ASP cc_start: 0.8339 (m-30) cc_final: 0.8074 (m-30) REVERT: F 58 GLU cc_start: 0.6887 (mp0) cc_final: 0.6620 (mp0) REVERT: F 92 TYR cc_start: 0.8357 (m-10) cc_final: 0.8022 (m-10) REVERT: X 100 MET cc_start: 0.7785 (ttp) cc_final: 0.7165 (ttp) REVERT: X 484 TYR cc_start: 0.8469 (p90) cc_final: 0.7992 (p90) REVERT: X 492 GLU cc_start: 0.8311 (tt0) cc_final: 0.7999 (tt0) REVERT: X 588 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9027 (tptt) REVERT: Y 97 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8343 (mttt) REVERT: Y 103 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8055 (tm-30) REVERT: Z 97 LYS cc_start: 0.8710 (tmtt) cc_final: 0.8097 (tmmt) REVERT: Z 112 TRP cc_start: 0.7912 (m100) cc_final: 0.7703 (m100) REVERT: Z 484 TYR cc_start: 0.8723 (p90) cc_final: 0.8493 (p90) REVERT: Z 486 TYR cc_start: 0.9137 (m-10) cc_final: 0.8714 (m-10) REVERT: Z 584 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8077 (tm-30) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1090 time to fit residues: 48.4979 Evaluate side-chains 225 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN X 99 ASN ** X 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.139235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116678 restraints weight = 31898.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119984 restraints weight = 19601.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122259 restraints weight = 14052.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123848 restraints weight = 11164.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124776 restraints weight = 9464.332| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16252 Z= 0.182 Angle : 0.734 13.439 22124 Z= 0.359 Chirality : 0.048 0.497 2592 Planarity : 0.004 0.060 2700 Dihedral : 9.261 118.823 3039 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.19), residues: 1854 helix: 1.65 (0.30), residues: 312 sheet: -0.56 (0.23), residues: 483 loop : -2.06 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 469 TYR 0.041 0.002 TYR Z 233 PHE 0.017 0.002 PHE X 53 TRP 0.033 0.002 TRP X 479 HIS 0.007 0.002 HIS Y 375 Details of bonding type rmsd covalent geometry : bond 0.00426 (16176) covalent geometry : angle 0.69532 (21924) SS BOND : bond 0.00558 ( 28) SS BOND : angle 1.28409 ( 56) hydrogen bonds : bond 0.04070 ( 544) hydrogen bonds : angle 5.20462 ( 1503) link_ALPHA1-3 : bond 0.01456 ( 3) link_ALPHA1-3 : angle 5.00748 ( 9) link_ALPHA1-6 : bond 0.00942 ( 3) link_ALPHA1-6 : angle 2.15473 ( 9) link_BETA1-4 : bond 0.00386 ( 12) link_BETA1-4 : angle 1.96225 ( 36) link_NAG-ASN : bond 0.00632 ( 30) link_NAG-ASN : angle 3.03114 ( 90) *********************** 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 283 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 THR cc_start: 0.8155 (p) cc_final: 0.7952 (p) REVERT: C 90 MET cc_start: 0.6288 (mmp) cc_final: 0.5881 (mmp) REVERT: C 101 MET cc_start: 0.6825 (ttm) cc_final: 0.6518 (mtp) REVERT: D 35 ASP cc_start: 0.8451 (m-30) cc_final: 0.8057 (m-30) REVERT: D 68 SER cc_start: 0.8315 (t) cc_final: 0.8001 (p) REVERT: E 47 TRP cc_start: 0.8759 (t60) cc_final: 0.7971 (t60) REVERT: E 50 GLU cc_start: 0.7160 (tt0) cc_final: 0.6649 (tt0) REVERT: E 90 MET cc_start: 0.6608 (mmt) cc_final: 0.6217 (mmt) REVERT: F 35 ASP cc_start: 0.8343 (m-30) cc_final: 0.8123 (m-30) REVERT: F 92 TYR cc_start: 0.8343 (m-10) cc_final: 0.8106 (m-10) REVERT: X 54 CYS cc_start: 0.6811 (t) cc_final: 0.6599 (t) REVERT: X 100 MET cc_start: 0.7789 (ttp) cc_final: 0.7197 (ttp) REVERT: X 484 TYR cc_start: 0.8451 (p90) cc_final: 0.7970 (p90) REVERT: X 492 GLU cc_start: 0.8290 (tt0) cc_final: 0.7982 (tt0) REVERT: X 588 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9054 (tptt) REVERT: Y 103 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8021 (tm-30) REVERT: Z 97 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8100 (tmmt) REVERT: Z 112 TRP cc_start: 0.7903 (m100) cc_final: 0.7655 (m100) REVERT: Z 484 TYR cc_start: 0.8689 (p90) cc_final: 0.8441 (p90) REVERT: Z 486 TYR cc_start: 0.9151 (m-10) cc_final: 0.8710 (m-10) REVERT: Z 530 MET cc_start: 0.8936 (tpt) cc_final: 0.8551 (tpt) REVERT: Z 584 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8089 (tm-30) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.0973 time to fit residues: 42.6701 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 : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN X 99 ASN X 374 HIS ** Y 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN Z 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.137825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116448 restraints weight = 32294.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119463 restraints weight = 20327.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121620 restraints weight = 14802.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123160 restraints weight = 11817.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124017 restraints weight = 10028.361| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16252 Z= 0.170 Angle : 0.741 13.423 22124 Z= 0.360 Chirality : 0.048 0.490 2592 Planarity : 0.004 0.059 2700 Dihedral : 9.157 118.466 3039 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.19), residues: 1854 helix: 1.69 (0.30), residues: 312 sheet: -0.54 (0.23), residues: 480 loop : -2.04 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 38 TYR 0.018 0.002 TYR X 619 PHE 0.017 0.002 PHE X 53 TRP 0.035 0.002 TRP X 479 HIS 0.008 0.002 HIS Y 374 Details of bonding type rmsd covalent geometry : bond 0.00397 (16176) covalent geometry : angle 0.69815 (21924) SS BOND : bond 0.00539 ( 28) SS BOND : angle 1.47758 ( 56) hydrogen bonds : bond 0.04055 ( 544) hydrogen bonds : angle 5.17984 ( 1503) link_ALPHA1-3 : bond 0.01483 ( 3) link_ALPHA1-3 : angle 4.98851 ( 9) link_ALPHA1-6 : bond 0.00991 ( 3) link_ALPHA1-6 : angle 2.16407 ( 9) link_BETA1-4 : bond 0.00393 ( 12) link_BETA1-4 : angle 1.93201 ( 36) link_NAG-ASN : bond 0.00628 ( 30) link_NAG-ASN : angle 3.24375 ( 90) ********************** 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 283 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 MET cc_start: 0.6404 (mmp) cc_final: 0.6079 (mmp) REVERT: C 101 MET cc_start: 0.6826 (ttm) cc_final: 0.6389 (mtp) REVERT: C 102 MET cc_start: 0.7558 (tpt) cc_final: 0.7247 (tpt) REVERT: D 35 ASP cc_start: 0.8510 (m-30) cc_final: 0.8106 (m-30) REVERT: E 36 TRP cc_start: 0.8963 (m100) cc_final: 0.8618 (m-10) REVERT: E 47 TRP cc_start: 0.8795 (t60) cc_final: 0.7981 (t60) REVERT: E 50 GLU cc_start: 0.7232 (tt0) cc_final: 0.6768 (tt0) REVERT: E 90 MET cc_start: 0.6611 (mmt) cc_final: 0.6183 (mmt) REVERT: F 35 ASP cc_start: 0.8401 (m-30) cc_final: 0.8136 (m-30) REVERT: F 92 TYR cc_start: 0.8387 (m-10) cc_final: 0.8067 (m-10) REVERT: F 110 GLU cc_start: 0.8172 (pp20) cc_final: 0.7970 (pp20) REVERT: X 54 CYS cc_start: 0.6832 (t) cc_final: 0.6517 (t) REVERT: X 100 MET cc_start: 0.7832 (ttp) cc_final: 0.7196 (ttp) REVERT: X 484 TYR cc_start: 0.8485 (p90) cc_final: 0.8084 (p90) REVERT: X 492 GLU cc_start: 0.8337 (tt0) cc_final: 0.8027 (tt0) REVERT: X 588 LYS cc_start: 0.9366 (tmtt) cc_final: 0.9037 (tptt) REVERT: Y 97 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8335 (mttt) REVERT: Y 100 MET cc_start: 0.8617 (mmm) cc_final: 0.8252 (mmm) REVERT: Y 103 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7958 (tm-30) REVERT: Y 530 MET cc_start: 0.7875 (ttt) cc_final: 0.7491 (mtp) REVERT: Z 112 TRP cc_start: 0.7948 (m100) cc_final: 0.7707 (m100) REVERT: Z 227 TYR cc_start: 0.7726 (m-80) cc_final: 0.7463 (m-80) REVERT: Z 484 TYR cc_start: 0.8703 (p90) cc_final: 0.8465 (p90) REVERT: Z 486 TYR cc_start: 0.9154 (m-10) cc_final: 0.8682 (m-10) REVERT: Z 584 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8083 (tm-30) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.1011 time to fit residues: 43.9582 Evaluate side-chains 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 141 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN F 6 GLN ** X 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 374 HIS ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.141169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119527 restraints weight = 32989.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122502 restraints weight = 21425.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124643 restraints weight = 15923.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126052 restraints weight = 12860.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127170 restraints weight = 11107.310| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16252 Z= 0.130 Angle : 0.713 13.390 22124 Z= 0.345 Chirality : 0.047 0.492 2592 Planarity : 0.004 0.055 2700 Dihedral : 8.764 118.072 3039 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.19), residues: 1854 helix: 1.76 (0.30), residues: 312 sheet: -0.32 (0.24), residues: 468 loop : -1.99 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 38 TYR 0.018 0.002 TYR X 227 PHE 0.026 0.002 PHE A 78 TRP 0.034 0.002 TRP A 36 HIS 0.006 0.001 HIS Y 375 Details of bonding type rmsd covalent geometry : bond 0.00301 (16176) covalent geometry : angle 0.67146 (21924) SS BOND : bond 0.00467 ( 28) SS BOND : angle 1.31525 ( 56) hydrogen bonds : bond 0.03605 ( 544) hydrogen bonds : angle 5.03222 ( 1503) link_ALPHA1-3 : bond 0.01521 ( 3) link_ALPHA1-3 : angle 4.94254 ( 9) link_ALPHA1-6 : bond 0.01091 ( 3) link_ALPHA1-6 : angle 2.19445 ( 9) link_BETA1-4 : bond 0.00376 ( 12) link_BETA1-4 : angle 1.88173 ( 36) link_NAG-ASN : bond 0.00618 ( 30) link_NAG-ASN : angle 3.12315 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.15 seconds wall clock time: 38 minutes 7.73 seconds (2287.73 seconds total)