Starting phenix.real_space_refine on Fri Jul 3 20:12:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gpg_34192/07_2026/8gpg_34192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpg_34192/07_2026/8gpg_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_34192/07_2026/8gpg_34192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpg_34192/07_2026/8gpg_34192.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpg_34192/07_2026/8gpg_34192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpg_34192/07_2026/8gpg_34192.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gpg_34192/07_2026/8gpg_34192.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gpg_34192/07_2026/8gpg_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 7 Time building chain proxies: 3.16, per 1000 atoms: 0.20 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: 1.40 Conformation dependent library (CDL) restraints added in 579.5 milliseconds 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: 0.48 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: 2.07 Time building geometry restraints manager: 1.85 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 - 17.97: 8328 17.97 - 35.93: 782 35.93 - 53.89: 142 53.89 - 71.86: 35 71.86 - 89.82: 16 Dihedral angle restraints: 9303 sinusoidal: 3792 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 9300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2313 0.082 - 0.164: 261 0.164 - 0.246: 10 0.246 - 0.328: 4 0.328 - 0.410: 4 Chirality restraints: 2592 Sorted by residual: chirality pdb=" C1 NAG Y 701 " pdb=" ND2 ASN Y 244 " pdb=" C2 NAG Y 701 " pdb=" O5 NAG Y 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C1 NAG Z 704 " pdb=" ND2 ASN Z 444 " pdb=" C2 NAG Z 704 " pdb=" O5 NAG Z 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C1 NAG Y 706 " pdb=" ND2 ASN Y 611 " pdb=" C2 NAG Y 706 " pdb=" O5 NAG Y 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2589 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN Z 444 " 0.002 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" CG ASN Z 444 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN Z 444 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN Z 444 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG Z 704 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 479 " 0.010 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP Y 479 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 479 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 479 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 479 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 479 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 479 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 479 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 479 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 479 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU X 106 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLU X 106 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU X 106 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP X 107 " -0.020 2.00e-02 2.50e+03 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 425 2.68 - 3.24: 15197 3.24 - 3.79: 23596 3.79 - 4.35: 29143 4.35 - 4.90: 47940 Nonbonded interactions: 116301 Sorted by model distance: nonbonded pdb=" OD2 ASP D 87 " pdb=" OH TYR D 91 " model vdw 2.130 3.040 nonbonded pdb=" OD2 ASP B 87 " pdb=" OH TYR B 91 " model vdw 2.131 3.040 nonbonded pdb=" ND2 ASN X 293 " pdb=" OD2 ASP X 477 " model vdw 2.145 3.120 nonbonded pdb=" O TYR D 37 " pdb=" OG1 THR D 96 " model vdw 2.157 3.040 nonbonded pdb=" OE2 GLU C 105 " pdb=" OH TYR D 37 " model vdw 2.169 3.040 ... (remaining 116296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.790 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 14.412 89.824 5661 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 are 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/Z covalent geometry : bond 0.00487 / 0.22 (16176) covalent geometry : angle 0.76174 / 0.38 (21924) SS BOND : bond 0.00455 / 0.23 ( 28) SS BOND : angle 1.44282 / 0.88 ( 56) hydrogen bonds : bond 0.11970 / 7.92 ( 544) hydrogen bonds : angle 6.37796 / 4.34 ( 1503) link_ALPHA1-3 : bond 0.01161 / 0.58 ( 3) link_ALPHA1-3 : angle 4.52553 / 2.93 ( 9) link_ALPHA1-6 : bond 0.00582 / 0.28 ( 3) link_ALPHA1-6 : angle 1.64784 / 1.05 ( 9) link_BETA1-4 : bond 0.00662 / 0.36 ( 12) link_BETA1-4 : angle 2.18505 / 1.33 ( 36) link_NAG-ASN : bond 0.00581 / 0.35 ( 30) link_NAG-ASN : angle 3.23805 / 2.24 ( 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 : 0.604 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: 0.7095 (tpp) REVERT: B 65 ASP cc_start: 0.7399 (t0) cc_final: 0.6980 (t0) REVERT: C 47 TRP cc_start: 0.8541 (t60) cc_final: 0.7498 (t60) REVERT: C 75 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7959 (mtmm) REVERT: D 35 ASP cc_start: 0.8692 (m-30) cc_final: 0.8339 (m-30) REVERT: D 97 ARG cc_start: 0.7939 (tmt-80) cc_final: 0.7594 (tpt-90) REVERT: E 47 TRP cc_start: 0.8707 (t60) cc_final: 0.8458 (t60) REVERT: F 35 ASP cc_start: 0.8367 (m-30) cc_final: 0.8118 (m-30) REVERT: F 57 SER cc_start: 0.8826 (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: 0.8089 (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: 0.1027 time to fit residues: 48.8390 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 : 0.427 ------------------------------------------------------------------------------- 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... A 39 GLN 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 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111028 restraints weight = 33724.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113886 restraints weight = 22180.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115895 restraints weight = 16681.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117299 restraints weight = 13683.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118124 restraints weight = 11879.344| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 16252 Z= 0.250 Angle : 0.754 12.826 22124 Z= 0.373 Chirality : 0.049 0.492 2592 Planarity : 0.005 0.065 2700 Dihedral : 5.107 28.391 2049 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.06 % Allowed : 7.67 % Favored : 92.27 % 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 are not related in a simple way. whole: -1.51 (0.19), residues: 1854 helix: 1.24 (0.29), residues: 315 sheet: -0.53 (0.24), residues: 441 loop : -1.99 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 99 TYR 0.025 0.002 TYR Z 227 PHE 0.018 0.002 PHE Z 376 TRP 0.042 0.002 TRP E 36 HIS 0.008 0.003 HIS X 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 (16176) covalent geometry : angle 0.71903 / 0.37 (21924) SS BOND : bond 0.00585 / 0.31 ( 28) SS BOND : angle 1.60098 / 1.00 ( 56) hydrogen bonds : bond 0.04738 / 3.08 ( 544) hydrogen bonds : angle 5.75553 / 3.90 ( 1503) link_ALPHA1-3 : bond 0.01207 / 0.60 ( 3) link_ALPHA1-3 : angle 4.97428 / 3.18 ( 9) link_ALPHA1-6 : bond 0.00619 / 0.30 ( 3) link_ALPHA1-6 : angle 1.56615 / 0.97 ( 9) link_BETA1-4 : bond 0.00411 / 0.18 ( 12) link_BETA1-4 : angle 1.71397 / 1.12 ( 36) link_NAG-ASN : bond 0.00609 / 0.36 ( 30) link_NAG-ASN : angle 2.85711 / 2.10 ( 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 283 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 ASP cc_start: 0.8524 (m-30) cc_final: 0.8206 (m-30) REVERT: D 58 GLU cc_start: 0.6076 (mp0) cc_final: 0.5800 (mp0) REVERT: D 97 ARG cc_start: 0.8078 (tmt-80) cc_final: 0.7695 (tpt-90) REVERT: E 47 TRP cc_start: 0.8794 (t60) cc_final: 0.8180 (t60) REVERT: E 50 GLU cc_start: 0.7703 (tt0) cc_final: 0.7431 (tt0) REVERT: F 35 ASP cc_start: 0.8456 (m-30) cc_final: 0.8240 (m-30) REVERT: F 58 GLU cc_start: 0.7204 (mp0) cc_final: 0.6966 (mp0) REVERT: X 292 LYS cc_start: 0.8073 (tptt) cc_final: 0.7641 (mmmt) REVERT: X 362 GLN cc_start: 0.4300 (mp10) cc_final: 0.4076 (mp10) REVERT: X 492 GLU cc_start: 0.8436 (tt0) cc_final: 0.8163 (tt0) REVERT: X 588 LYS cc_start: 0.9342 (tmtt) cc_final: 0.8968 (tptt) REVERT: Y 353 PHE cc_start: 0.5721 (m-10) cc_final: 0.5482 (m-10) REVERT: Y 479 TRP cc_start: 0.7120 (m100) cc_final: 0.6708 (m100) REVERT: Z 484 TYR cc_start: 0.8718 (p90) cc_final: 0.8234 (p90) REVERT: Z 486 TYR cc_start: 0.9061 (m-10) cc_final: 0.8773 (m-10) REVERT: Z 584 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8122 (tm-30) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.1106 time to fit residues: 48.0112 Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 8.9990 chunk 175 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 374 HIS ** 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 = 0.3842 r_free = 0.3842 target = 0.138212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115651 restraints weight = 33666.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118731 restraints weight = 21373.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120921 restraints weight = 15739.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122420 restraints weight = 12672.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123262 restraints weight = 10874.550| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16252 Z= 0.136 Angle : 0.681 12.049 22124 Z= 0.332 Chirality : 0.047 0.419 2592 Planarity : 0.004 0.043 2700 Dihedral : 4.870 28.740 2049 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.12 % Allowed : 4.01 % Favored : 95.87 % 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 are not related in a simple way. whole: -1.28 (0.19), residues: 1854 helix: 1.61 (0.30), residues: 309 sheet: -0.39 (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 0.018 0.002 TYR X 619 PHE 0.015 0.001 PHE Z 376 TRP 0.024 0.002 TRP E 36 HIS 0.008 0.001 HIS X 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (16176) covalent geometry : angle 0.64227 / 0.32 (21924) SS BOND : bond 0.00475 / 0.25 ( 28) SS BOND : angle 1.57018 / 0.94 ( 56) hydrogen bonds : bond 0.03925 / 2.54 ( 544) hydrogen bonds : angle 5.38655 / 3.65 ( 1503) link_ALPHA1-3 : bond 0.01394 / 0.70 ( 3) link_ALPHA1-3 : angle 4.58820 / 2.99 ( 9) link_ALPHA1-6 : bond 0.00766 / 0.38 ( 3) link_ALPHA1-6 : angle 1.50297 / 0.94 ( 9) link_BETA1-4 : bond 0.00380 / 0.20 ( 12) link_BETA1-4 : angle 1.67822 / 1.09 ( 36) link_NAG-ASN : bond 0.00648 / 0.39 ( 30) link_NAG-ASN : angle 2.89481 / 2.19 ( 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 324 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 CYS cc_start: 0.6367 (m) cc_final: 0.6119 (m) REVERT: D 35 ASP cc_start: 0.8536 (m-30) cc_final: 0.8200 (m-30) REVERT: D 58 GLU cc_start: 0.5920 (mp0) cc_final: 0.5627 (mp0) REVERT: D 97 ARG cc_start: 0.8063 (tmt-80) cc_final: 0.7780 (tpt-90) REVERT: E 47 TRP cc_start: 0.8764 (t60) cc_final: 0.7981 (t60) REVERT: E 90 MET cc_start: 0.6448 (mmt) cc_final: 0.6152 (mmt) REVERT: F 8 PRO cc_start: 0.8294 (Cg_endo) cc_final: 0.8047 (Cg_exo) REVERT: F 58 GLU cc_start: 0.6958 (mp0) cc_final: 0.6704 (mp0) REVERT: F 92 TYR cc_start: 0.8397 (m-10) cc_final: 0.8162 (m-10) REVERT: F 97 ARG cc_start: 0.8301 (tpt90) cc_final: 0.7996 (tpt-90) REVERT: F 111 ILE cc_start: 0.7339 (tt) cc_final: 0.7131 (mt) REVERT: X 54 CYS cc_start: 0.7057 (t) cc_final: 0.6785 (t) REVERT: X 100 MET cc_start: 0.7922 (ttp) cc_final: 0.7234 (ttp) REVERT: X 484 TYR cc_start: 0.8505 (p90) cc_final: 0.7959 (p90) REVERT: X 492 GLU cc_start: 0.8445 (tt0) cc_final: 0.8135 (tt0) REVERT: X 588 LYS cc_start: 0.9333 (tmtt) cc_final: 0.8981 (tptt) REVERT: Y 103 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8069 (tm-30) REVERT: Y 227 TYR cc_start: 0.7204 (m-80) cc_final: 0.7004 (m-80) REVERT: Y 353 PHE cc_start: 0.5715 (m-10) cc_final: 0.5412 (m-10) REVERT: Y 479 TRP cc_start: 0.6974 (m100) cc_final: 0.6764 (m100) REVERT: Y 484 TYR cc_start: 0.8243 (p90) cc_final: 0.7975 (p90) REVERT: Z 104 MET cc_start: 0.9178 (mmm) cc_final: 0.8879 (tpp) REVERT: Z 484 TYR cc_start: 0.8701 (p90) cc_final: 0.8191 (p90) REVERT: Z 486 TYR cc_start: 0.9037 (m-10) cc_final: 0.8653 (m-10) outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.1102 time to fit residues: 54.6740 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 : 0.588 ------------------------------------------------------------------------------- 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: 4.9990 chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 6 GLN F 6 GLN ** X 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 478 ASN ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110777 restraints weight = 33567.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113567 restraints weight = 22163.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115583 restraints weight = 16809.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117014 restraints weight = 13777.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118023 restraints weight = 11918.446| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16252 Z= 0.229 Angle : 0.741 12.166 22124 Z= 0.366 Chirality : 0.048 0.413 2592 Planarity : 0.005 0.046 2700 Dihedral : 5.076 39.362 2049 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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 are not related in a simple way. whole: -1.51 (0.19), residues: 1854 helix: 1.47 (0.30), residues: 309 sheet: -0.52 (0.24), residues: 453 loop : -2.07 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 99 TYR 0.025 0.002 TYR X 619 PHE 0.017 0.002 PHE A 78 TRP 0.026 0.002 TRP E 36 HIS 0.010 0.002 HIS X 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (16176) covalent geometry : angle 0.70562 / 0.36 (21924) SS BOND : bond 0.00610 / 0.33 ( 28) SS BOND : angle 1.63165 / 1.01 ( 56) hydrogen bonds : bond 0.04454 / 2.92 ( 544) hydrogen bonds : angle 5.49447 / 3.73 ( 1503) link_ALPHA1-3 : bond 0.01336 / 0.67 ( 3) link_ALPHA1-3 : angle 4.60608 / 3.00 ( 9) link_ALPHA1-6 : bond 0.00602 / 0.29 ( 3) link_ALPHA1-6 : angle 1.55640 / 0.98 ( 9) link_BETA1-4 : bond 0.00442 / 0.22 ( 12) link_BETA1-4 : angle 1.67563 / 1.05 ( 36) link_NAG-ASN : bond 0.00605 / 0.37 ( 30) link_NAG-ASN : angle 2.93305 / 2.18 ( 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 286 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8393 (pttm) cc_final: 0.8135 (mttp) REVERT: A 102 MET cc_start: 0.7882 (tpp) cc_final: 0.7681 (tpp) REVERT: C 38 ARG cc_start: 0.8130 (ptt180) cc_final: 0.7917 (ptt180) REVERT: C 102 MET cc_start: 0.7398 (tpt) cc_final: 0.7191 (tpp) REVERT: D 35 ASP cc_start: 0.8512 (m-30) cc_final: 0.8205 (m-30) REVERT: D 58 GLU cc_start: 0.6072 (mp0) cc_final: 0.5683 (mp0) REVERT: D 97 ARG cc_start: 0.8127 (tmt-80) cc_final: 0.7892 (tpt-90) REVERT: E 47 TRP cc_start: 0.8850 (t60) cc_final: 0.8195 (t60) REVERT: E 77 GLN cc_start: 0.6736 (pm20) cc_final: 0.6495 (pm20) REVERT: F 97 ARG cc_start: 0.8335 (tpt90) cc_final: 0.8099 (tpt-90) REVERT: F 111 ILE cc_start: 0.7511 (tt) cc_final: 0.7256 (mt) REVERT: X 100 MET cc_start: 0.7946 (ttp) cc_final: 0.7270 (ttp) REVERT: X 484 TYR cc_start: 0.8507 (p90) cc_final: 0.7789 (p90) REVERT: X 492 GLU cc_start: 0.8441 (tt0) cc_final: 0.8169 (tt0) REVERT: X 588 LYS cc_start: 0.9375 (tmtt) cc_final: 0.9015 (tptt) REVERT: X 635 ILE cc_start: 0.8933 (mm) cc_final: 0.8675 (tt) REVERT: Y 97 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8364 (tmtt) REVERT: Y 103 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8138 (tm-30) REVERT: Y 479 TRP cc_start: 0.7047 (m100) cc_final: 0.6188 (m100) REVERT: Z 97 LYS cc_start: 0.8766 (tttm) cc_final: 0.8454 (tmmt) REVERT: Z 484 TYR cc_start: 0.8679 (p90) cc_final: 0.8340 (p90) REVERT: Z 486 TYR cc_start: 0.9130 (m-10) cc_final: 0.8799 (m-10) REVERT: Z 584 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8315 (tm-30) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1063 time to fit residues: 46.9865 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 : 0.480 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 111 optimal weight: 0.0050 chunk 5 optimal weight: 0.9980 overall best weight: 1.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 6 GLN F 6 GLN ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Z 490 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114931 restraints weight = 33343.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117906 restraints weight = 21699.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120040 restraints weight = 16165.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121521 restraints weight = 13115.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122481 restraints weight = 11291.331| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16252 Z= 0.142 Angle : 0.688 13.599 22124 Z= 0.335 Chirality : 0.046 0.417 2592 Planarity : 0.004 0.043 2700 Dihedral : 4.908 35.602 2049 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % 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 are not related in a simple way. whole: -1.29 (0.19), residues: 1854 helix: 1.66 (0.30), residues: 309 sheet: -0.39 (0.24), residues: 468 loop : -1.93 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 99 TYR 0.020 0.002 TYR X 619 PHE 0.015 0.002 PHE X 53 TRP 0.032 0.002 TRP E 36 HIS 0.007 0.001 HIS X 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16176) covalent geometry : angle 0.65162 / 0.33 (21924) SS BOND : bond 0.00526 / 0.27 ( 28) SS BOND : angle 1.36851 / 0.81 ( 56) hydrogen bonds : bond 0.03862 / 2.51 ( 544) hydrogen bonds : angle 5.31174 / 3.60 ( 1503) link_ALPHA1-3 : bond 0.01394 / 0.70 ( 3) link_ALPHA1-3 : angle 4.55189 / 2.97 ( 9) link_ALPHA1-6 : bond 0.00727 / 0.36 ( 3) link_ALPHA1-6 : angle 1.49470 / 0.94 ( 9) link_BETA1-4 : bond 0.00410 / 0.20 ( 12) link_BETA1-4 : angle 1.63295 / 1.04 ( 36) link_NAG-ASN : bond 0.00626 / 0.37 ( 30) link_NAG-ASN : angle 2.89977 / 2.20 ( 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 313 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ARG cc_start: 0.8103 (ptt180) cc_final: 0.7863 (ptt180) REVERT: C 90 MET cc_start: 0.6284 (mmp) cc_final: 0.5883 (mmp) REVERT: C 102 MET cc_start: 0.7284 (tpt) cc_final: 0.7020 (tpp) REVERT: D 35 ASP cc_start: 0.8481 (m-30) cc_final: 0.8170 (m-30) REVERT: D 68 SER cc_start: 0.8318 (t) cc_final: 0.7946 (p) REVERT: E 47 TRP cc_start: 0.8781 (t60) cc_final: 0.8032 (t60) REVERT: E 90 MET cc_start: 0.6507 (mmt) cc_final: 0.6206 (mmt) REVERT: E 101 MET cc_start: 0.7794 (ttt) cc_final: 0.7521 (ttt) REVERT: F 35 ASP cc_start: 0.8320 (m-30) cc_final: 0.8034 (m-30) REVERT: F 92 TYR cc_start: 0.8447 (m-10) cc_final: 0.8227 (m-10) REVERT: F 97 ARG cc_start: 0.8379 (tpt90) cc_final: 0.8015 (tpt-90) REVERT: F 111 ILE cc_start: 0.7383 (tt) cc_final: 0.7085 (mt) REVERT: X 100 MET cc_start: 0.7781 (ttp) cc_final: 0.7118 (ttp) REVERT: X 484 TYR cc_start: 0.8433 (p90) cc_final: 0.7932 (p90) REVERT: X 492 GLU cc_start: 0.8385 (tt0) cc_final: 0.8111 (tt0) REVERT: X 588 LYS cc_start: 0.9332 (tmtt) cc_final: 0.9014 (tptt) REVERT: Y 103 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8086 (tm-30) REVERT: Y 383 PHE cc_start: 0.7935 (m-80) cc_final: 0.7715 (m-80) REVERT: Y 530 MET cc_start: 0.7837 (ttt) cc_final: 0.7496 (mtp) REVERT: Y 622 ILE cc_start: 0.9425 (mt) cc_final: 0.9209 (mt) REVERT: Z 383 PHE cc_start: 0.7907 (m-80) cc_final: 0.7619 (m-80) REVERT: Z 484 TYR cc_start: 0.8664 (p90) cc_final: 0.8367 (p90) REVERT: Z 486 TYR cc_start: 0.9130 (m-10) cc_final: 0.8607 (m-10) REVERT: Z 584 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8082 (tm-30) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.1044 time to fit residues: 49.9421 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 : 0.466 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN ** Z 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111065 restraints weight = 33385.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114191 restraints weight = 21716.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116334 restraints weight = 16200.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117852 restraints weight = 13258.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118785 restraints weight = 11488.624| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16252 Z= 0.220 Angle : 0.742 13.092 22124 Z= 0.366 Chirality : 0.048 0.411 2592 Planarity : 0.005 0.054 2700 Dihedral : 5.139 45.720 2049 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % 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 are not related in a simple way. whole: -1.49 (0.19), residues: 1854 helix: 1.55 (0.30), residues: 309 sheet: -0.62 (0.23), residues: 474 loop : -2.04 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Z 469 TYR 0.022 0.002 TYR X 619 PHE 0.017 0.002 PHE A 78 TRP 0.031 0.002 TRP E 36 HIS 0.009 0.002 HIS Z 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (16176) covalent geometry : angle 0.70697 / 0.36 (21924) SS BOND : bond 0.00603 / 0.31 ( 28) SS BOND : angle 1.65540 / 0.97 ( 56) hydrogen bonds : bond 0.04403 / 2.88 ( 544) hydrogen bonds : angle 5.46056 / 3.70 ( 1503) link_ALPHA1-3 : bond 0.01282 / 0.64 ( 3) link_ALPHA1-3 : angle 4.58012 / 2.99 ( 9) link_ALPHA1-6 : bond 0.00593 / 0.29 ( 3) link_ALPHA1-6 : angle 1.53384 / 0.97 ( 9) link_BETA1-4 : bond 0.00472 / 0.23 ( 12) link_BETA1-4 : angle 1.68738 / 1.08 ( 36) link_NAG-ASN : bond 0.00625 / 0.40 ( 30) link_NAG-ASN : angle 2.90509 / 2.19 ( 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 273 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 MET cc_start: 0.6442 (mmp) cc_final: 0.6031 (mmp) REVERT: D 35 ASP cc_start: 0.8378 (m-30) cc_final: 0.8116 (m-30) REVERT: E 36 TRP cc_start: 0.8938 (m-10) cc_final: 0.8670 (m-10) REVERT: E 47 TRP cc_start: 0.8865 (t60) cc_final: 0.8199 (t60) REVERT: E 72 ASP cc_start: 0.7430 (t70) cc_final: 0.6895 (p0) REVERT: E 90 MET cc_start: 0.6658 (mmt) cc_final: 0.6354 (mmt) REVERT: F 97 ARG cc_start: 0.8354 (tpt90) cc_final: 0.8111 (tpt-90) REVERT: X 100 MET cc_start: 0.7904 (ttp) cc_final: 0.7160 (ttp) REVERT: X 484 TYR cc_start: 0.8458 (p90) cc_final: 0.7853 (p90) REVERT: X 492 GLU cc_start: 0.8382 (tt0) cc_final: 0.8129 (tt0) REVERT: X 588 LYS cc_start: 0.9380 (tmtt) cc_final: 0.9061 (tptt) REVERT: Y 103 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8053 (tm-30) REVERT: Z 97 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8296 (tmmt) REVERT: Z 484 TYR cc_start: 0.8642 (p90) cc_final: 0.8377 (p90) REVERT: Z 486 TYR cc_start: 0.9159 (m-10) cc_final: 0.8723 (m-10) REVERT: Z 584 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8138 (tm-30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1173 time to fit residues: 49.1212 Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 0.0870 chunk 105 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 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 374 HIS ** X 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113940 restraints weight = 33132.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117106 restraints weight = 21082.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119305 restraints weight = 15624.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120890 restraints weight = 12692.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121986 restraints weight = 10949.401| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16252 Z= 0.167 Angle : 0.715 12.612 22124 Z= 0.351 Chirality : 0.047 0.416 2592 Planarity : 0.004 0.058 2700 Dihedral : 5.072 42.361 2049 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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 are not related in a simple way. whole: -1.40 (0.19), residues: 1854 helix: 1.68 (0.30), residues: 309 sheet: -0.53 (0.24), residues: 471 loop : -2.01 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 59 TYR 0.030 0.002 TYR Z 233 PHE 0.015 0.002 PHE X 53 TRP 0.044 0.002 TRP C 114 HIS 0.007 0.002 HIS Z 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16176) covalent geometry : angle 0.67701 / 0.34 (21924) SS BOND : bond 0.00559 / 0.28 ( 28) SS BOND : angle 1.34793 / 0.80 ( 56) hydrogen bonds : bond 0.04041 / 2.62 ( 544) hydrogen bonds : angle 5.38050 / 3.65 ( 1503) link_ALPHA1-3 : bond 0.01345 / 0.67 ( 3) link_ALPHA1-3 : angle 4.55532 / 2.97 ( 9) link_ALPHA1-6 : bond 0.00640 / 0.31 ( 3) link_ALPHA1-6 : angle 1.48908 / 0.94 ( 9) link_BETA1-4 : bond 0.00421 / 0.21 ( 12) link_BETA1-4 : angle 1.64794 / 1.05 ( 36) link_NAG-ASN : bond 0.00636 / 0.40 ( 30) link_NAG-ASN : angle 3.05715 / 2.23 ( 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 302 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 MET cc_start: 0.6364 (mmp) cc_final: 0.5985 (mmp) REVERT: C 102 MET cc_start: 0.7580 (tpp) cc_final: 0.7147 (tpt) REVERT: C 111 MET cc_start: 0.7485 (mtp) cc_final: 0.7274 (mtp) REVERT: D 35 ASP cc_start: 0.8413 (m-30) cc_final: 0.8078 (m-30) REVERT: E 36 TRP cc_start: 0.8966 (m-10) cc_final: 0.8669 (m-10) REVERT: E 47 TRP cc_start: 0.8847 (t60) cc_final: 0.8146 (t60) REVERT: E 50 GLU cc_start: 0.7546 (tt0) cc_final: 0.7253 (tt0) REVERT: E 72 ASP cc_start: 0.7413 (t70) cc_final: 0.6795 (p0) REVERT: E 90 MET cc_start: 0.6641 (mmt) cc_final: 0.6316 (mmt) REVERT: F 35 ASP cc_start: 0.8332 (m-30) cc_final: 0.8057 (m-30) REVERT: F 92 TYR cc_start: 0.8443 (m-10) cc_final: 0.8221 (m-10) REVERT: F 97 ARG cc_start: 0.8408 (tpt90) cc_final: 0.8132 (tpt-90) REVERT: X 54 CYS cc_start: 0.7008 (t) cc_final: 0.6700 (t) REVERT: X 100 MET cc_start: 0.7785 (ttp) cc_final: 0.7209 (ttp) REVERT: X 484 TYR cc_start: 0.8431 (p90) cc_final: 0.7955 (p90) REVERT: X 492 GLU cc_start: 0.8314 (tt0) cc_final: 0.8045 (tt0) REVERT: X 588 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9020 (tptt) REVERT: Y 103 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7981 (tm-30) REVERT: Y 530 MET cc_start: 0.7772 (ttt) cc_final: 0.7352 (mtp) REVERT: Y 622 ILE cc_start: 0.9451 (mt) cc_final: 0.9219 (mt) REVERT: Z 97 LYS cc_start: 0.8749 (tmtt) cc_final: 0.8229 (tmmt) REVERT: Z 469 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8028 (tpt-90) REVERT: Z 486 TYR cc_start: 0.9215 (m-10) cc_final: 0.8755 (m-10) REVERT: Z 584 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8058 (tm-30) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1141 time to fit residues: 52.9411 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 : 0.732 ------------------------------------------------------------------------------- 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: 1.9990 chunk 138 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN 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 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113993 restraints weight = 32163.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117059 restraints weight = 19886.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119263 restraints weight = 14380.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120741 restraints weight = 11391.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121688 restraints weight = 9680.667| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16252 Z= 0.141 Angle : 0.694 12.120 22124 Z= 0.340 Chirality : 0.047 0.415 2592 Planarity : 0.004 0.057 2700 Dihedral : 4.989 39.954 2049 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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 are not related in a simple way. whole: -1.32 (0.19), residues: 1854 helix: 1.76 (0.30), residues: 309 sheet: -0.41 (0.24), residues: 465 loop : -2.00 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 108 TYR 0.023 0.002 TYR Z 233 PHE 0.015 0.001 PHE X 53 TRP 0.041 0.002 TRP E 98 HIS 0.012 0.001 HIS Y 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (16176) covalent geometry : angle 0.65748 / 0.33 (21924) SS BOND : bond 0.00587 / 0.35 ( 28) SS BOND : angle 1.23251 / 0.76 ( 56) hydrogen bonds : bond 0.03830 / 2.51 ( 544) hydrogen bonds : angle 5.20184 / 3.52 ( 1503) link_ALPHA1-3 : bond 0.01348 / 0.67 ( 3) link_ALPHA1-3 : angle 4.53515 / 2.96 ( 9) link_ALPHA1-6 : bond 0.00687 / 0.34 ( 3) link_ALPHA1-6 : angle 1.47540 / 0.93 ( 9) link_BETA1-4 : bond 0.00414 / 0.21 ( 12) link_BETA1-4 : angle 1.61913 / 1.04 ( 36) link_NAG-ASN : bond 0.00626 / 0.39 ( 30) link_NAG-ASN : angle 2.95081 / 2.14 ( 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 296 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.6841 (mp10) cc_final: 0.6638 (mp10) REVERT: C 90 MET cc_start: 0.6345 (mmp) cc_final: 0.5964 (mmp) REVERT: C 101 MET cc_start: 0.7176 (ttp) cc_final: 0.6718 (ttp) REVERT: C 102 MET cc_start: 0.7686 (tpp) cc_final: 0.7404 (tpt) REVERT: D 35 ASP cc_start: 0.8360 (m-30) cc_final: 0.8021 (m-30) REVERT: D 68 SER cc_start: 0.8284 (t) cc_final: 0.7939 (p) REVERT: E 36 TRP cc_start: 0.9000 (m-10) cc_final: 0.8592 (m-10) REVERT: E 47 TRP cc_start: 0.8857 (t60) cc_final: 0.8118 (t60) REVERT: E 50 GLU cc_start: 0.7518 (tt0) cc_final: 0.7112 (tt0) REVERT: E 72 ASP cc_start: 0.7527 (t70) cc_final: 0.6889 (p0) REVERT: E 90 MET cc_start: 0.6508 (mmt) cc_final: 0.6154 (mmt) REVERT: F 92 TYR cc_start: 0.8473 (m-10) cc_final: 0.8246 (m-10) REVERT: F 97 ARG cc_start: 0.8356 (tpt90) cc_final: 0.8136 (tpt-90) REVERT: X 100 MET cc_start: 0.7758 (ttp) cc_final: 0.7139 (ttp) REVERT: X 484 TYR cc_start: 0.8480 (p90) cc_final: 0.8088 (p90) REVERT: X 492 GLU cc_start: 0.8373 (tt0) cc_final: 0.8105 (tt0) REVERT: X 588 LYS cc_start: 0.9342 (tmtt) cc_final: 0.9027 (tptt) REVERT: Y 103 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8032 (tm-30) REVERT: Z 383 PHE cc_start: 0.7944 (m-80) cc_final: 0.7570 (m-80) REVERT: Z 469 ARG cc_start: 0.8237 (tpp80) cc_final: 0.8008 (tpt-90) REVERT: Z 484 TYR cc_start: 0.8721 (p90) cc_final: 0.8476 (p90) REVERT: Z 486 TYR cc_start: 0.9176 (m-10) cc_final: 0.8728 (m-10) REVERT: Z 584 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8080 (tm-30) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1179 time to fit residues: 53.3841 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 : 0.598 ------------------------------------------------------------------------------- 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: 0.9980 chunk 149 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118984 restraints weight = 31984.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122309 restraints weight = 19436.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124640 restraints weight = 13879.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126234 restraints weight = 10950.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127420 restraints weight = 9242.458| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16252 Z= 0.145 Angle : 0.706 12.106 22124 Z= 0.346 Chirality : 0.047 0.414 2592 Planarity : 0.005 0.098 2700 Dihedral : 4.965 42.285 2049 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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 are not related in a simple way. whole: -1.30 (0.19), residues: 1854 helix: 1.77 (0.30), residues: 309 sheet: -0.48 (0.23), residues: 480 loop : -1.95 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 108 TYR 0.016 0.002 TYR X 619 PHE 0.014 0.002 PHE X 53 TRP 0.038 0.002 TRP X 479 HIS 0.006 0.001 HIS X 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (16176) covalent geometry : angle 0.66852 / 0.34 (21924) SS BOND : bond 0.00513 / 0.26 ( 28) SS BOND : angle 1.31033 / 0.77 ( 56) hydrogen bonds : bond 0.03787 / 2.45 ( 544) hydrogen bonds : angle 5.21032 / 3.52 ( 1503) link_ALPHA1-3 : bond 0.01336 / 0.67 ( 3) link_ALPHA1-3 : angle 4.52238 / 2.95 ( 9) link_ALPHA1-6 : bond 0.00654 / 0.32 ( 3) link_ALPHA1-6 : angle 1.47491 / 0.94 ( 9) link_BETA1-4 : bond 0.00431 / 0.22 ( 12) link_BETA1-4 : angle 1.61010 / 1.03 ( 36) link_NAG-ASN : bond 0.00624 / 0.39 ( 30) link_NAG-ASN : angle 3.07608 / 2.29 ( 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 295 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7427 (ptp90) cc_final: 0.7179 (ptp-170) REVERT: C 38 ARG cc_start: 0.8197 (ptt180) cc_final: 0.7964 (ptt180) REVERT: C 90 MET cc_start: 0.6296 (mmp) cc_final: 0.5937 (mmp) REVERT: C 102 MET cc_start: 0.7660 (tpp) cc_final: 0.7435 (tpt) REVERT: D 35 ASP cc_start: 0.8455 (m-30) cc_final: 0.8054 (m-30) REVERT: D 110 GLU cc_start: 0.8155 (pp20) cc_final: 0.7918 (pp20) REVERT: E 36 TRP cc_start: 0.9011 (m-10) cc_final: 0.8580 (m-10) REVERT: E 47 TRP cc_start: 0.8863 (t60) cc_final: 0.8083 (t60) REVERT: E 50 GLU cc_start: 0.7559 (tt0) cc_final: 0.7175 (tt0) REVERT: E 72 ASP cc_start: 0.7556 (t70) cc_final: 0.6949 (p0) REVERT: E 90 MET cc_start: 0.6401 (mmt) cc_final: 0.6008 (mmt) REVERT: F 35 ASP cc_start: 0.8439 (m-30) cc_final: 0.8136 (m-30) REVERT: F 58 GLU cc_start: 0.6872 (mp0) cc_final: 0.6579 (mp0) REVERT: F 92 TYR cc_start: 0.8508 (m-10) cc_final: 0.8275 (m-10) REVERT: X 100 MET cc_start: 0.7780 (ttp) cc_final: 0.7148 (ttp) REVERT: X 103 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8365 (tm-30) REVERT: X 484 TYR cc_start: 0.8488 (p90) cc_final: 0.8095 (p90) REVERT: X 492 GLU cc_start: 0.8406 (tt0) cc_final: 0.8110 (tt0) REVERT: X 588 LYS cc_start: 0.9322 (tmtt) cc_final: 0.9006 (tptt) REVERT: Y 97 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8315 (mttt) REVERT: Y 103 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8038 (tm-30) REVERT: Y 353 PHE cc_start: 0.5785 (m-10) cc_final: 0.5500 (m-80) REVERT: Y 486 TYR cc_start: 0.8926 (m-80) cc_final: 0.8678 (m-80) REVERT: Y 530 MET cc_start: 0.7942 (ttt) cc_final: 0.7546 (mtp) REVERT: Y 622 ILE cc_start: 0.9413 (mt) cc_final: 0.9166 (mt) REVERT: Z 469 ARG cc_start: 0.8272 (tpp80) cc_final: 0.7982 (tpt-90) REVERT: Z 486 TYR cc_start: 0.9184 (m-10) cc_final: 0.8754 (m-10) REVERT: Z 584 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8073 (tm-30) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1177 time to fit residues: 53.2199 Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 0.5980 chunk 87 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 6 GLN F 6 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 ASN X 374 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.138043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113445 restraints weight = 33213.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116611 restraints weight = 21354.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118819 restraints weight = 15864.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120377 restraints weight = 12903.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121472 restraints weight = 11129.887| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16252 Z= 0.170 Angle : 0.718 12.102 22124 Z= 0.353 Chirality : 0.047 0.412 2592 Planarity : 0.004 0.057 2700 Dihedral : 5.025 41.904 2049 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % 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 : 0.06 % 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 are not related in a simple way. whole: -1.36 (0.19), residues: 1854 helix: 1.71 (0.30), residues: 309 sheet: -0.53 (0.23), residues: 480 loop : -1.98 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 108 TYR 0.018 0.002 TYR X 227 PHE 0.018 0.002 PHE X 53 TRP 0.033 0.002 TRP Z 45 HIS 0.006 0.001 HIS Z 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (16176) covalent geometry : angle 0.68037 / 0.34 (21924) SS BOND : bond 0.00523 / 0.27 ( 28) SS BOND : angle 1.50048 / 0.94 ( 56) hydrogen bonds : bond 0.03938 / 2.58 ( 544) hydrogen bonds : angle 5.22616 / 3.54 ( 1503) link_ALPHA1-3 : bond 0.01302 / 0.65 ( 3) link_ALPHA1-3 : angle 4.52946 / 2.96 ( 9) link_ALPHA1-6 : bond 0.00608 / 0.30 ( 3) link_ALPHA1-6 : angle 1.49715 / 0.95 ( 9) link_BETA1-4 : bond 0.00434 / 0.22 ( 12) link_BETA1-4 : angle 1.63566 / 1.04 ( 36) link_NAG-ASN : bond 0.00614 / 0.39 ( 30) link_NAG-ASN : angle 3.01010 / 2.25 ( 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 289 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7436 (ptp90) cc_final: 0.7201 (ptp-170) REVERT: C 90 MET cc_start: 0.6443 (mmp) cc_final: 0.6118 (mmp) REVERT: C 102 MET cc_start: 0.7597 (tpp) cc_final: 0.7352 (tpt) REVERT: D 35 ASP cc_start: 0.8451 (m-30) cc_final: 0.8079 (m-30) REVERT: E 36 TRP cc_start: 0.9081 (m-10) cc_final: 0.8681 (m-10) REVERT: E 47 TRP cc_start: 0.8859 (t60) cc_final: 0.8190 (t60) REVERT: E 50 GLU cc_start: 0.7443 (tt0) cc_final: 0.7114 (tt0) REVERT: E 72 ASP cc_start: 0.7577 (t70) cc_final: 0.6999 (p0) REVERT: E 77 GLN cc_start: 0.6440 (mp10) cc_final: 0.5774 (mp10) REVERT: E 80 LEU cc_start: 0.7793 (pp) cc_final: 0.7551 (pp) REVERT: E 90 MET cc_start: 0.6549 (mmt) cc_final: 0.6154 (mmt) REVERT: F 35 ASP cc_start: 0.8378 (m-30) cc_final: 0.8130 (m-30) REVERT: F 92 TYR cc_start: 0.8402 (m-10) cc_final: 0.8183 (m-10) REVERT: X 54 CYS cc_start: 0.6846 (t) cc_final: 0.6591 (t) REVERT: X 100 MET cc_start: 0.7785 (ttp) cc_final: 0.7176 (ttp) REVERT: X 484 TYR cc_start: 0.8457 (p90) cc_final: 0.8060 (p90) REVERT: X 492 GLU cc_start: 0.8322 (tt0) cc_final: 0.8026 (tt0) REVERT: X 588 LYS cc_start: 0.9360 (tmtt) cc_final: 0.9030 (tptt) REVERT: Y 103 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8027 (tm-30) REVERT: Y 104 MET cc_start: 0.8453 (tmm) cc_final: 0.8247 (tmm) REVERT: Y 383 PHE cc_start: 0.7866 (m-80) cc_final: 0.7654 (m-80) REVERT: Y 486 TYR cc_start: 0.8939 (m-80) cc_final: 0.8676 (m-80) REVERT: Z 486 TYR cc_start: 0.9174 (m-10) cc_final: 0.8666 (m-10) REVERT: Z 584 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8091 (tm-30) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1138 time to fit residues: 50.3249 Evaluate side-chains 226 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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: 1.9990 chunk 134 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 20 optimal weight: 0.0570 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 6 GLN F 6 GLN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 ASN ** X 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112137 restraints weight = 33335.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115159 restraints weight = 21672.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117242 restraints weight = 16115.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118738 restraints weight = 13107.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119666 restraints weight = 11308.069| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16252 Z= 0.186 Angle : 0.734 12.090 22124 Z= 0.361 Chirality : 0.048 0.411 2592 Planarity : 0.005 0.058 2700 Dihedral : 5.092 42.192 2049 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.19), residues: 1854 helix: 1.57 (0.30), residues: 312 sheet: -0.59 (0.23), residues: 474 loop : -2.08 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 108 TYR 0.039 0.002 TYR X 227 PHE 0.017 0.002 PHE X 53 TRP 0.035 0.002 TRP Z 45 HIS 0.007 0.002 HIS X 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (16176) covalent geometry : angle 0.69787 / 0.35 (21924) SS BOND : bond 0.00536 / 0.27 ( 28) SS BOND : angle 1.48698 / 0.94 ( 56) hydrogen bonds : bond 0.04054 / 2.65 ( 544) hydrogen bonds : angle 5.27774 / 3.58 ( 1503) link_ALPHA1-3 : bond 0.01261 / 0.63 ( 3) link_ALPHA1-3 : angle 4.53204 / 2.96 ( 9) link_ALPHA1-6 : bond 0.00601 / 0.29 ( 3) link_ALPHA1-6 : angle 1.49889 / 0.95 ( 9) link_BETA1-4 : bond 0.00440 / 0.22 ( 12) link_BETA1-4 : angle 1.64626 / 1.04 ( 36) link_NAG-ASN : bond 0.00614 / 0.39 ( 30) link_NAG-ASN : angle 3.00757 / 2.24 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2332.90 seconds wall clock time: 41 minutes 27.41 seconds (2487.41 seconds total)