Starting phenix.real_space_refine on Sun Jun 15 02:58:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cxi_27058/06_2025/8cxi_27058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cxi_27058/06_2025/8cxi_27058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cxi_27058/06_2025/8cxi_27058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cxi_27058/06_2025/8cxi_27058.map" model { file = "/net/cci-nas-00/data/ceres_data/8cxi_27058/06_2025/8cxi_27058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cxi_27058/06_2025/8cxi_27058.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 98 atoms to isotropic. 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 114 5.16 5 C 10612 2.51 5 N 2902 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16832 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1036 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 761 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1024 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 743 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.47, per 1000 atoms: 0.56 Number of scatterers: 16832 At special positions: 0 Unit cell: (106, 203.52, 121.9, 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 114 16.00 O 3204 8.00 N 2902 7.00 C 10612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.95 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.31 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=1.90 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=0.96 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.82 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.05 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 339 " distance=2.93 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 Atom "HETATM16746 O5 NAG G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " NAG-ASN " NAG G 1 " - " ASN A 154 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 2.1 seconds 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 40 sheets defined 23.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 461 through 478 Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.535A pdb=" N GLY A 492 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 41 through 53 removed outlier: 3.563A pdb=" N LEU D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 97 through 100B removed outlier: 4.058A pdb=" N TYR H 100A" --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 27C through 32 removed outlier: 3.930A pdb=" N ASN L 31 " --> pdb=" O ALA L 27C" (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 32 " --> pdb=" O ASP L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 27C through 32' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.985A pdb=" N ILE B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.923A pdb=" N GLU B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.781A pdb=" N VAL B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 426 through 429 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 482 through 500 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.956A pdb=" N THR E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.910A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.553A pdb=" N LYS E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 83 through 87 removed outlier: 3.508A pdb=" N ASP h 86 " --> pdb=" O THR h 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 33 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.605A pdb=" N GLU l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.872A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 457 Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 483 through 500 removed outlier: 3.566A pdb=" N LEU C 498 " --> pdb=" O VAL C 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 11 removed outlier: 3.604A pdb=" N LYS F 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 39 Processing helix chain 'F' and resid 40 through 52 Processing helix chain 'F' and resid 56 through 74 removed outlier: 3.702A pdb=" N LYS F 60 " --> pdb=" O SER F 56 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.684A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS A 210 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N MET A 125 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 58 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 127 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 54 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.684A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG A 138 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 26 removed outlier: 4.511A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 65 removed outlier: 3.982A pdb=" N SER A 112 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA6, first strand: chain 'A' and resid 243 through 247 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.587A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.587A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.399A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.716A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 48 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 281 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 276 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS B 210 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 54 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.716A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG B 138 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 48 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU B 136 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.434A pdb=" N ASP B 296 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER B 185 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 72 removed outlier: 6.411A pdb=" N LYS B 118 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 116 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 114 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 112 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 320 removed outlier: 7.088A pdb=" N THR B 315 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLN B 331 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE B 317 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 329 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.859A pdb=" N CYS B 339 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 365 " --> pdb=" O CYS B 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AC7, first strand: chain 'h' and resid 3 through 7 removed outlier: 3.635A pdb=" N GLN h 3 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER h 25 " --> pdb=" O GLN h 3 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 11 through 12 removed outlier: 3.555A pdb=" N TRP h 33 " --> pdb=" O ASP h 95 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET h 34 " --> pdb=" O ARG h 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 11 through 12 removed outlier: 4.509A pdb=" N VAL h 102 " --> pdb=" O ARG h 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'l' and resid 9 through 12 removed outlier: 7.123A pdb=" N VAL l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP l 35 " --> pdb=" O MET l 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 9 through 12 removed outlier: 7.123A pdb=" N VAL l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.606A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 127 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 54 " --> pdb=" O SER C 129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.606A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG C 138 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR C 48 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 20 through 26 Processing sheet with id=AD7, first strand: chain 'C' and resid 63 through 65 Processing sheet with id=AD8, first strand: chain 'C' and resid 63 through 65 Processing sheet with id=AD9, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AE1, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AE4, first strand: chain 'C' and resid 343 through 346 753 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2730 1.27 - 1.41: 4286 1.41 - 1.54: 9975 1.54 - 1.68: 26 1.68 - 1.81: 179 Bond restraints: 17196 Sorted by residual: bond pdb=" CA SER C 72 " pdb=" C SER C 72 " ideal model delta sigma weight residual 1.520 1.415 0.105 1.20e-02 6.94e+03 7.65e+01 bond pdb=" CA MET A 125 " pdb=" C MET A 125 " ideal model delta sigma weight residual 1.522 1.425 0.098 1.19e-02 7.06e+03 6.78e+01 bond pdb=" C ARG C 73 " pdb=" O ARG C 73 " ideal model delta sigma weight residual 1.234 1.139 0.095 1.20e-02 6.94e+03 6.27e+01 bond pdb=" C MET A 125 " pdb=" O MET A 125 " ideal model delta sigma weight residual 1.235 1.146 0.089 1.23e-02 6.61e+03 5.26e+01 bond pdb=" CA LYS A 316 " pdb=" C LYS A 316 " ideal model delta sigma weight residual 1.522 1.426 0.095 1.37e-02 5.33e+03 4.83e+01 ... (remaining 17191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 22964 3.13 - 6.26: 289 6.26 - 9.40: 33 9.40 - 12.53: 11 12.53 - 15.66: 7 Bond angle restraints: 23304 Sorted by residual: angle pdb=" C CYS B 74 " pdb=" N PRO B 75 " pdb=" CA PRO B 75 " ideal model delta sigma weight residual 119.84 135.50 -15.66 1.25e+00 6.40e-01 1.57e+02 angle pdb=" N LYS A 316 " pdb=" CA LYS A 316 " pdb=" C LYS A 316 " ideal model delta sigma weight residual 113.23 100.07 13.16 1.24e+00 6.50e-01 1.13e+02 angle pdb=" N ARG B 73 " pdb=" CA ARG B 73 " pdb=" C ARG B 73 " ideal model delta sigma weight residual 112.92 125.37 -12.45 1.23e+00 6.61e-01 1.02e+02 angle pdb=" N THR A 315 " pdb=" CA THR A 315 " pdb=" C THR A 315 " ideal model delta sigma weight residual 111.40 123.14 -11.74 1.22e+00 6.72e-01 9.26e+01 angle pdb=" C CYS C 74 " pdb=" N PRO C 75 " pdb=" CA PRO C 75 " ideal model delta sigma weight residual 119.84 131.79 -11.95 1.25e+00 6.40e-01 9.14e+01 ... (remaining 23299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 9746 24.85 - 49.70: 412 49.70 - 74.55: 51 74.55 - 99.40: 28 99.40 - 124.25: 2 Dihedral angle restraints: 10239 sinusoidal: 4036 harmonic: 6203 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -168.58 82.58 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -153.39 67.39 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sinusoidal sigma weight residual -86.00 -152.73 66.73 1 1.00e+01 1.00e-02 5.81e+01 ... (remaining 10236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.648: 2640 0.648 - 1.296: 0 1.296 - 1.944: 0 1.944 - 2.592: 0 2.592 - 3.240: 1 Chirality restraints: 2641 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 154 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 0.84 -3.24 2.00e-01 2.50e+01 2.62e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.15e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.04e+01 ... (remaining 2638 not shown) Planarity restraints: 2943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 154 " -0.031 2.00e-02 2.50e+03 2.51e-01 7.90e+02 pdb=" CG ASN A 154 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 154 " -0.172 2.00e-02 2.50e+03 pdb=" ND2 ASN A 154 " 0.432 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.305 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 239 " -0.031 2.00e-02 2.50e+03 6.49e-02 4.22e+01 pdb=" C LYS C 239 " 0.112 2.00e-02 2.50e+03 pdb=" O LYS C 239 " -0.043 2.00e-02 2.50e+03 pdb=" N GLU C 240 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 1 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" C ILE C 1 " 0.084 2.00e-02 2.50e+03 pdb=" O ILE C 1 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG C 2 " -0.028 2.00e-02 2.50e+03 ... (remaining 2940 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 9 1.67 - 2.47: 178 2.47 - 3.28: 18102 3.28 - 4.09: 39051 4.09 - 4.90: 71646 Warning: very small nonbonded interaction distances. Nonbonded interactions: 128986 Sorted by model distance: nonbonded pdb=" OD2 ASP B 10 " pdb=" NH2 ARG B 420 " model vdw 0.857 3.120 nonbonded pdb=" CD2 TYR l 36 " pdb=" CD2 LEU l 46 " model vdw 1.362 3.760 nonbonded pdb=" O PHE B 312 " pdb=" CD1 ILE B 396 " model vdw 1.364 3.460 nonbonded pdb=" CD2 LEU B 472 " pdb=" CE MET B 487 " model vdw 1.472 3.880 nonbonded pdb=" OG SER h 100J" pdb=" NE ARG C 73 " model vdw 1.517 3.120 ... (remaining 128981 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = (chain 'H' and (resid 1 through 100 or resid 100B through 112)) selection = chain 'h' } ncs_group { reference = (chain 'L' and resid 8 through 105) selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.130 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.016 1.074 17222 Z= 0.829 Angle : 1.210 63.517 23361 Z= 0.656 Chirality : 0.086 3.240 2641 Planarity : 0.006 0.099 2942 Dihedral : 14.268 124.253 6237 Min Nonbonded Distance : 0.857 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.57 % Favored : 89.74 % Rotamer: Outliers : 3.00 % Allowed : 9.45 % Favored : 87.55 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.16), residues: 2174 helix: -1.25 (0.21), residues: 450 sheet: -0.32 (0.19), residues: 733 loop : -3.08 (0.16), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 400 HIS 0.006 0.001 HIS A 235 PHE 0.016 0.002 PHE A 431 TYR 0.020 0.002 TYR A 61 ARG 0.011 0.001 ARG C 73 Details of bonding type rmsd link_NAG-ASN : bond 0.15690 ( 1) link_NAG-ASN : angle 31.98488 ( 3) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 6.01168 ( 12) hydrogen bonds : bond 0.13754 ( 706) hydrogen bonds : angle 7.44257 ( 1968) link_BETA1-6 : bond 0.03696 ( 2) link_BETA1-6 : angle 2.29616 ( 6) SS BOND : bond 0.44207 ( 18) SS BOND : angle 15.58891 ( 36) covalent geometry : bond 0.00802 (17196) covalent geometry : angle 0.96936 (23304) Misc. bond : bond 0.11072 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 457 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8108 (p0) cc_final: 0.7795 (p0) REVERT: A 276 GLU cc_start: 0.6129 (pt0) cc_final: 0.5909 (pt0) REVERT: A 395 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7698 (ptpp) REVERT: A 495 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7944 (mp) REVERT: H 32 HIS cc_start: 0.6889 (m90) cc_final: 0.6579 (m90) REVERT: B 136 GLU cc_start: 0.6794 (tt0) cc_final: 0.5990 (tt0) REVERT: B 140 MET cc_start: 0.7585 (mmt) cc_final: 0.7324 (mmm) REVERT: B 247 ASP cc_start: 0.6537 (t0) cc_final: 0.6318 (t0) REVERT: B 429 TRP cc_start: 0.7361 (m100) cc_final: 0.7066 (m100) REVERT: E 14 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7886 (m) REVERT: E 38 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6522 (mmt90) REVERT: C 67 ASP cc_start: 0.8344 (p0) cc_final: 0.8042 (p0) REVERT: C 87 ASP cc_start: 0.7556 (t0) cc_final: 0.7133 (t0) REVERT: C 134 ASN cc_start: 0.8427 (p0) cc_final: 0.8064 (p0) outliers start: 54 outliers final: 19 residues processed: 497 average time/residue: 0.2933 time to fit residues: 213.7422 Evaluate side-chains 354 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN A 148 HIS A 163 ASN A 288 HIS ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 85 GLN B 134 ASN B 163 ASN B 261 GLN B 344 GLN B 350 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN E 7 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 HIS C 154 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS C 350 GLN F 7 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.187410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126634 restraints weight = 20047.470| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.18 r_work: 0.3263 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17222 Z= 0.157 Angle : 0.805 24.179 23361 Z= 0.403 Chirality : 0.053 1.181 2641 Planarity : 0.006 0.147 2942 Dihedral : 11.406 109.511 2548 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.48 % Favored : 90.39 % Rotamer: Outliers : 3.72 % Allowed : 14.90 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.17), residues: 2174 helix: 0.11 (0.25), residues: 429 sheet: -0.13 (0.19), residues: 706 loop : -2.69 (0.16), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 36 HIS 0.032 0.001 HIS A 27 PHE 0.036 0.002 PHE A 314 TYR 0.015 0.002 TYR D 25 ARG 0.006 0.001 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.01023 ( 1) link_NAG-ASN : angle 17.20593 ( 3) link_BETA1-4 : bond 0.00982 ( 4) link_BETA1-4 : angle 2.17918 ( 12) hydrogen bonds : bond 0.05147 ( 706) hydrogen bonds : angle 6.07370 ( 1968) link_BETA1-6 : bond 0.00733 ( 2) link_BETA1-6 : angle 2.87929 ( 6) SS BOND : bond 0.00602 ( 18) SS BOND : angle 1.24614 ( 36) covalent geometry : bond 0.00332 (17196) covalent geometry : angle 0.77742 (23304) Misc. bond : bond 0.00426 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 350 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.8966 (tp40) cc_final: 0.8735 (tp-100) REVERT: A 66 SER cc_start: 0.8517 (t) cc_final: 0.8214 (m) REVERT: A 72 SER cc_start: 0.8777 (p) cc_final: 0.8332 (m) REVERT: A 90 TYR cc_start: 0.8734 (m-80) cc_final: 0.8503 (m-80) REVERT: A 121 CYS cc_start: 0.8866 (p) cc_final: 0.8200 (t) REVERT: A 151 MET cc_start: 0.7975 (mmm) cc_final: 0.7373 (mmm) REVERT: A 221 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 276 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6662 (pt0) REVERT: A 294 LYS cc_start: 0.8438 (mttt) cc_final: 0.8202 (mttt) REVERT: A 382 PHE cc_start: 0.8600 (m-80) cc_final: 0.8190 (m-10) REVERT: H 34 MET cc_start: 0.7932 (mmm) cc_final: 0.7656 (mmm) REVERT: B 26 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8592 (mt-10) REVERT: B 70 SER cc_start: 0.8882 (p) cc_final: 0.8494 (t) REVERT: B 136 GLU cc_start: 0.7884 (tt0) cc_final: 0.7457 (tt0) REVERT: B 168 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 193 ARG cc_start: 0.9137 (mtt-85) cc_final: 0.8907 (mtt-85) REVERT: B 197 ASP cc_start: 0.8010 (t0) cc_final: 0.7702 (t0) REVERT: B 237 ASN cc_start: 0.8065 (t0) cc_final: 0.7860 (t0) REVERT: B 254 THR cc_start: 0.6994 (OUTLIER) cc_final: 0.6736 (p) REVERT: B 421 MET cc_start: 0.8593 (mtt) cc_final: 0.8384 (mtt) REVERT: B 430 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7836 (t0) REVERT: l 47 MET cc_start: 0.8132 (mtm) cc_final: 0.7748 (ptp) REVERT: C 87 ASP cc_start: 0.8497 (t0) cc_final: 0.8043 (m-30) REVERT: C 125 MET cc_start: 0.6613 (tpp) cc_final: 0.6180 (ttt) REVERT: C 151 MET cc_start: 0.8569 (mmm) cc_final: 0.8267 (mtt) REVERT: C 164 ARG cc_start: 0.7271 (mtm-85) cc_final: 0.6974 (mtm110) REVERT: C 473 MET cc_start: 0.7336 (tpp) cc_final: 0.7116 (mmm) REVERT: C 487 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.6063 (mmt) REVERT: F 8 SER cc_start: 0.8863 (p) cc_final: 0.8434 (t) outliers start: 67 outliers final: 41 residues processed: 396 average time/residue: 0.2621 time to fit residues: 159.5326 Evaluate side-chains 367 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 321 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 45 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 65 optimal weight: 40.0000 chunk 113 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 115 optimal weight: 0.3980 chunk 47 optimal weight: 0.0980 chunk 74 optimal weight: 50.0000 chunk 43 optimal weight: 8.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 447 GLN h 35 HIS C 103 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.183202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122090 restraints weight = 19872.971| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.09 r_work: 0.3207 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17222 Z= 0.216 Angle : 0.785 24.436 23361 Z= 0.397 Chirality : 0.051 0.975 2641 Planarity : 0.005 0.104 2942 Dihedral : 10.665 98.740 2526 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.21 % Favored : 89.70 % Rotamer: Outliers : 5.00 % Allowed : 16.45 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2174 helix: 0.26 (0.26), residues: 429 sheet: 0.06 (0.20), residues: 682 loop : -2.52 (0.16), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 400 HIS 0.023 0.001 HIS C 288 PHE 0.018 0.002 PHE A 314 TYR 0.014 0.002 TYR D 25 ARG 0.006 0.001 ARG l 95 Details of bonding type rmsd link_NAG-ASN : bond 0.01187 ( 1) link_NAG-ASN : angle 16.94807 ( 3) link_BETA1-4 : bond 0.00734 ( 4) link_BETA1-4 : angle 2.43920 ( 12) hydrogen bonds : bond 0.05217 ( 706) hydrogen bonds : angle 5.76929 ( 1968) link_BETA1-6 : bond 0.00603 ( 2) link_BETA1-6 : angle 2.92510 ( 6) SS BOND : bond 0.00449 ( 18) SS BOND : angle 1.05246 ( 36) covalent geometry : bond 0.00499 (17196) covalent geometry : angle 0.75762 (23304) Misc. bond : bond 0.00578 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 345 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.9034 (tp40) cc_final: 0.8767 (tp-100) REVERT: A 66 SER cc_start: 0.8561 (t) cc_final: 0.8292 (m) REVERT: A 72 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8249 (t) REVERT: A 121 CYS cc_start: 0.8785 (p) cc_final: 0.8444 (t) REVERT: A 177 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: A 221 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7988 (mt) REVERT: A 276 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: A 345 MET cc_start: 0.8609 (mmm) cc_final: 0.7897 (mmm) REVERT: A 379 ASP cc_start: 0.8485 (t0) cc_final: 0.8250 (t0) REVERT: D 70 ILE cc_start: 0.8222 (tt) cc_final: 0.8018 (tt) REVERT: H 32 HIS cc_start: 0.7119 (m90) cc_final: 0.5551 (m90) REVERT: H 34 MET cc_start: 0.8003 (mmm) cc_final: 0.7630 (mmm) REVERT: H 94 ARG cc_start: 0.3587 (ttp-170) cc_final: 0.2979 (ttp-170) REVERT: L 47 MET cc_start: 0.7223 (mmt) cc_final: 0.6853 (mtt) REVERT: L 90 SER cc_start: 0.7383 (OUTLIER) cc_final: 0.7170 (m) REVERT: B 13 GLU cc_start: 0.8393 (tt0) cc_final: 0.7771 (pt0) REVERT: B 70 SER cc_start: 0.8896 (p) cc_final: 0.8596 (t) REVERT: B 166 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8635 (ttmt) REVERT: B 193 ARG cc_start: 0.9178 (mtt-85) cc_final: 0.8955 (mtt-85) REVERT: B 197 ASP cc_start: 0.8096 (t0) cc_final: 0.7673 (t0) REVERT: B 283 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7836 (mtm110) REVERT: B 430 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7738 (t0) REVERT: B 460 MET cc_start: 0.8558 (mtp) cc_final: 0.8141 (mtp) REVERT: E 38 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6840 (mmt90) REVERT: h 34 MET cc_start: 0.7465 (mmt) cc_final: 0.7096 (mmt) REVERT: l 47 MET cc_start: 0.8190 (mtm) cc_final: 0.7873 (ptp) REVERT: C 40 THR cc_start: 0.8728 (m) cc_final: 0.8398 (p) REVERT: C 87 ASP cc_start: 0.8600 (t0) cc_final: 0.8086 (t0) REVERT: C 125 MET cc_start: 0.6935 (tpp) cc_final: 0.6708 (ttt) REVERT: C 151 MET cc_start: 0.8585 (mmm) cc_final: 0.8093 (mtt) REVERT: C 164 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.6914 (mtm110) REVERT: C 177 GLU cc_start: 0.8375 (pt0) cc_final: 0.8052 (pm20) REVERT: C 276 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: C 329 GLU cc_start: 0.8565 (tt0) cc_final: 0.8333 (tt0) REVERT: C 344 GLN cc_start: 0.7653 (pt0) cc_final: 0.7424 (pt0) REVERT: C 494 VAL cc_start: 0.5916 (OUTLIER) cc_final: 0.5706 (t) REVERT: F 8 SER cc_start: 0.8965 (p) cc_final: 0.8522 (t) outliers start: 90 outliers final: 50 residues processed: 408 average time/residue: 0.2789 time to fit residues: 177.2095 Evaluate side-chains 384 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 325 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 192 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 157 optimal weight: 50.0000 chunk 83 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 75 optimal weight: 40.0000 chunk 77 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 362 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 = 0.4021 r_free = 0.4021 target = 0.183608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121740 restraints weight = 20192.659| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.16 r_work: 0.3202 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17222 Z= 0.219 Angle : 0.766 23.565 23361 Z= 0.387 Chirality : 0.050 0.896 2641 Planarity : 0.005 0.091 2942 Dihedral : 10.129 95.748 2522 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.76 % Favored : 89.10 % Rotamer: Outliers : 6.06 % Allowed : 16.23 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2174 helix: 0.17 (0.25), residues: 447 sheet: 0.20 (0.20), residues: 679 loop : -2.49 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 400 HIS 0.010 0.001 HIS A 27 PHE 0.024 0.002 PHE A 382 TYR 0.014 0.002 TYR D 25 ARG 0.007 0.001 ARG B 99 Details of bonding type rmsd link_NAG-ASN : bond 0.01262 ( 1) link_NAG-ASN : angle 16.24605 ( 3) link_BETA1-4 : bond 0.00809 ( 4) link_BETA1-4 : angle 2.54417 ( 12) hydrogen bonds : bond 0.05107 ( 706) hydrogen bonds : angle 5.62605 ( 1968) link_BETA1-6 : bond 0.01151 ( 2) link_BETA1-6 : angle 2.70600 ( 6) SS BOND : bond 0.00356 ( 18) SS BOND : angle 0.94687 ( 36) covalent geometry : bond 0.00510 (17196) covalent geometry : angle 0.74003 (23304) Misc. bond : bond 0.00716 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 345 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6004 (ptp) cc_final: 0.5705 (ptt) REVERT: A 36 GLN cc_start: 0.9052 (tp40) cc_final: 0.8774 (tp-100) REVERT: A 72 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8522 (t) REVERT: A 151 MET cc_start: 0.8007 (mmm) cc_final: 0.7600 (mmm) REVERT: A 177 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: A 221 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (mt) REVERT: A 276 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6732 (pt0) REVERT: A 345 MET cc_start: 0.8813 (mmm) cc_final: 0.7808 (mmm) REVERT: A 379 ASP cc_start: 0.8469 (t0) cc_final: 0.8224 (t0) REVERT: A 382 PHE cc_start: 0.8652 (m-80) cc_final: 0.8365 (m-10) REVERT: D 70 ILE cc_start: 0.8222 (tt) cc_final: 0.8021 (tt) REVERT: H 32 HIS cc_start: 0.7105 (m90) cc_final: 0.5604 (m90) REVERT: H 94 ARG cc_start: 0.3819 (ttp-170) cc_final: 0.3115 (ttp-170) REVERT: L 47 MET cc_start: 0.7189 (mmt) cc_final: 0.6872 (mtt) REVERT: B 13 GLU cc_start: 0.8691 (tt0) cc_final: 0.7840 (pt0) REVERT: B 30 CYS cc_start: 0.8704 (p) cc_final: 0.8401 (p) REVERT: B 87 ASP cc_start: 0.8030 (t0) cc_final: 0.7686 (t0) REVERT: B 136 GLU cc_start: 0.7998 (tt0) cc_final: 0.7667 (tt0) REVERT: B 166 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8611 (ttmt) REVERT: B 168 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7635 (mt-10) REVERT: B 197 ASP cc_start: 0.8067 (t0) cc_final: 0.7678 (t0) REVERT: B 283 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7781 (mtm110) REVERT: B 382 PHE cc_start: 0.8854 (m-80) cc_final: 0.8347 (m-80) REVERT: B 460 MET cc_start: 0.8548 (mtp) cc_final: 0.8133 (mtp) REVERT: B 487 MET cc_start: 0.6841 (mmt) cc_final: 0.6605 (mmp) REVERT: h 34 MET cc_start: 0.7574 (mmt) cc_final: 0.7263 (mmt) REVERT: h 77 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7148 (p) REVERT: l 47 MET cc_start: 0.8217 (mtm) cc_final: 0.7886 (ptp) REVERT: C 40 THR cc_start: 0.8695 (m) cc_final: 0.8375 (p) REVERT: C 79 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 87 ASP cc_start: 0.8565 (t0) cc_final: 0.8079 (t0) REVERT: C 133 GLU cc_start: 0.8433 (pt0) cc_final: 0.8153 (pp20) REVERT: C 151 MET cc_start: 0.8481 (mmm) cc_final: 0.8216 (mtt) REVERT: C 164 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6881 (mtm110) REVERT: C 177 GLU cc_start: 0.8469 (pt0) cc_final: 0.8146 (pm20) REVERT: C 316 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7615 (mtmm) REVERT: C 329 GLU cc_start: 0.8584 (tt0) cc_final: 0.8322 (tt0) REVERT: C 374 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6891 (ppp) REVERT: C 395 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8417 (mtmm) REVERT: C 494 VAL cc_start: 0.5859 (OUTLIER) cc_final: 0.5653 (t) REVERT: F 8 SER cc_start: 0.8924 (p) cc_final: 0.8454 (t) outliers start: 109 outliers final: 67 residues processed: 421 average time/residue: 0.2466 time to fit residues: 162.2586 Evaluate side-chains 398 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 185 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 chunk 62 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.179930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120040 restraints weight = 20353.890| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.42 r_work: 0.3135 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17222 Z= 0.293 Angle : 0.819 23.209 23361 Z= 0.417 Chirality : 0.052 0.883 2641 Planarity : 0.005 0.086 2942 Dihedral : 9.377 93.988 2517 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.27 % Favored : 88.59 % Rotamer: Outliers : 6.39 % Allowed : 18.23 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2174 helix: -0.10 (0.25), residues: 450 sheet: 0.19 (0.21), residues: 661 loop : -2.45 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 400 HIS 0.010 0.001 HIS A 27 PHE 0.024 0.002 PHE A 382 TYR 0.016 0.002 TYR D 25 ARG 0.004 0.001 ARG B 99 Details of bonding type rmsd link_NAG-ASN : bond 0.01337 ( 1) link_NAG-ASN : angle 15.76448 ( 3) link_BETA1-4 : bond 0.00769 ( 4) link_BETA1-4 : angle 2.58675 ( 12) hydrogen bonds : bond 0.05636 ( 706) hydrogen bonds : angle 5.68544 ( 1968) link_BETA1-6 : bond 0.02127 ( 2) link_BETA1-6 : angle 2.10909 ( 6) SS BOND : bond 0.00610 ( 18) SS BOND : angle 1.23280 ( 36) covalent geometry : bond 0.00692 (17196) covalent geometry : angle 0.79641 (23304) Misc. bond : bond 0.00344 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 324 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6706 (ptp) cc_final: 0.6141 (ptt) REVERT: A 36 GLN cc_start: 0.9075 (tp40) cc_final: 0.8527 (tp-100) REVERT: A 67 ASP cc_start: 0.8697 (p0) cc_final: 0.8352 (p0) REVERT: A 72 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8660 (t) REVERT: A 151 MET cc_start: 0.7936 (mmm) cc_final: 0.7671 (mmm) REVERT: A 276 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6792 (pt0) REVERT: A 345 MET cc_start: 0.8891 (mmm) cc_final: 0.8259 (mmm) REVERT: A 382 PHE cc_start: 0.8778 (m-80) cc_final: 0.8536 (m-80) REVERT: D 70 ILE cc_start: 0.8261 (tt) cc_final: 0.8034 (tt) REVERT: L 47 MET cc_start: 0.7117 (mmt) cc_final: 0.6686 (mtt) REVERT: B 30 CYS cc_start: 0.8649 (p) cc_final: 0.8266 (p) REVERT: B 60 CYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9105 (t) REVERT: B 87 ASP cc_start: 0.8073 (t0) cc_final: 0.7646 (t0) REVERT: B 164 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8446 (mtm-85) REVERT: B 166 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8320 (ttmm) REVERT: B 197 ASP cc_start: 0.8265 (t0) cc_final: 0.7799 (t0) REVERT: B 213 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8489 (m) REVERT: B 283 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7766 (mtm110) REVERT: B 382 PHE cc_start: 0.8932 (m-80) cc_final: 0.8406 (m-80) REVERT: B 460 MET cc_start: 0.8716 (mtp) cc_final: 0.8324 (mtp) REVERT: h 34 MET cc_start: 0.7449 (mmt) cc_final: 0.7140 (mmt) REVERT: h 77 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7017 (p) REVERT: l 47 MET cc_start: 0.8216 (mtm) cc_final: 0.7847 (ptp) REVERT: C 13 GLU cc_start: 0.8646 (tt0) cc_final: 0.8441 (tt0) REVERT: C 15 MET cc_start: 0.5328 (tpt) cc_final: 0.5127 (tpt) REVERT: C 87 ASP cc_start: 0.8547 (t0) cc_final: 0.8081 (t0) REVERT: C 151 MET cc_start: 0.8595 (mmm) cc_final: 0.8214 (mtt) REVERT: C 164 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.7012 (mtm110) REVERT: C 175 ARG cc_start: 0.5850 (ptt-90) cc_final: 0.5348 (ptp90) REVERT: C 177 GLU cc_start: 0.8489 (pt0) cc_final: 0.8218 (tt0) REVERT: C 395 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8429 (mtmm) REVERT: C 460 MET cc_start: 0.8965 (mtm) cc_final: 0.8448 (mtp) outliers start: 115 outliers final: 83 residues processed: 405 average time/residue: 0.2529 time to fit residues: 159.3305 Evaluate side-chains 406 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 318 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 50.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 148 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN C 144 HIS ** C 362 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 = 0.4044 r_free = 0.4044 target = 0.185915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124273 restraints weight = 20124.952| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.15 r_work: 0.3218 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17222 Z= 0.143 Angle : 0.696 22.677 23361 Z= 0.352 Chirality : 0.048 0.883 2641 Planarity : 0.005 0.076 2942 Dihedral : 8.830 91.993 2515 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.98 % Favored : 89.88 % Rotamer: Outliers : 4.67 % Allowed : 19.79 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2174 helix: 0.29 (0.26), residues: 450 sheet: 0.29 (0.21), residues: 652 loop : -2.42 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 400 HIS 0.009 0.001 HIS A 27 PHE 0.019 0.001 PHE F 42 TYR 0.016 0.001 TYR C 61 ARG 0.004 0.000 ARG B 164 Details of bonding type rmsd link_NAG-ASN : bond 0.01557 ( 1) link_NAG-ASN : angle 15.48542 ( 3) link_BETA1-4 : bond 0.00774 ( 4) link_BETA1-4 : angle 2.62873 ( 12) hydrogen bonds : bond 0.04498 ( 706) hydrogen bonds : angle 5.32969 ( 1968) link_BETA1-6 : bond 0.01753 ( 2) link_BETA1-6 : angle 1.33035 ( 6) SS BOND : bond 0.00287 ( 18) SS BOND : angle 1.00384 ( 36) covalent geometry : bond 0.00315 (17196) covalent geometry : angle 0.67042 (23304) Misc. bond : bond 0.00265 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 314 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6567 (ptp) cc_final: 0.6122 (ptt) REVERT: A 36 GLN cc_start: 0.8999 (tp40) cc_final: 0.8637 (tp-100) REVERT: A 72 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8773 (t) REVERT: A 151 MET cc_start: 0.7924 (mmm) cc_final: 0.7665 (mmm) REVERT: A 166 LYS cc_start: 0.8824 (tttt) cc_final: 0.8543 (tttm) REVERT: A 276 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6800 (pt0) REVERT: A 345 MET cc_start: 0.8789 (mmm) cc_final: 0.7564 (mmm) REVERT: D 25 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.4594 (p90) REVERT: D 70 ILE cc_start: 0.8224 (tt) cc_final: 0.8016 (tt) REVERT: H 94 ARG cc_start: 0.4031 (ttp-170) cc_final: 0.3332 (ttp-170) REVERT: L 47 MET cc_start: 0.7150 (mmt) cc_final: 0.6847 (mtt) REVERT: B 60 CYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9053 (t) REVERT: B 87 ASP cc_start: 0.8086 (t0) cc_final: 0.7668 (t0) REVERT: B 164 ARG cc_start: 0.8725 (mtm-85) cc_final: 0.8395 (mtm-85) REVERT: B 166 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8324 (ttmm) REVERT: B 197 ASP cc_start: 0.8266 (t0) cc_final: 0.7805 (t0) REVERT: B 238 ASN cc_start: 0.8180 (t0) cc_final: 0.7883 (t0) REVERT: B 283 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7834 (mtm110) REVERT: B 295 MET cc_start: 0.9111 (mtm) cc_final: 0.8748 (ptp) REVERT: B 336 ASP cc_start: 0.7028 (m-30) cc_final: 0.6699 (m-30) REVERT: B 382 PHE cc_start: 0.8862 (m-80) cc_final: 0.8349 (m-80) REVERT: B 460 MET cc_start: 0.8402 (mtp) cc_final: 0.7914 (mtm) REVERT: h 34 MET cc_start: 0.7472 (mmt) cc_final: 0.7132 (mmt) REVERT: h 77 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7077 (p) REVERT: l 47 MET cc_start: 0.8233 (mtm) cc_final: 0.7857 (ptp) REVERT: C 15 MET cc_start: 0.5303 (tpt) cc_final: 0.4688 (tpp) REVERT: C 40 THR cc_start: 0.8668 (m) cc_final: 0.8407 (p) REVERT: C 151 MET cc_start: 0.8530 (mmm) cc_final: 0.8048 (mtt) REVERT: C 164 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.6943 (mtm110) REVERT: C 175 ARG cc_start: 0.5604 (ptt-90) cc_final: 0.5045 (ptp90) REVERT: C 316 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7590 (mtmm) REVERT: C 329 GLU cc_start: 0.8598 (tt0) cc_final: 0.8283 (tt0) REVERT: C 374 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7048 (ppp) REVERT: C 395 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8361 (mtmm) REVERT: C 460 MET cc_start: 0.8771 (mtm) cc_final: 0.8332 (mtp) REVERT: C 473 MET cc_start: 0.7347 (tpp) cc_final: 0.6848 (tpt) outliers start: 84 outliers final: 52 residues processed: 370 average time/residue: 0.2674 time to fit residues: 151.5519 Evaluate side-chains 362 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 203 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 62 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 153 optimal weight: 40.0000 chunk 37 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.180439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120761 restraints weight = 20203.848| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.51 r_work: 0.3163 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17222 Z= 0.233 Angle : 0.761 22.635 23361 Z= 0.385 Chirality : 0.050 0.858 2641 Planarity : 0.005 0.090 2942 Dihedral : 8.704 89.901 2515 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.09 % Favored : 88.78 % Rotamer: Outliers : 5.45 % Allowed : 19.68 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2174 helix: 0.05 (0.25), residues: 456 sheet: 0.25 (0.21), residues: 663 loop : -2.39 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 400 HIS 0.014 0.001 HIS A 27 PHE 0.026 0.002 PHE E 37 TYR 0.014 0.002 TYR B 137 ARG 0.006 0.001 ARG B 420 Details of bonding type rmsd link_NAG-ASN : bond 0.01357 ( 1) link_NAG-ASN : angle 15.39623 ( 3) link_BETA1-4 : bond 0.00706 ( 4) link_BETA1-4 : angle 2.71204 ( 12) hydrogen bonds : bond 0.05097 ( 706) hydrogen bonds : angle 5.41091 ( 1968) link_BETA1-6 : bond 0.01735 ( 2) link_BETA1-6 : angle 1.32886 ( 6) SS BOND : bond 0.00420 ( 18) SS BOND : angle 1.03280 ( 36) covalent geometry : bond 0.00547 (17196) covalent geometry : angle 0.73734 (23304) Misc. bond : bond 0.00802 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 324 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6587 (ptp) cc_final: 0.6231 (ptt) REVERT: A 52 ASN cc_start: 0.7825 (p0) cc_final: 0.7556 (p0) REVERT: A 57 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8209 (tpp80) REVERT: A 72 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8780 (t) REVERT: A 151 MET cc_start: 0.7978 (mmm) cc_final: 0.7688 (mmm) REVERT: A 276 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6867 (pt0) REVERT: A 316 LYS cc_start: 0.3849 (tttt) cc_final: 0.3363 (tttp) REVERT: A 345 MET cc_start: 0.8898 (mmm) cc_final: 0.8071 (mmm) REVERT: A 481 ASN cc_start: 0.6373 (t0) cc_final: 0.6166 (t0) REVERT: D 25 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.4799 (p90) REVERT: D 70 ILE cc_start: 0.8284 (tt) cc_final: 0.8078 (tt) REVERT: H 94 ARG cc_start: 0.4065 (ttp-170) cc_final: 0.3360 (ttp-170) REVERT: L 47 MET cc_start: 0.7081 (mmt) cc_final: 0.6612 (mtt) REVERT: B 13 GLU cc_start: 0.8613 (tt0) cc_final: 0.7623 (pt0) REVERT: B 26 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8801 (mt-10) REVERT: B 87 ASP cc_start: 0.8121 (t0) cc_final: 0.7708 (t0) REVERT: B 164 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8402 (mtm-85) REVERT: B 166 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8221 (ttmm) REVERT: B 168 GLU cc_start: 0.8664 (mt-10) cc_final: 0.7635 (mt-10) REVERT: B 197 ASP cc_start: 0.8359 (t0) cc_final: 0.7879 (t0) REVERT: B 283 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7683 (mtm110) REVERT: B 295 MET cc_start: 0.9205 (mtm) cc_final: 0.8827 (ptp) REVERT: B 336 ASP cc_start: 0.7051 (m-30) cc_final: 0.6721 (m-30) REVERT: B 382 PHE cc_start: 0.8882 (m-80) cc_final: 0.8438 (m-80) REVERT: B 460 MET cc_start: 0.8604 (mtp) cc_final: 0.8244 (mtp) REVERT: B 487 MET cc_start: 0.6887 (mmt) cc_final: 0.6655 (mmp) REVERT: h 34 MET cc_start: 0.7565 (mmt) cc_final: 0.7271 (mmt) REVERT: h 77 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.7029 (p) REVERT: l 47 MET cc_start: 0.8208 (mtm) cc_final: 0.7767 (ptp) REVERT: C 15 MET cc_start: 0.5312 (tpt) cc_final: 0.4671 (tpp) REVERT: C 151 MET cc_start: 0.8424 (mmm) cc_final: 0.8007 (mtt) REVERT: C 164 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7146 (mtm110) REVERT: C 175 ARG cc_start: 0.5538 (ptt-90) cc_final: 0.5180 (ptt-90) REVERT: C 177 GLU cc_start: 0.8416 (pt0) cc_final: 0.7954 (tt0) REVERT: C 316 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7649 (mtmm) REVERT: C 329 GLU cc_start: 0.8538 (tt0) cc_final: 0.8239 (tt0) REVERT: C 374 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7064 (ppp) REVERT: C 384 ASP cc_start: 0.7881 (m-30) cc_final: 0.7666 (t0) REVERT: C 385 SER cc_start: 0.8727 (t) cc_final: 0.8456 (t) REVERT: C 395 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8345 (mtmm) REVERT: C 460 MET cc_start: 0.8843 (mtm) cc_final: 0.8353 (mtp) outliers start: 98 outliers final: 75 residues processed: 390 average time/residue: 0.2604 time to fit residues: 156.9209 Evaluate side-chains 392 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 312 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 69 optimal weight: 0.4980 chunk 152 optimal weight: 0.0770 chunk 33 optimal weight: 0.4980 chunk 206 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 155 optimal weight: 50.0000 chunk 58 optimal weight: 40.0000 chunk 212 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.188064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126952 restraints weight = 20084.636| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.26 r_work: 0.3273 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17222 Z= 0.120 Angle : 0.672 25.996 23361 Z= 0.338 Chirality : 0.045 0.583 2641 Planarity : 0.005 0.083 2942 Dihedral : 8.175 86.341 2514 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.11 % Favored : 90.75 % Rotamer: Outliers : 3.17 % Allowed : 21.96 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2174 helix: 0.33 (0.25), residues: 465 sheet: 0.54 (0.21), residues: 628 loop : -2.42 (0.17), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 400 HIS 0.009 0.001 HIS A 27 PHE 0.022 0.002 PHE E 37 TYR 0.011 0.001 TYR C 61 ARG 0.006 0.000 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01970 ( 1) link_NAG-ASN : angle 17.75806 ( 3) link_BETA1-4 : bond 0.00770 ( 4) link_BETA1-4 : angle 2.84023 ( 12) hydrogen bonds : bond 0.04052 ( 706) hydrogen bonds : angle 5.10496 ( 1968) link_BETA1-6 : bond 0.01606 ( 2) link_BETA1-6 : angle 1.37400 ( 6) SS BOND : bond 0.00236 ( 18) SS BOND : angle 0.93878 ( 36) covalent geometry : bond 0.00248 (17196) covalent geometry : angle 0.63720 (23304) Misc. bond : bond 0.00237 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 329 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.9040 (tp40) cc_final: 0.8759 (tp-100) REVERT: A 57 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7548 (mtp-110) REVERT: A 151 MET cc_start: 0.7899 (mmm) cc_final: 0.7653 (mmm) REVERT: A 276 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7087 (pt0) REVERT: A 316 LYS cc_start: 0.4068 (tttt) cc_final: 0.3505 (tttp) REVERT: A 345 MET cc_start: 0.8773 (mmm) cc_final: 0.7497 (mmm) REVERT: A 466 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6826 (mm) REVERT: D 25 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.4704 (p90) REVERT: H 34 MET cc_start: 0.8075 (mmm) cc_final: 0.7685 (mmm) REVERT: L 47 MET cc_start: 0.7113 (mmt) cc_final: 0.6821 (mtt) REVERT: B 13 GLU cc_start: 0.8522 (tt0) cc_final: 0.7541 (pt0) REVERT: B 57 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7442 (ttm170) REVERT: B 87 ASP cc_start: 0.8068 (t0) cc_final: 0.7603 (t0) REVERT: B 89 GLN cc_start: 0.7472 (mt0) cc_final: 0.7031 (tt0) REVERT: B 164 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8255 (mtm-85) REVERT: B 166 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8320 (ttmm) REVERT: B 168 GLU cc_start: 0.8664 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 197 ASP cc_start: 0.8297 (t0) cc_final: 0.7904 (t0) REVERT: B 238 ASN cc_start: 0.8211 (t0) cc_final: 0.7907 (t0) REVERT: B 283 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7844 (mtm110) REVERT: B 295 MET cc_start: 0.9094 (mtm) cc_final: 0.8714 (ptp) REVERT: B 336 ASP cc_start: 0.6944 (m-30) cc_final: 0.6638 (m-30) REVERT: B 382 PHE cc_start: 0.8725 (m-80) cc_final: 0.8226 (m-80) REVERT: B 426 ASP cc_start: 0.8514 (p0) cc_final: 0.8217 (p0) REVERT: B 460 MET cc_start: 0.8313 (mtp) cc_final: 0.7916 (mtm) REVERT: E 52 LEU cc_start: 0.8463 (mp) cc_final: 0.8035 (tt) REVERT: h 34 MET cc_start: 0.7617 (mmt) cc_final: 0.7372 (mmt) REVERT: l 47 MET cc_start: 0.8185 (mtm) cc_final: 0.7739 (ptp) REVERT: C 15 MET cc_start: 0.5515 (tpt) cc_final: 0.4974 (tpp) REVERT: C 151 MET cc_start: 0.8348 (mmm) cc_final: 0.7936 (mtt) REVERT: C 164 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6894 (mtm110) REVERT: C 175 ARG cc_start: 0.5640 (ptt-90) cc_final: 0.5095 (ptp90) REVERT: C 177 GLU cc_start: 0.8471 (pt0) cc_final: 0.8066 (tt0) REVERT: C 316 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7553 (mtmm) REVERT: C 329 GLU cc_start: 0.8534 (tt0) cc_final: 0.8244 (tt0) REVERT: C 374 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7129 (ppp) REVERT: C 395 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8391 (mtmm) REVERT: C 473 MET cc_start: 0.7222 (tpp) cc_final: 0.6727 (tpt) REVERT: F 8 SER cc_start: 0.8880 (p) cc_final: 0.8622 (t) outliers start: 57 outliers final: 43 residues processed: 367 average time/residue: 0.2640 time to fit residues: 147.4943 Evaluate side-chains 359 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 312 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 177 optimal weight: 0.0470 chunk 107 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 168 optimal weight: 0.0970 chunk 83 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 overall best weight: 3.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.184654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122869 restraints weight = 20319.922| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.26 r_work: 0.3234 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17222 Z= 0.165 Angle : 0.700 25.010 23361 Z= 0.350 Chirality : 0.046 0.627 2641 Planarity : 0.005 0.082 2942 Dihedral : 7.905 84.698 2512 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.07 % Favored : 89.79 % Rotamer: Outliers : 3.28 % Allowed : 22.51 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 2174 helix: 0.32 (0.25), residues: 465 sheet: 0.59 (0.21), residues: 631 loop : -2.43 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 400 HIS 0.013 0.001 HIS A 27 PHE 0.016 0.001 PHE F 42 TYR 0.016 0.001 TYR h 100N ARG 0.007 0.000 ARG B 420 Details of bonding type rmsd link_NAG-ASN : bond 0.01398 ( 1) link_NAG-ASN : angle 17.33007 ( 3) link_BETA1-4 : bond 0.00659 ( 4) link_BETA1-4 : angle 2.87806 ( 12) hydrogen bonds : bond 0.04363 ( 706) hydrogen bonds : angle 5.08825 ( 1968) link_BETA1-6 : bond 0.01520 ( 2) link_BETA1-6 : angle 1.29601 ( 6) SS BOND : bond 0.00312 ( 18) SS BOND : angle 0.89879 ( 36) covalent geometry : bond 0.00378 (17196) covalent geometry : angle 0.66821 (23304) Misc. bond : bond 0.00363 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 312 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.9168 (tp40) cc_final: 0.8599 (tp-100) REVERT: A 151 MET cc_start: 0.7969 (mmm) cc_final: 0.7751 (mmm) REVERT: A 276 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7109 (pt0) REVERT: A 316 LYS cc_start: 0.3974 (tttt) cc_final: 0.3338 (tttp) REVERT: A 336 ASP cc_start: 0.8276 (m-30) cc_final: 0.7985 (m-30) REVERT: A 345 MET cc_start: 0.8812 (mmm) cc_final: 0.7439 (mmm) REVERT: D 25 TYR cc_start: 0.6013 (OUTLIER) cc_final: 0.4862 (p90) REVERT: B 13 GLU cc_start: 0.8519 (tt0) cc_final: 0.7523 (pt0) REVERT: B 57 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7468 (ttm170) REVERT: B 87 ASP cc_start: 0.8137 (t0) cc_final: 0.7681 (t0) REVERT: B 89 GLN cc_start: 0.7500 (mt0) cc_final: 0.7063 (tt0) REVERT: B 164 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8353 (mtm-85) REVERT: B 166 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8265 (ttmm) REVERT: B 168 GLU cc_start: 0.8671 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 197 ASP cc_start: 0.8330 (t0) cc_final: 0.7957 (t0) REVERT: B 283 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7803 (mtm110) REVERT: B 295 MET cc_start: 0.9156 (mtm) cc_final: 0.8713 (ptp) REVERT: B 336 ASP cc_start: 0.7013 (m-30) cc_final: 0.6693 (m-30) REVERT: B 382 PHE cc_start: 0.8778 (m-80) cc_final: 0.8243 (m-80) REVERT: B 460 MET cc_start: 0.8502 (mtp) cc_final: 0.8103 (mtp) REVERT: E 52 LEU cc_start: 0.8573 (mp) cc_final: 0.8094 (tt) REVERT: h 77 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.7049 (p) REVERT: l 47 MET cc_start: 0.8151 (mtm) cc_final: 0.7906 (ptp) REVERT: C 15 MET cc_start: 0.5407 (tpt) cc_final: 0.4916 (tpp) REVERT: C 151 MET cc_start: 0.8375 (mmm) cc_final: 0.7952 (mtt) REVERT: C 164 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.6933 (mtm110) REVERT: C 175 ARG cc_start: 0.5376 (ptt-90) cc_final: 0.5097 (ptt-90) REVERT: C 177 GLU cc_start: 0.8502 (pt0) cc_final: 0.8114 (tt0) REVERT: C 316 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7528 (mtmm) REVERT: C 374 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7202 (ppp) REVERT: C 395 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8408 (mtmm) REVERT: F 8 SER cc_start: 0.8894 (p) cc_final: 0.8615 (t) outliers start: 59 outliers final: 48 residues processed: 355 average time/residue: 0.3672 time to fit residues: 206.2079 Evaluate side-chains 357 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 103 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.189708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127844 restraints weight = 20211.236| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.30 r_work: 0.3272 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17222 Z= 0.123 Angle : 0.671 24.703 23361 Z= 0.335 Chirality : 0.046 0.645 2641 Planarity : 0.004 0.079 2942 Dihedral : 7.654 81.923 2512 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.25 % Favored : 90.62 % Rotamer: Outliers : 3.06 % Allowed : 22.96 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2174 helix: 0.53 (0.26), residues: 465 sheet: 0.62 (0.21), residues: 624 loop : -2.42 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 400 HIS 0.008 0.001 HIS A 27 PHE 0.019 0.001 PHE F 42 TYR 0.015 0.001 TYR h 100N ARG 0.007 0.000 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.01582 ( 1) link_NAG-ASN : angle 17.07732 ( 3) link_BETA1-4 : bond 0.00544 ( 4) link_BETA1-4 : angle 2.91473 ( 12) hydrogen bonds : bond 0.04001 ( 706) hydrogen bonds : angle 4.95004 ( 1968) link_BETA1-6 : bond 0.01338 ( 2) link_BETA1-6 : angle 1.17734 ( 6) SS BOND : bond 0.00211 ( 18) SS BOND : angle 0.85597 ( 36) covalent geometry : bond 0.00264 (17196) covalent geometry : angle 0.63866 (23304) Misc. bond : bond 0.00182 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 314 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.9143 (tp40) cc_final: 0.8562 (tp-100) REVERT: A 166 LYS cc_start: 0.8795 (tptt) cc_final: 0.8263 (tptp) REVERT: A 276 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7097 (pt0) REVERT: A 316 LYS cc_start: 0.3831 (tttt) cc_final: 0.3257 (tttp) REVERT: A 336 ASP cc_start: 0.8265 (m-30) cc_final: 0.7973 (m-30) REVERT: A 345 MET cc_start: 0.8725 (mmm) cc_final: 0.7304 (mmm) REVERT: D 25 TYR cc_start: 0.5808 (OUTLIER) cc_final: 0.4760 (p90) REVERT: H 34 MET cc_start: 0.7860 (mmm) cc_final: 0.7510 (mmm) REVERT: H 94 ARG cc_start: 0.4161 (ttp-170) cc_final: 0.3481 (ttp-170) REVERT: L 47 MET cc_start: 0.6958 (mmt) cc_final: 0.6597 (mtt) REVERT: L 95 ARG cc_start: 0.1855 (OUTLIER) cc_final: 0.1072 (mtm-85) REVERT: B 13 GLU cc_start: 0.8584 (tt0) cc_final: 0.7521 (pt0) REVERT: B 57 ARG cc_start: 0.7791 (ttm170) cc_final: 0.7441 (ttm170) REVERT: B 77 GLN cc_start: 0.6756 (mm-40) cc_final: 0.6368 (tt0) REVERT: B 87 ASP cc_start: 0.8069 (t0) cc_final: 0.7648 (t0) REVERT: B 89 GLN cc_start: 0.7457 (mt0) cc_final: 0.7036 (tt0) REVERT: B 143 VAL cc_start: 0.8843 (t) cc_final: 0.8569 (t) REVERT: B 152 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7451 (pt) REVERT: B 164 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8248 (mtm-85) REVERT: B 166 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8275 (ttmm) REVERT: B 168 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7656 (mt-10) REVERT: B 197 ASP cc_start: 0.8364 (t0) cc_final: 0.7977 (t0) REVERT: B 238 ASN cc_start: 0.8238 (t0) cc_final: 0.7926 (t0) REVERT: B 283 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7810 (mtm110) REVERT: B 295 MET cc_start: 0.9073 (mtm) cc_final: 0.8826 (ptp) REVERT: B 336 ASP cc_start: 0.6887 (m-30) cc_final: 0.6584 (m-30) REVERT: B 382 PHE cc_start: 0.8685 (m-80) cc_final: 0.8133 (m-80) REVERT: B 460 MET cc_start: 0.8343 (mtp) cc_final: 0.7933 (mtm) REVERT: E 52 LEU cc_start: 0.8503 (mp) cc_final: 0.8089 (tt) REVERT: h 77 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.7015 (p) REVERT: l 47 MET cc_start: 0.8126 (mtm) cc_final: 0.7887 (ptp) REVERT: C 15 MET cc_start: 0.5480 (tpt) cc_final: 0.5144 (tpp) REVERT: C 151 MET cc_start: 0.8328 (mmm) cc_final: 0.7894 (mtt) REVERT: C 164 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6840 (mtm110) REVERT: C 175 ARG cc_start: 0.5264 (ptt-90) cc_final: 0.4233 (ptp90) REVERT: C 177 GLU cc_start: 0.8641 (pt0) cc_final: 0.8241 (tt0) REVERT: C 316 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7769 (mtmm) REVERT: C 329 GLU cc_start: 0.8486 (tt0) cc_final: 0.8104 (tt0) REVERT: C 374 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7183 (ppp) REVERT: C 377 GLU cc_start: 0.7409 (pt0) cc_final: 0.7048 (pt0) REVERT: C 395 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8350 (mtmm) REVERT: C 473 MET cc_start: 0.7226 (tpp) cc_final: 0.6951 (mmm) REVERT: F 8 SER cc_start: 0.8902 (p) cc_final: 0.8665 (t) outliers start: 55 outliers final: 44 residues processed: 351 average time/residue: 0.2622 time to fit residues: 140.8086 Evaluate side-chains 361 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 311 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 9 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 40.0000 chunk 61 optimal weight: 50.0000 chunk 76 optimal weight: 40.0000 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 199 optimal weight: 8.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.181564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121213 restraints weight = 20292.337| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.53 r_work: 0.3182 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17222 Z= 0.245 Angle : 0.754 24.745 23361 Z= 0.380 Chirality : 0.049 0.652 2641 Planarity : 0.005 0.079 2942 Dihedral : 7.658 80.949 2512 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.63 % Favored : 89.24 % Rotamer: Outliers : 3.45 % Allowed : 22.73 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2174 helix: 0.24 (0.25), residues: 465 sheet: 0.33 (0.21), residues: 668 loop : -2.40 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 400 HIS 0.016 0.001 HIS A 27 PHE 0.014 0.002 PHE A 382 TYR 0.018 0.002 TYR E 25 ARG 0.011 0.001 ARG B 420 Details of bonding type rmsd link_NAG-ASN : bond 0.01432 ( 1) link_NAG-ASN : angle 17.08218 ( 3) link_BETA1-4 : bond 0.00441 ( 4) link_BETA1-4 : angle 2.90962 ( 12) hydrogen bonds : bond 0.04883 ( 706) hydrogen bonds : angle 5.17725 ( 1968) link_BETA1-6 : bond 0.01297 ( 2) link_BETA1-6 : angle 1.38142 ( 6) SS BOND : bond 0.00421 ( 18) SS BOND : angle 1.00212 ( 36) covalent geometry : bond 0.00578 (17196) covalent geometry : angle 0.72546 (23304) Misc. bond : bond 0.00524 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8811.97 seconds wall clock time: 153 minutes 30.17 seconds (9210.17 seconds total)