Starting phenix.real_space_refine on Wed Mar 4 22:18:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cxi_27058/03_2026/8cxi_27058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cxi_27058/03_2026/8cxi_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cxi_27058/03_2026/8cxi_27058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cxi_27058/03_2026/8cxi_27058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cxi_27058/03_2026/8cxi_27058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cxi_27058/03_2026/8cxi_27058.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.78, per 1000 atoms: 0.22 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: 1.28 Conformation dependent library (CDL) restraints added in 650.9 milliseconds 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: 0.76 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: 3.85 Time building geometry restraints manager: 1.69 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.950 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.011 0.001 ARG C 73 TYR 0.020 0.002 TYR A 61 PHE 0.016 0.002 PHE A 431 TRP 0.017 0.002 TRP B 400 HIS 0.006 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00802 (17196) covalent geometry : angle 0.96936 (23304) SS BOND : bond 0.44207 ( 18) SS BOND : angle 15.58891 ( 36) hydrogen bonds : bond 0.13754 ( 706) hydrogen bonds : angle 7.44257 ( 1968) Misc. bond : bond 0.11072 ( 1) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 6.01168 ( 12) link_BETA1-6 : bond 0.03696 ( 2) link_BETA1-6 : angle 2.29616 ( 6) link_NAG-ASN : bond 0.15690 ( 1) link_NAG-ASN : angle 31.98488 ( 3) *********************** 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 : 0.436 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: 0.6521 (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: 0.1289 time to fit residues: 94.5301 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 : 0.610 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 A 465 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 85 GLN B 134 ASN B 163 ASN 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 446 HIS ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 HIS C 154 ASN C 261 GLN C 350 GLN F 7 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.186234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124965 restraints weight = 20043.239| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.15 r_work: 0.3240 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17222 Z= 0.199 Angle : 0.835 24.703 23361 Z= 0.418 Chirality : 0.053 1.100 2641 Planarity : 0.006 0.148 2942 Dihedral : 11.477 110.271 2548 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.80 % Favored : 90.06 % Rotamer: Outliers : 4.22 % Allowed : 15.12 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2174 helix: -0.04 (0.25), residues: 429 sheet: -0.13 (0.19), residues: 718 loop : -2.74 (0.16), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 99 TYR 0.016 0.002 TYR D 25 PHE 0.038 0.002 PHE A 314 TRP 0.025 0.002 TRP H 36 HIS 0.017 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00445 (17196) covalent geometry : angle 0.80809 (23304) SS BOND : bond 0.00601 ( 18) SS BOND : angle 1.18875 ( 36) hydrogen bonds : bond 0.05380 ( 706) hydrogen bonds : angle 6.10441 ( 1968) Misc. bond : bond 0.01161 ( 1) link_BETA1-4 : bond 0.00601 ( 4) link_BETA1-4 : angle 2.27594 ( 12) link_BETA1-6 : bond 0.00760 ( 2) link_BETA1-6 : angle 2.98293 ( 6) link_NAG-ASN : bond 0.01011 ( 1) link_NAG-ASN : angle 17.36524 ( 3) *********************** 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 427 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 351 time to evaluate : 0.565 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 66 SER cc_start: 0.8575 (t) cc_final: 0.8223 (m) REVERT: A 67 ASP cc_start: 0.8767 (p0) cc_final: 0.8562 (p0) REVERT: A 72 SER cc_start: 0.8820 (p) cc_final: 0.8374 (t) REVERT: A 90 TYR cc_start: 0.8759 (m-80) cc_final: 0.8499 (m-80) REVERT: A 121 CYS cc_start: 0.8863 (p) cc_final: 0.8291 (t) REVERT: A 151 MET cc_start: 0.8043 (mmm) cc_final: 0.7509 (mmm) REVERT: A 221 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 276 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6585 (pt0) REVERT: A 294 LYS cc_start: 0.8482 (mttt) cc_final: 0.8235 (mttt) REVERT: A 382 PHE cc_start: 0.8640 (m-80) cc_final: 0.8207 (m-80) REVERT: D 70 ILE cc_start: 0.8208 (tt) cc_final: 0.7988 (tt) REVERT: H 32 HIS cc_start: 0.7158 (m90) cc_final: 0.5471 (m90) REVERT: H 34 MET cc_start: 0.7995 (mmm) cc_final: 0.7744 (mmm) REVERT: H 94 ARG cc_start: 0.4021 (ttp-170) cc_final: 0.3342 (ttp-170) REVERT: B 26 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8618 (mt-10) REVERT: B 70 SER cc_start: 0.8920 (p) cc_final: 0.8547 (t) REVERT: B 87 ASP cc_start: 0.8034 (t0) cc_final: 0.7711 (t0) REVERT: B 140 MET cc_start: 0.8056 (mmt) cc_final: 0.7760 (mmm) REVERT: B 148 HIS cc_start: 0.7528 (t-90) cc_final: 0.7286 (t-90) REVERT: B 193 ARG cc_start: 0.9192 (mtt-85) cc_final: 0.8974 (mtt-85) REVERT: B 197 ASP cc_start: 0.8024 (t0) cc_final: 0.7713 (t0) REVERT: B 254 THR cc_start: 0.7031 (OUTLIER) cc_final: 0.6771 (p) REVERT: B 294 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7345 (mttt) REVERT: B 430 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7789 (t0) REVERT: l 47 MET cc_start: 0.8105 (mtm) cc_final: 0.7760 (ptp) REVERT: C 87 ASP cc_start: 0.8560 (t0) cc_final: 0.8031 (t0) REVERT: C 151 MET cc_start: 0.8589 (mmm) cc_final: 0.8292 (mtt) REVERT: C 164 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.7063 (mtm110) REVERT: C 344 GLN cc_start: 0.7744 (pt0) cc_final: 0.7429 (pt0) REVERT: C 460 MET cc_start: 0.8897 (mtm) cc_final: 0.8527 (mtp) REVERT: C 473 MET cc_start: 0.7390 (tpp) cc_final: 0.7162 (mmm) REVERT: C 499 SER cc_start: 0.8551 (m) cc_final: 0.8314 (t) REVERT: F 8 SER cc_start: 0.8866 (p) cc_final: 0.8403 (t) outliers start: 76 outliers final: 50 residues processed: 407 average time/residue: 0.1128 time to fit residues: 71.9402 Evaluate side-chains 375 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 122 SER 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 265 VAL 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 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 16 SER 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 C residue 56 VAL 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 266 HIS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 478 ASN 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 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 29 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN A 371 ASN ** 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** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 35 HIS ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.183057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124073 restraints weight = 20270.218| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.29 r_work: 0.3205 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17222 Z= 0.205 Angle : 0.773 24.252 23361 Z= 0.391 Chirality : 0.050 0.952 2641 Planarity : 0.005 0.103 2942 Dihedral : 10.579 96.656 2528 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.76 % Favored : 89.14 % Rotamer: Outliers : 5.34 % Allowed : 16.45 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2174 helix: 0.25 (0.26), residues: 429 sheet: 0.05 (0.20), residues: 694 loop : -2.52 (0.16), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 283 TYR 0.015 0.002 TYR h 29 PHE 0.019 0.002 PHE A 382 TRP 0.014 0.002 TRP B 400 HIS 0.009 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00474 (17196) covalent geometry : angle 0.74486 (23304) SS BOND : bond 0.00334 ( 18) SS BOND : angle 1.32848 ( 36) hydrogen bonds : bond 0.05134 ( 706) hydrogen bonds : angle 5.76033 ( 1968) Misc. bond : bond 0.01002 ( 1) link_BETA1-4 : bond 0.01018 ( 4) link_BETA1-4 : angle 2.44216 ( 12) link_BETA1-6 : bond 0.01085 ( 2) link_BETA1-6 : angle 2.98606 ( 6) link_NAG-ASN : bond 0.01379 ( 1) link_NAG-ASN : angle 16.72504 ( 3) *********************** 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 446 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 350 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.9029 (tp40) cc_final: 0.8770 (tp-100) REVERT: A 66 SER cc_start: 0.8572 (t) cc_final: 0.8323 (m) REVERT: A 72 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8554 (t) REVERT: A 121 CYS cc_start: 0.8765 (p) cc_final: 0.8550 (t) REVERT: A 151 MET cc_start: 0.7991 (mmm) cc_final: 0.7568 (mmm) REVERT: A 177 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7897 (tt0) REVERT: A 221 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7985 (mt) REVERT: A 345 MET cc_start: 0.8641 (mmm) cc_final: 0.7737 (mmm) REVERT: A 379 ASP cc_start: 0.8488 (t0) cc_final: 0.8237 (t0) REVERT: D 70 ILE cc_start: 0.8232 (tt) cc_final: 0.8025 (tt) REVERT: H 32 HIS cc_start: 0.7049 (m90) cc_final: 0.5508 (m90) REVERT: H 34 MET cc_start: 0.7982 (mmm) cc_final: 0.7668 (mmm) REVERT: H 94 ARG cc_start: 0.3901 (ttp-170) cc_final: 0.3255 (ttp-170) REVERT: L 47 MET cc_start: 0.7219 (mmt) cc_final: 0.6843 (mtt) REVERT: B 13 GLU cc_start: 0.8329 (tt0) cc_final: 0.7699 (pt0) REVERT: B 70 SER cc_start: 0.8905 (p) cc_final: 0.8582 (t) REVERT: B 164 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8447 (mtm-85) REVERT: B 193 ARG cc_start: 0.9174 (mtt-85) cc_final: 0.8964 (mtt-85) REVERT: B 197 ASP cc_start: 0.8079 (t0) cc_final: 0.7647 (t0) REVERT: B 283 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7812 (mtm110) REVERT: B 382 PHE cc_start: 0.8823 (m-80) cc_final: 0.8273 (m-80) REVERT: B 430 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7692 (t0) REVERT: B 460 MET cc_start: 0.8482 (mtp) cc_final: 0.8071 (mtp) REVERT: h 34 MET cc_start: 0.7342 (mmt) cc_final: 0.6991 (mmt) REVERT: l 47 MET cc_start: 0.8220 (mtm) cc_final: 0.7912 (ptp) REVERT: C 87 ASP cc_start: 0.8589 (t0) cc_final: 0.8070 (m-30) REVERT: C 151 MET cc_start: 0.8583 (mmm) cc_final: 0.8090 (mtt) REVERT: C 164 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.7041 (mtm110) REVERT: C 177 GLU cc_start: 0.8397 (pt0) cc_final: 0.8040 (tt0) REVERT: C 242 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8405 (mp) REVERT: C 344 GLN cc_start: 0.7640 (pt0) cc_final: 0.7404 (pt0) REVERT: C 499 SER cc_start: 0.8492 (m) cc_final: 0.8266 (t) REVERT: F 8 SER cc_start: 0.8958 (p) cc_final: 0.8523 (t) outliers start: 96 outliers final: 51 residues processed: 416 average time/residue: 0.1117 time to fit residues: 72.9819 Evaluate side-chains 378 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 323 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 ILE 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 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 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 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 h residue 100 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 479 THR 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 44 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 137 optimal weight: 40.0000 chunk 143 optimal weight: 30.0000 chunk 201 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 0.0970 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 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** E 7 HIS ** C 103 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 = 0.4050 r_free = 0.4050 target = 0.186549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127259 restraints weight = 20282.926| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.55 r_work: 0.3230 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17222 Z= 0.154 Angle : 0.717 23.346 23361 Z= 0.361 Chirality : 0.048 0.896 2641 Planarity : 0.005 0.091 2942 Dihedral : 9.945 95.716 2522 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.12 % Favored : 89.79 % Rotamer: Outliers : 5.34 % Allowed : 16.73 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 2174 helix: 0.28 (0.25), residues: 453 sheet: 0.25 (0.20), residues: 679 loop : -2.45 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.013 0.001 TYR h 29 PHE 0.021 0.001 PHE A 382 TRP 0.011 0.001 TRP B 400 HIS 0.009 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00347 (17196) covalent geometry : angle 0.68877 (23304) SS BOND : bond 0.00215 ( 18) SS BOND : angle 1.11039 ( 36) hydrogen bonds : bond 0.04630 ( 706) hydrogen bonds : angle 5.51453 ( 1968) Misc. bond : bond 0.00087 ( 1) link_BETA1-4 : bond 0.00836 ( 4) link_BETA1-4 : angle 2.54497 ( 12) link_BETA1-6 : bond 0.01325 ( 2) link_BETA1-6 : angle 2.67391 ( 6) link_NAG-ASN : bond 0.01435 ( 1) link_NAG-ASN : angle 16.10490 ( 3) *********************** 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 421 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 325 time to evaluate : 0.577 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: 0.9024 (tp40) cc_final: 0.8749 (tp-100) REVERT: A 72 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8527 (t) REVERT: A 151 MET cc_start: 0.7908 (mmm) cc_final: 0.7532 (mmm) REVERT: A 221 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7926 (mt) REVERT: A 276 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6746 (pt0) REVERT: A 345 MET cc_start: 0.8673 (mmm) cc_final: 0.7734 (mmm) REVERT: A 379 ASP cc_start: 0.8448 (t0) cc_final: 0.8196 (t0) REVERT: A 382 PHE cc_start: 0.8579 (m-80) cc_final: 0.8250 (m-10) REVERT: D 25 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.4475 (p90) REVERT: H 32 HIS cc_start: 0.6939 (m90) cc_final: 0.5538 (m90) REVERT: H 94 ARG cc_start: 0.4143 (ttp-170) cc_final: 0.3431 (ttp-170) REVERT: L 47 MET cc_start: 0.7089 (mmt) cc_final: 0.6778 (mtt) REVERT: B 13 GLU cc_start: 0.8645 (tt0) cc_final: 0.7717 (pt0) REVERT: B 57 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7684 (ttm170) REVERT: B 87 ASP cc_start: 0.7917 (t0) cc_final: 0.7624 (t0) REVERT: B 168 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 193 ARG cc_start: 0.9125 (mtt-85) cc_final: 0.8916 (mtt-85) REVERT: B 197 ASP cc_start: 0.8083 (t0) cc_final: 0.7693 (t0) REVERT: B 238 ASN cc_start: 0.8157 (t0) cc_final: 0.7835 (t0) REVERT: B 283 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7860 (mtm110) REVERT: B 320 GLU cc_start: 0.7942 (tt0) cc_final: 0.7740 (tt0) REVERT: B 382 PHE cc_start: 0.8809 (m-80) cc_final: 0.8239 (m-80) REVERT: B 460 MET cc_start: 0.8468 (mtp) cc_final: 0.8029 (mtp) REVERT: B 487 MET cc_start: 0.6740 (mmt) cc_final: 0.6520 (mmp) REVERT: h 34 MET cc_start: 0.7387 (mmt) cc_final: 0.7028 (mmt) REVERT: h 77 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7117 (p) REVERT: l 47 MET cc_start: 0.8173 (mtm) cc_final: 0.7814 (ptp) REVERT: C 26 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8748 (mt-10) REVERT: C 40 THR cc_start: 0.8640 (m) cc_final: 0.8390 (p) REVERT: C 87 ASP cc_start: 0.8513 (t0) cc_final: 0.8033 (m-30) REVERT: C 164 ARG cc_start: 0.7265 (mtm-85) cc_final: 0.6901 (mtm110) REVERT: C 177 GLU cc_start: 0.8426 (pt0) cc_final: 0.8122 (pm20) REVERT: C 374 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6860 (ppp) REVERT: C 375 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.9039 (ttm) REVERT: C 473 MET cc_start: 0.7338 (tpp) cc_final: 0.6827 (tpt) REVERT: F 8 SER cc_start: 0.8908 (p) cc_final: 0.8498 (t) REVERT: F 16 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8961 (p) outliers start: 96 outliers final: 55 residues processed: 389 average time/residue: 0.1095 time to fit residues: 66.9281 Evaluate side-chains 372 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 49 THR 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 141 LEU 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 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 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 126 THR 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 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 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 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 h residue 77 THR Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 56 VAL 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 213 VAL 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 359 ILE Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 14 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 135 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** 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** C 103 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 = 0.4034 r_free = 0.4034 target = 0.184924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125811 restraints weight = 20273.970| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.49 r_work: 0.3229 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17222 Z= 0.159 Angle : 0.705 22.984 23361 Z= 0.353 Chirality : 0.048 0.894 2641 Planarity : 0.004 0.083 2942 Dihedral : 9.116 94.512 2517 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.21 % Favored : 89.65 % Rotamer: Outliers : 5.50 % Allowed : 18.40 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.18), residues: 2174 helix: 0.35 (0.25), residues: 456 sheet: 0.45 (0.21), residues: 652 loop : -2.46 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 38 TYR 0.011 0.001 TYR h 29 PHE 0.024 0.002 PHE E 37 TRP 0.013 0.001 TRP B 400 HIS 0.008 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00362 (17196) covalent geometry : angle 0.67815 (23304) SS BOND : bond 0.00296 ( 18) SS BOND : angle 1.11575 ( 36) hydrogen bonds : bond 0.04548 ( 706) hydrogen bonds : angle 5.33513 ( 1968) Misc. bond : bond 0.00199 ( 1) link_BETA1-4 : bond 0.00853 ( 4) link_BETA1-4 : angle 2.58992 ( 12) link_BETA1-6 : bond 0.01849 ( 2) link_BETA1-6 : angle 2.04723 ( 6) link_NAG-ASN : bond 0.01591 ( 1) link_NAG-ASN : angle 15.66963 ( 3) *********************** 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 426 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 327 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6305 (ptp) cc_final: 0.5984 (ptt) REVERT: A 36 GLN cc_start: 0.9029 (tp40) cc_final: 0.8737 (tp-100) REVERT: A 72 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8552 (t) REVERT: A 151 MET cc_start: 0.7959 (mmm) cc_final: 0.7657 (mmm) REVERT: A 276 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6760 (pt0) REVERT: A 295 MET cc_start: 0.8807 (ptm) cc_final: 0.8309 (ptt) REVERT: A 345 MET cc_start: 0.8677 (mmm) cc_final: 0.7693 (mmm) REVERT: A 382 PHE cc_start: 0.8609 (m-80) cc_final: 0.8315 (m-10) REVERT: D 25 TYR cc_start: 0.6197 (OUTLIER) cc_final: 0.4587 (p90) REVERT: D 52 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7298 (mp) REVERT: H 94 ARG cc_start: 0.4222 (ttp-170) cc_final: 0.3504 (ttp-170) REVERT: L 47 MET cc_start: 0.7091 (mmt) cc_final: 0.6784 (mtt) REVERT: B 13 GLU cc_start: 0.8607 (tt0) cc_final: 0.7743 (pt0) REVERT: B 57 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7694 (ttm170) REVERT: B 60 CYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9081 (t) REVERT: B 87 ASP cc_start: 0.8004 (t0) cc_final: 0.7585 (t0) REVERT: B 89 GLN cc_start: 0.7470 (mt0) cc_final: 0.6744 (tt0) REVERT: B 164 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8402 (mtm-85) REVERT: B 168 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 197 ASP cc_start: 0.8258 (t0) cc_final: 0.7798 (t0) REVERT: B 238 ASN cc_start: 0.8165 (t0) cc_final: 0.7824 (t0) REVERT: B 283 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7876 (mtm110) REVERT: B 382 PHE cc_start: 0.8815 (m-80) cc_final: 0.8278 (m-80) REVERT: B 460 MET cc_start: 0.8478 (mtp) cc_final: 0.7918 (mtm) REVERT: B 487 MET cc_start: 0.6829 (mmt) cc_final: 0.6616 (mmp) REVERT: h 34 MET cc_start: 0.7491 (mmt) cc_final: 0.7069 (mmt) REVERT: h 77 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.7122 (p) REVERT: l 47 MET cc_start: 0.8196 (mtm) cc_final: 0.7819 (ptp) REVERT: C 26 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8762 (mt-10) REVERT: C 79 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7355 (mt-10) REVERT: C 87 ASP cc_start: 0.8568 (t0) cc_final: 0.8061 (m-30) REVERT: C 151 MET cc_start: 0.8586 (mmm) cc_final: 0.8240 (mtt) REVERT: C 164 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.6842 (mtm110) REVERT: C 177 GLU cc_start: 0.8482 (pt0) cc_final: 0.8052 (pm20) REVERT: C 395 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8320 (mtmm) REVERT: F 8 SER cc_start: 0.8945 (p) cc_final: 0.8558 (t) REVERT: F 16 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8984 (p) outliers start: 99 outliers final: 60 residues processed: 393 average time/residue: 0.1109 time to fit residues: 67.9005 Evaluate side-chains 382 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 315 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 49 THR 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 213 VAL 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 D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 52 LEU 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 60 CYS Chi-restraints excluded: chain B residue 97 VAL 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 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 448 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 25 TYR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain h residue 77 THR Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 56 VAL 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 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 389 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR 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 44 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 59 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 147 optimal weight: 30.0000 chunk 211 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 148 HIS ** 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 = 0.4015 r_free = 0.4015 target = 0.182801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123465 restraints weight = 20118.270| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.28 r_work: 0.3203 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17222 Z= 0.205 Angle : 0.729 22.569 23361 Z= 0.367 Chirality : 0.049 0.869 2641 Planarity : 0.005 0.079 2942 Dihedral : 8.799 92.311 2515 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.63 % Favored : 89.24 % Rotamer: Outliers : 5.39 % Allowed : 19.12 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2174 helix: 0.16 (0.25), residues: 462 sheet: 0.32 (0.21), residues: 661 loop : -2.41 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 193 TYR 0.013 0.002 TYR B 203 PHE 0.014 0.002 PHE A 382 TRP 0.015 0.001 TRP B 400 HIS 0.013 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00478 (17196) covalent geometry : angle 0.70428 (23304) SS BOND : bond 0.00379 ( 18) SS BOND : angle 1.16155 ( 36) hydrogen bonds : bond 0.04842 ( 706) hydrogen bonds : angle 5.33971 ( 1968) Misc. bond : bond 0.00674 ( 1) link_BETA1-4 : bond 0.00766 ( 4) link_BETA1-4 : angle 2.65911 ( 12) link_BETA1-6 : bond 0.01691 ( 2) link_BETA1-6 : angle 1.33525 ( 6) link_NAG-ASN : bond 0.01371 ( 1) link_NAG-ASN : angle 15.42327 ( 3) *********************** 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 412 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 315 time to evaluate : 0.534 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: 0.6460 (ptp) cc_final: 0.5983 (ptt) REVERT: A 36 GLN cc_start: 0.9059 (tp40) cc_final: 0.8742 (tp-100) REVERT: A 72 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8707 (t) REVERT: A 151 MET cc_start: 0.8026 (mmm) cc_final: 0.7771 (mmm) REVERT: A 166 LYS cc_start: 0.8785 (tttt) cc_final: 0.8502 (tttm) REVERT: A 276 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6751 (pt0) REVERT: A 345 MET cc_start: 0.8764 (mmm) cc_final: 0.7632 (mmm) REVERT: A 497 PHE cc_start: 0.6645 (m-80) cc_final: 0.6413 (m-80) REVERT: D 25 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.4898 (p90) REVERT: H 94 ARG cc_start: 0.4584 (ttp-170) cc_final: 0.3747 (ttp-170) REVERT: L 47 MET cc_start: 0.7130 (mmt) cc_final: 0.6811 (mtt) REVERT: B 13 GLU cc_start: 0.8638 (tt0) cc_final: 0.7778 (pt0) REVERT: B 57 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7621 (ttm170) REVERT: B 60 CYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9050 (t) REVERT: B 87 ASP cc_start: 0.8104 (t0) cc_final: 0.7677 (t0) REVERT: B 89 GLN cc_start: 0.7450 (mt0) cc_final: 0.6824 (tt0) REVERT: B 164 ARG cc_start: 0.8747 (mtm-85) cc_final: 0.8462 (mtm-85) REVERT: B 168 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7755 (mt-10) REVERT: B 197 ASP cc_start: 0.8216 (t0) cc_final: 0.7791 (t0) REVERT: B 276 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: B 283 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7886 (mtm110) REVERT: B 382 PHE cc_start: 0.8877 (m-80) cc_final: 0.8345 (m-80) REVERT: B 460 MET cc_start: 0.8548 (mtp) cc_final: 0.8167 (mtp) REVERT: h 34 MET cc_start: 0.7545 (mmt) cc_final: 0.7219 (mmt) REVERT: h 77 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.7085 (p) REVERT: l 47 MET cc_start: 0.8224 (mtm) cc_final: 0.7828 (ptp) REVERT: C 79 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 87 ASP cc_start: 0.8625 (t0) cc_final: 0.8039 (m-30) REVERT: C 151 MET cc_start: 0.8424 (mmm) cc_final: 0.8132 (mtt) REVERT: C 164 ARG cc_start: 0.7314 (mtm-85) cc_final: 0.6887 (mtm110) REVERT: C 395 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8383 (mtmm) REVERT: C 460 MET cc_start: 0.8905 (mtm) cc_final: 0.8661 (mtm) REVERT: F 8 SER cc_start: 0.8955 (p) cc_final: 0.8541 (t) REVERT: F 16 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8989 (p) outliers start: 97 outliers final: 74 residues processed: 381 average time/residue: 0.1083 time to fit residues: 64.9946 Evaluate side-chains 386 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 179 THR 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 364 VAL Chi-restraints excluded: chain A residue 426 ASP 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 30 ILE 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 60 CYS Chi-restraints excluded: chain B residue 97 VAL 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 253 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL 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 347 VAL 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 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 h residue 77 THR Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 56 VAL 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 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 389 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 448 ILE 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 36 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 197 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 145 optimal weight: 50.0000 chunk 208 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 200 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 B 144 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.181118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120845 restraints weight = 20127.704| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.51 r_work: 0.3128 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3084 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= 0.264 Angle : 0.782 22.530 23361 Z= 0.396 Chirality : 0.050 0.855 2641 Planarity : 0.005 0.075 2942 Dihedral : 8.749 89.902 2515 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.81 % Favored : 89.01 % Rotamer: Outliers : 6.06 % Allowed : 18.90 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.18), residues: 2174 helix: -0.02 (0.25), residues: 456 sheet: 0.19 (0.21), residues: 663 loop : -2.39 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 193 TYR 0.015 0.002 TYR D 25 PHE 0.021 0.002 PHE F 37 TRP 0.018 0.002 TRP B 400 HIS 0.015 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00621 (17196) covalent geometry : angle 0.75896 (23304) SS BOND : bond 0.00459 ( 18) SS BOND : angle 1.27647 ( 36) hydrogen bonds : bond 0.05349 ( 706) hydrogen bonds : angle 5.47721 ( 1968) Misc. bond : bond 0.00511 ( 1) link_BETA1-4 : bond 0.00694 ( 4) link_BETA1-4 : angle 2.69503 ( 12) link_BETA1-6 : bond 0.01600 ( 2) link_BETA1-6 : angle 1.31965 ( 6) link_NAG-ASN : bond 0.01288 ( 1) link_NAG-ASN : angle 15.33972 ( 3) *********************** 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 432 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 323 time to evaluate : 0.480 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: 0.6553 (ptp) cc_final: 0.6118 (ptt) REVERT: A 67 ASP cc_start: 0.8677 (p0) cc_final: 0.8358 (p0) REVERT: A 72 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8759 (t) REVERT: A 151 MET cc_start: 0.7996 (mmm) cc_final: 0.7642 (mmm) REVERT: A 276 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6904 (pt0) REVERT: A 316 LYS cc_start: 0.3830 (tttt) cc_final: 0.2893 (tttm) REVERT: A 345 MET cc_start: 0.8895 (mmm) cc_final: 0.8157 (mmm) REVERT: A 481 ASN cc_start: 0.6503 (t0) cc_final: 0.6275 (t0) REVERT: D 25 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.4841 (p90) REVERT: L 47 MET cc_start: 0.7086 (mmt) cc_final: 0.6746 (mtt) REVERT: B 13 GLU cc_start: 0.8609 (tt0) cc_final: 0.7796 (pt0) REVERT: B 77 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6447 (tt0) REVERT: B 87 ASP cc_start: 0.8173 (t0) cc_final: 0.7773 (t0) REVERT: B 168 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 197 ASP cc_start: 0.8242 (t0) cc_final: 0.7809 (t0) REVERT: B 283 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7669 (mtm110) REVERT: B 382 PHE cc_start: 0.8882 (m-80) cc_final: 0.8419 (m-80) REVERT: B 460 MET cc_start: 0.8610 (mtp) cc_final: 0.8238 (mtp) REVERT: h 34 MET cc_start: 0.7541 (mmt) cc_final: 0.7259 (mmt) REVERT: h 77 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7035 (p) REVERT: l 47 MET cc_start: 0.8241 (mtm) cc_final: 0.7829 (ptp) REVERT: C 79 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7572 (mt-10) REVERT: C 87 ASP cc_start: 0.8638 (t0) cc_final: 0.8145 (t0) REVERT: C 134 ASN cc_start: 0.8976 (p0) cc_final: 0.8707 (p0) REVERT: C 151 MET cc_start: 0.8430 (mmm) cc_final: 0.8039 (mtt) REVERT: C 164 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7175 (mtm110) REVERT: C 175 ARG cc_start: 0.4990 (ptt-90) cc_final: 0.4530 (ptt-90) REVERT: C 177 GLU cc_start: 0.8436 (pt0) cc_final: 0.7987 (tt0) REVERT: C 374 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7391 (ppp) REVERT: C 395 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8364 (mtmm) REVERT: F 16 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8968 (p) outliers start: 109 outliers final: 82 residues processed: 399 average time/residue: 0.1140 time to fit residues: 72.0648 Evaluate side-chains 393 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 305 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 33 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 179 THR 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 359 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 30 ILE 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 31 VAL 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 253 GLN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 303 VAL 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 355 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 407 ILE 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 25 TYR Chi-restraints excluded: chain E residue 30 ILE 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 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 72 SER 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 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 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 396 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 448 ILE 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 36 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 50.0000 chunk 70 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 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 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 = 0.4006 r_free = 0.4006 target = 0.181328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119102 restraints weight = 20403.962| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.22 r_work: 0.3180 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17222 Z= 0.218 Angle : 0.752 26.329 23361 Z= 0.381 Chirality : 0.047 0.546 2641 Planarity : 0.005 0.071 2942 Dihedral : 8.496 88.035 2514 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.72 % Favored : 89.10 % Rotamer: Outliers : 5.61 % Allowed : 19.73 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.18), residues: 2174 helix: 0.04 (0.25), residues: 459 sheet: 0.22 (0.21), residues: 672 loop : -2.41 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 193 TYR 0.013 0.002 TYR D 25 PHE 0.021 0.002 PHE F 37 TRP 0.028 0.002 TRP B 400 HIS 0.088 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00508 (17196) covalent geometry : angle 0.72024 (23304) SS BOND : bond 0.00367 ( 18) SS BOND : angle 1.25037 ( 36) hydrogen bonds : bond 0.05025 ( 706) hydrogen bonds : angle 5.41929 ( 1968) Misc. bond : bond 0.02027 ( 1) link_BETA1-4 : bond 0.00610 ( 4) link_BETA1-4 : angle 2.69160 ( 12) link_BETA1-6 : bond 0.01617 ( 2) link_BETA1-6 : angle 1.35192 ( 6) link_NAG-ASN : bond 0.01014 ( 1) link_NAG-ASN : angle 17.87076 ( 3) *********************** 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 405 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 304 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6403 (ptp) cc_final: 0.6011 (ptt) REVERT: A 72 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8761 (t) REVERT: A 151 MET cc_start: 0.7930 (mmm) cc_final: 0.7610 (mmm) REVERT: A 166 LYS cc_start: 0.8815 (tttt) cc_final: 0.8538 (tttm) REVERT: A 276 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6821 (pt0) REVERT: A 316 LYS cc_start: 0.4043 (tttt) cc_final: 0.3038 (tttm) REVERT: A 345 MET cc_start: 0.8874 (mmm) cc_final: 0.8119 (mmm) REVERT: D 25 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.4705 (p90) REVERT: H 94 ARG cc_start: 0.4779 (ttp-170) cc_final: 0.3872 (ttp-170) REVERT: L 47 MET cc_start: 0.7157 (mmt) cc_final: 0.6831 (mtt) REVERT: B 13 GLU cc_start: 0.8617 (tt0) cc_final: 0.7760 (pt0) REVERT: B 77 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6344 (tt0) REVERT: B 87 ASP cc_start: 0.8148 (t0) cc_final: 0.7651 (t0) REVERT: B 89 GLN cc_start: 0.7485 (mt0) cc_final: 0.6754 (tt0) REVERT: B 164 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8489 (mtm-85) REVERT: B 168 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 197 ASP cc_start: 0.8328 (t0) cc_final: 0.7862 (t0) REVERT: B 238 ASN cc_start: 0.8176 (t0) cc_final: 0.7798 (t0) REVERT: B 254 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.7241 (t) REVERT: B 276 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: B 283 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7694 (mtm110) REVERT: B 336 ASP cc_start: 0.7047 (m-30) cc_final: 0.6712 (m-30) REVERT: B 382 PHE cc_start: 0.8896 (m-80) cc_final: 0.8419 (m-80) REVERT: B 460 MET cc_start: 0.8508 (mtp) cc_final: 0.8162 (mtp) REVERT: h 34 MET cc_start: 0.7583 (mmt) cc_final: 0.7290 (mmt) REVERT: h 77 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.7035 (p) REVERT: l 47 MET cc_start: 0.8234 (mtm) cc_final: 0.7806 (ptp) REVERT: C 15 MET cc_start: 0.5106 (tpt) cc_final: 0.4611 (tpp) REVERT: C 79 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7514 (mt-10) REVERT: C 151 MET cc_start: 0.8394 (mmm) cc_final: 0.7985 (mtt) REVERT: C 164 ARG cc_start: 0.7591 (mtm-85) cc_final: 0.7186 (mtm110) REVERT: C 175 ARG cc_start: 0.4836 (ptt-90) cc_final: 0.4172 (ptt-90) REVERT: C 177 GLU cc_start: 0.8476 (pt0) cc_final: 0.7989 (tt0) REVERT: C 316 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7594 (mtmm) REVERT: C 374 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7476 (ppp) REVERT: C 395 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8357 (mtmm) REVERT: C 460 MET cc_start: 0.9019 (mtm) cc_final: 0.8671 (mtp) outliers start: 101 outliers final: 79 residues processed: 372 average time/residue: 0.1136 time to fit residues: 65.9651 Evaluate side-chains 387 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 301 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 179 THR 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 359 ILE Chi-restraints excluded: chain A residue 426 ASP 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 30 ILE 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 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 253 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL 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 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 407 ILE 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 25 TYR Chi-restraints excluded: chain E residue 30 ILE 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 23 VAL Chi-restraints excluded: chain C residue 40 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 97 VAL 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 249 HIS Chi-restraints excluded: chain C residue 266 HIS 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 396 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain F residue 4 LEU 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 52 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 74 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 13 optimal weight: 0.0470 chunk 208 optimal weight: 7.9990 chunk 151 optimal weight: 50.0000 overall best weight: 3.4086 ------------------------------------------------------------------------------- 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 85 GLN B 148 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS ** 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 = 0.4053 r_free = 0.4053 target = 0.186364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124872 restraints weight = 20238.498| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.23 r_work: 0.3213 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17222 Z= 0.168 Angle : 0.711 25.194 23361 Z= 0.357 Chirality : 0.046 0.612 2641 Planarity : 0.004 0.063 2942 Dihedral : 8.173 85.298 2514 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.53 % Favored : 89.28 % Rotamer: Outliers : 4.50 % Allowed : 20.79 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2174 helix: 0.20 (0.25), residues: 459 sheet: 0.25 (0.21), residues: 665 loop : -2.37 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 193 TYR 0.010 0.001 TYR C 202 PHE 0.021 0.001 PHE F 37 TRP 0.023 0.001 TRP B 400 HIS 0.065 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00383 (17196) covalent geometry : angle 0.67961 (23304) SS BOND : bond 0.00321 ( 18) SS BOND : angle 1.15579 ( 36) hydrogen bonds : bond 0.04576 ( 706) hydrogen bonds : angle 5.26800 ( 1968) Misc. bond : bond 0.01106 ( 1) link_BETA1-4 : bond 0.00551 ( 4) link_BETA1-4 : angle 2.81848 ( 12) link_BETA1-6 : bond 0.01665 ( 2) link_BETA1-6 : angle 1.34192 ( 6) link_NAG-ASN : bond 0.01418 ( 1) link_NAG-ASN : angle 17.39523 ( 3) *********************** 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 386 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6362 (ptp) cc_final: 0.6058 (ptt) REVERT: A 166 LYS cc_start: 0.8797 (tttt) cc_final: 0.8487 (tttp) REVERT: A 276 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6879 (pt0) REVERT: A 316 LYS cc_start: 0.4051 (tttt) cc_final: 0.2954 (tttm) REVERT: A 345 MET cc_start: 0.8832 (mmm) cc_final: 0.8057 (mmm) REVERT: D 25 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.4730 (p90) REVERT: H 34 MET cc_start: 0.7910 (mmm) cc_final: 0.7508 (mmm) REVERT: H 94 ARG cc_start: 0.4727 (ttp-170) cc_final: 0.3842 (ttp-170) REVERT: B 13 GLU cc_start: 0.8482 (tt0) cc_final: 0.7568 (pt0) REVERT: B 77 GLN cc_start: 0.6808 (mm-40) cc_final: 0.6354 (tt0) REVERT: B 87 ASP cc_start: 0.8106 (t0) cc_final: 0.7600 (t0) REVERT: B 89 GLN cc_start: 0.7461 (mt0) cc_final: 0.6730 (tt0) REVERT: B 168 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 197 ASP cc_start: 0.8335 (t0) cc_final: 0.7908 (t0) REVERT: B 238 ASN cc_start: 0.8155 (t0) cc_final: 0.7773 (t0) REVERT: B 254 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7226 (t) REVERT: B 283 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7699 (mtm110) REVERT: B 295 MET cc_start: 0.9171 (mtm) cc_final: 0.8890 (ptp) REVERT: B 336 ASP cc_start: 0.7050 (m-30) cc_final: 0.6744 (m-30) REVERT: B 382 PHE cc_start: 0.8865 (m-80) cc_final: 0.8378 (m-80) REVERT: B 460 MET cc_start: 0.8448 (mtp) cc_final: 0.7987 (mtm) REVERT: h 34 MET cc_start: 0.7567 (mmt) cc_final: 0.7319 (mmt) REVERT: h 77 THR cc_start: 0.7311 (OUTLIER) cc_final: 0.7003 (p) REVERT: l 47 MET cc_start: 0.8202 (mtm) cc_final: 0.7756 (ptp) REVERT: C 15 MET cc_start: 0.4933 (tpt) cc_final: 0.4510 (tpp) REVERT: C 151 MET cc_start: 0.8335 (mmm) cc_final: 0.7926 (mtt) REVERT: C 164 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.6962 (mtm110) REVERT: C 175 ARG cc_start: 0.4833 (ptt-90) cc_final: 0.4204 (ptt-90) REVERT: C 177 GLU cc_start: 0.8519 (pt0) cc_final: 0.8027 (tt0) REVERT: C 316 LYS cc_start: 0.8283 (mtpp) cc_final: 0.7480 (mtmm) REVERT: C 374 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7488 (ppp) REVERT: C 395 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8372 (mtmm) REVERT: C 433 SER cc_start: 0.7522 (t) cc_final: 0.7191 (t) REVERT: C 460 MET cc_start: 0.9064 (mtm) cc_final: 0.8703 (mtp) outliers start: 81 outliers final: 68 residues processed: 354 average time/residue: 0.1149 time to fit residues: 63.3407 Evaluate side-chains 370 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 297 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 179 THR 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 359 ILE Chi-restraints excluded: chain A residue 426 ASP 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 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 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL 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 253 GLN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 307 LEU 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 407 ILE 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 25 TYR 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 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS 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 235 HIS Chi-restraints excluded: chain C residue 249 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 389 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain F residue 4 LEU 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 52 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 112 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 0.0670 chunk 206 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 overall best weight: 1.9722 ------------------------------------------------------------------------------- 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 85 GLN ** 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 = 0.4077 r_free = 0.4077 target = 0.188366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126117 restraints weight = 20175.326| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.29 r_work: 0.3256 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3630 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= 0.132 Angle : 0.681 24.946 23361 Z= 0.341 Chirality : 0.046 0.648 2641 Planarity : 0.004 0.058 2942 Dihedral : 7.820 81.894 2514 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.52 % Favored : 90.34 % Rotamer: Outliers : 3.78 % Allowed : 21.57 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2174 helix: 0.41 (0.26), residues: 459 sheet: 0.44 (0.21), residues: 627 loop : -2.40 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 283 TYR 0.010 0.001 TYR B 332 PHE 0.019 0.001 PHE F 42 TRP 0.020 0.001 TRP B 400 HIS 0.051 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00292 (17196) covalent geometry : angle 0.64797 (23304) SS BOND : bond 0.00357 ( 18) SS BOND : angle 1.07033 ( 36) hydrogen bonds : bond 0.04169 ( 706) hydrogen bonds : angle 5.08818 ( 1968) Misc. bond : bond 0.00829 ( 1) link_BETA1-4 : bond 0.00612 ( 4) link_BETA1-4 : angle 2.93359 ( 12) link_BETA1-6 : bond 0.01598 ( 2) link_BETA1-6 : angle 1.32119 ( 6) link_NAG-ASN : bond 0.01586 ( 1) link_NAG-ASN : angle 17.18530 ( 3) ********************** 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 387 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 319 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6339 (ptp) cc_final: 0.6054 (ptt) REVERT: A 151 MET cc_start: 0.7946 (mmm) cc_final: 0.7573 (mmm) REVERT: A 276 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6901 (pt0) REVERT: A 316 LYS cc_start: 0.3864 (tttt) cc_final: 0.3119 (tttt) REVERT: A 345 MET cc_start: 0.8807 (mmm) cc_final: 0.7480 (mmm) REVERT: D 25 TYR cc_start: 0.5889 (OUTLIER) cc_final: 0.4709 (p90) REVERT: H 34 MET cc_start: 0.7927 (mmm) cc_final: 0.7534 (mmm) REVERT: H 94 ARG cc_start: 0.4789 (ttp-170) cc_final: 0.3924 (ttp-170) REVERT: L 47 MET cc_start: 0.6976 (mmt) cc_final: 0.6644 (mtt) REVERT: B 13 GLU cc_start: 0.8456 (tt0) cc_final: 0.7497 (pt0) REVERT: B 57 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7501 (ttm170) REVERT: B 77 GLN cc_start: 0.6798 (mm-40) cc_final: 0.6378 (tt0) REVERT: B 87 ASP cc_start: 0.8074 (t0) cc_final: 0.7639 (t0) REVERT: B 164 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8442 (mtm-85) REVERT: B 168 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7652 (mt-10) REVERT: B 197 ASP cc_start: 0.8312 (t0) cc_final: 0.7925 (t0) REVERT: B 238 ASN cc_start: 0.8184 (t0) cc_final: 0.7867 (t0) REVERT: B 283 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7855 (mtm110) REVERT: B 336 ASP cc_start: 0.6977 (m-30) cc_final: 0.6650 (m-30) REVERT: B 382 PHE cc_start: 0.8719 (m-80) cc_final: 0.8188 (m-80) REVERT: E 52 LEU cc_start: 0.8483 (mp) cc_final: 0.8043 (tt) REVERT: h 77 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7010 (p) REVERT: l 47 MET cc_start: 0.8151 (mtm) cc_final: 0.7706 (ptp) REVERT: C 13 GLU cc_start: 0.8393 (tt0) cc_final: 0.7819 (mt-10) REVERT: C 15 MET cc_start: 0.5128 (tpt) cc_final: 0.4470 (tpp) REVERT: C 151 MET cc_start: 0.8316 (mmm) cc_final: 0.7880 (mtt) REVERT: C 164 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.6932 (mtm110) REVERT: C 175 ARG cc_start: 0.4801 (ptt-90) cc_final: 0.4167 (ptt-90) REVERT: C 177 GLU cc_start: 0.8561 (pt0) cc_final: 0.8109 (tt0) REVERT: C 292 ARG cc_start: 0.6651 (ttm110) cc_final: 0.5780 (ttt180) REVERT: C 316 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7729 (mtmm) REVERT: C 374 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7220 (ppp) REVERT: C 460 MET cc_start: 0.8976 (mtm) cc_final: 0.8715 (mtm) REVERT: C 473 MET cc_start: 0.7236 (tpp) cc_final: 0.6965 (mmm) REVERT: F 8 SER cc_start: 0.8880 (p) cc_final: 0.8634 (t) outliers start: 68 outliers final: 53 residues processed: 363 average time/residue: 0.1199 time to fit residues: 66.5056 Evaluate side-chains 362 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 305 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 179 THR 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 426 ASP 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 56 SER Chi-restraints excluded: chain H residue 92 CYS 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 177 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 391 VAL 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 25 TYR 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 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 CYS 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 249 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 389 ILE Chi-restraints excluded: chain C residue 396 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 81 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 147 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** 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 = 0.4055 r_free = 0.4055 target = 0.186423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124664 restraints weight = 20099.562| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.25 r_work: 0.3248 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3710 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= 0.146 Angle : 0.697 24.585 23361 Z= 0.347 Chirality : 0.047 0.659 2641 Planarity : 0.004 0.055 2942 Dihedral : 7.604 79.711 2514 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.80 % Favored : 90.06 % Rotamer: Outliers : 3.61 % Allowed : 22.23 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.18), residues: 2174 helix: 0.38 (0.25), residues: 465 sheet: 0.44 (0.21), residues: 627 loop : -2.42 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 193 TYR 0.018 0.001 TYR F 25 PHE 0.030 0.002 PHE B 245 TRP 0.023 0.001 TRP B 400 HIS 0.048 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00333 (17196) covalent geometry : angle 0.66529 (23304) SS BOND : bond 0.00279 ( 18) SS BOND : angle 1.04710 ( 36) hydrogen bonds : bond 0.04242 ( 706) hydrogen bonds : angle 5.06055 ( 1968) Misc. bond : bond 0.00772 ( 1) link_BETA1-4 : bond 0.00467 ( 4) link_BETA1-4 : angle 2.96728 ( 12) link_BETA1-6 : bond 0.01473 ( 2) link_BETA1-6 : angle 1.30861 ( 6) link_NAG-ASN : bond 0.01585 ( 1) link_NAG-ASN : angle 16.98916 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3948.79 seconds wall clock time: 68 minutes 27.12 seconds (4107.12 seconds total)