Starting phenix.real_space_refine on Mon Nov 18 15:56:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2024/8cxi_27058.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2024/8cxi_27058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2024/8cxi_27058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2024/8cxi_27058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2024/8cxi_27058.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxi_27058/11_2024/8cxi_27058.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 98 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 10612 2.51 5 N 2902 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16832 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1036 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 761 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1024 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 743 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.17, per 1000 atoms: 0.60 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=0, 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 " Time building additional restraints: 4.57 Conformation dependent library (CDL) restraints added in 2.2 seconds 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 40 sheets defined 23.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 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: 6.75 Time building geometry restraints manager: 5.19 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: 10 1.67 - 2.47: 180 2.47 - 3.28: 18104 3.28 - 4.09: 39051 4.09 - 4.90: 71646 Warning: very small nonbonded interaction distances. Nonbonded interactions: 128991 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 128986 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.170 Process input model: 40.310 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.720 ------------------------------------------------------------------------------- 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 : 0.008 0.105 17196 Z= 0.536 Angle : 0.969 15.659 23304 Z= 0.574 Chirality : 0.086 3.240 2641 Planarity : 0.006 0.099 2942 Dihedral : 14.268 124.253 6237 Min Nonbonded Distance : 0.857 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.57 % Favored : 89.74 % Rotamer: Outliers : 3.00 % Allowed : 9.45 % Favored : 87.55 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.16), residues: 2174 helix: -1.25 (0.21), residues: 450 sheet: -0.32 (0.19), residues: 733 loop : -3.08 (0.16), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 400 HIS 0.006 0.001 HIS A 235 PHE 0.016 0.002 PHE A 431 TYR 0.020 0.002 TYR A 61 ARG 0.011 0.001 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 457 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8108 (p0) cc_final: 0.7795 (p0) REVERT: A 276 GLU cc_start: 0.6129 (pt0) cc_final: 0.5909 (pt0) REVERT: A 395 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7698 (ptpp) REVERT: A 495 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7944 (mp) REVERT: H 32 HIS cc_start: 0.6889 (m90) cc_final: 0.6579 (m90) REVERT: B 136 GLU cc_start: 0.6794 (tt0) cc_final: 0.5990 (tt0) REVERT: B 140 MET cc_start: 0.7585 (mmt) cc_final: 0.7324 (mmm) REVERT: B 247 ASP cc_start: 0.6537 (t0) cc_final: 0.6318 (t0) REVERT: B 429 TRP cc_start: 0.7361 (m100) cc_final: 0.7066 (m100) REVERT: E 14 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7886 (m) REVERT: E 38 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6522 (mmt90) REVERT: C 67 ASP cc_start: 0.8344 (p0) cc_final: 0.8042 (p0) REVERT: C 87 ASP cc_start: 0.7556 (t0) cc_final: 0.7133 (t0) REVERT: C 134 ASN cc_start: 0.8427 (p0) cc_final: 0.8064 (p0) outliers start: 54 outliers final: 19 residues processed: 497 average time/residue: 0.3139 time to fit residues: 228.6897 Evaluate side-chains 354 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 134 ASN A 148 HIS A 163 ASN A 288 HIS ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 85 GLN B 134 ASN B 163 ASN B 261 GLN B 344 GLN B 350 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN E 7 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 HIS C 154 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS C 350 GLN F 7 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17196 Z= 0.228 Angle : 0.779 19.340 23304 Z= 0.399 Chirality : 0.052 1.143 2641 Planarity : 0.006 0.145 2942 Dihedral : 11.409 109.627 2548 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.57 % Favored : 90.29 % Rotamer: Outliers : 3.78 % Allowed : 15.06 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2174 helix: 0.14 (0.25), residues: 429 sheet: -0.12 (0.19), residues: 706 loop : -2.70 (0.16), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 36 HIS 0.005 0.001 HIS A 148 PHE 0.037 0.002 PHE A 314 TYR 0.016 0.002 TYR l 36 ARG 0.006 0.001 ARG A 99 *********************** 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 419 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 1.930 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 90 TYR cc_start: 0.8489 (m-80) cc_final: 0.8280 (m-80) REVERT: A 151 MET cc_start: 0.6373 (mmm) cc_final: 0.5945 (mmm) REVERT: A 221 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 426 ASP cc_start: 0.5722 (m-30) cc_final: 0.5463 (m-30) REVERT: B 85 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: C 125 MET cc_start: 0.6957 (tpp) cc_final: 0.6251 (ttt) REVERT: C 487 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.6087 (mmt) outliers start: 68 outliers final: 44 residues processed: 398 average time/residue: 0.2836 time to fit residues: 173.2235 Evaluate side-chains 368 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 97 VAL 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 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 85 GLN 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 313 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 391 VAL 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 E residue 38 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 235 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 7.9990 chunk 61 optimal weight: 50.0000 chunk 164 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 175 optimal weight: 30.0000 chunk 195 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 158 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS A 465 GLN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 226 HIS ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 447 GLN h 35 HIS C 103 ASN C 134 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 HIS ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17196 Z= 0.401 Angle : 0.798 17.997 23304 Z= 0.412 Chirality : 0.052 0.997 2641 Planarity : 0.005 0.105 2942 Dihedral : 10.849 101.459 2527 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.72 % Favored : 89.19 % Rotamer: Outliers : 4.95 % Allowed : 16.40 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2174 helix: 0.15 (0.25), residues: 429 sheet: 0.01 (0.20), residues: 682 loop : -2.58 (0.16), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 400 HIS 0.010 0.001 HIS C 288 PHE 0.016 0.002 PHE A 314 TYR 0.016 0.002 TYR D 25 ARG 0.006 0.001 ARG l 95 *********************** 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 437 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 348 time to evaluate : 2.027 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 221 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 345 MET cc_start: 0.6929 (mmm) cc_final: 0.6625 (mmm) REVERT: A 426 ASP cc_start: 0.5937 (m-30) cc_final: 0.5731 (m-30) REVERT: H 94 ARG cc_start: 0.6851 (ttp-170) cc_final: 0.6235 (ttp-170) REVERT: B 253 GLN cc_start: 0.6918 (mt0) cc_final: 0.6715 (mt0) REVERT: B 317 ILE cc_start: 0.7142 (pt) cc_final: 0.6872 (pt) REVERT: h 34 MET cc_start: 0.7051 (mmt) cc_final: 0.6821 (mmt) REVERT: C 125 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6857 (ttt) REVERT: C 164 ARG cc_start: 0.7658 (mtm110) cc_final: 0.7363 (mtm110) REVERT: C 487 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.6071 (mmt) REVERT: C 494 VAL cc_start: 0.7143 (OUTLIER) cc_final: 0.6924 (t) outliers start: 89 outliers final: 54 residues processed: 406 average time/residue: 0.2677 time to fit residues: 168.7336 Evaluate side-chains 391 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 333 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 140 MET 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 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 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 48 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 274 GLU 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 487 MET Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 209 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** 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** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17196 Z= 0.193 Angle : 0.689 13.277 23304 Z= 0.355 Chirality : 0.048 0.922 2641 Planarity : 0.005 0.088 2942 Dihedral : 10.122 96.028 2524 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.52 % Favored : 90.34 % Rotamer: Outliers : 4.28 % Allowed : 17.73 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2174 helix: 0.36 (0.26), residues: 453 sheet: 0.37 (0.21), residues: 649 loop : -2.50 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.005 0.001 HIS H 32 PHE 0.023 0.001 PHE E 37 TYR 0.013 0.001 TYR h 29 ARG 0.012 0.001 ARG B 283 *********************** 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 399 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 322 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6198 (mmm) cc_final: 0.5906 (mmm) REVERT: A 221 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7970 (mt) REVERT: A 345 MET cc_start: 0.7056 (mmm) cc_final: 0.6663 (mmm) REVERT: A 475 LEU cc_start: 0.8012 (tt) cc_final: 0.7682 (tt) REVERT: H 94 ARG cc_start: 0.6636 (ttp-170) cc_final: 0.6097 (ttp-170) REVERT: h 34 MET cc_start: 0.6751 (mmt) cc_final: 0.6543 (mmt) REVERT: C 125 MET cc_start: 0.7050 (tpp) cc_final: 0.6706 (ttt) REVERT: C 191 GLU cc_start: 0.6369 (tp30) cc_final: 0.5052 (tp30) REVERT: C 487 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5884 (mmt) outliers start: 77 outliers final: 43 residues processed: 372 average time/residue: 0.2760 time to fit residues: 157.8751 Evaluate side-chains 336 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 291 time to evaluate : 1.999 ------------------------------------------------------------------------------- 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 97 VAL 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 313 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 177 GLU 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 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 h residue 100 SER 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 266 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 156 optimal weight: 50.0000 chunk 86 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 50.0000 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17196 Z= 0.386 Angle : 0.771 14.965 23304 Z= 0.395 Chirality : 0.051 0.892 2641 Planarity : 0.005 0.082 2942 Dihedral : 9.427 94.515 2517 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.99 % Favored : 88.87 % Rotamer: Outliers : 5.00 % Allowed : 17.68 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2174 helix: 0.13 (0.25), residues: 456 sheet: 0.23 (0.20), residues: 676 loop : -2.45 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 400 HIS 0.008 0.001 HIS C 210 PHE 0.014 0.002 PHE C 463 TYR 0.014 0.002 TYR B 137 ARG 0.007 0.001 ARG B 99 *********************** 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 416 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 326 time to evaluate : 1.829 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 151 MET cc_start: 0.6512 (mmm) cc_final: 0.6262 (mmm) REVERT: A 382 PHE cc_start: 0.7890 (m-10) cc_final: 0.7474 (m-80) REVERT: H 11 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6594 (tp) REVERT: H 94 ARG cc_start: 0.6853 (ttp-170) cc_final: 0.6322 (ttp-170) REVERT: B 4 ILE cc_start: 0.7942 (mm) cc_final: 0.7725 (mm) REVERT: B 168 GLU cc_start: 0.6494 (mt-10) cc_final: 0.5912 (mt-10) REVERT: B 430 ASP cc_start: 0.7304 (t0) cc_final: 0.7101 (t0) REVERT: C 125 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7126 (ttt) REVERT: C 191 GLU cc_start: 0.6411 (tp30) cc_final: 0.5182 (tp30) outliers start: 90 outliers final: 65 residues processed: 388 average time/residue: 0.2643 time to fit residues: 160.1709 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 : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 45 LEU 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 364 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 14 THR 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 H residue 11 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 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 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 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 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 49 THR 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 125 MET 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 317 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain 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 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 50.0000 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 40.0000 chunk 110 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17196 Z= 0.338 Angle : 0.734 13.539 23304 Z= 0.378 Chirality : 0.050 0.888 2641 Planarity : 0.005 0.071 2942 Dihedral : 9.017 92.953 2515 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.86 % Favored : 89.01 % Rotamer: Outliers : 5.17 % Allowed : 18.84 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2174 helix: 0.12 (0.25), residues: 462 sheet: 0.25 (0.20), residues: 676 loop : -2.47 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 400 HIS 0.008 0.001 HIS A 288 PHE 0.019 0.002 PHE F 37 TYR 0.016 0.002 TYR h 79 ARG 0.006 0.001 ARG C 292 *********************** 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 406 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 313 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6527 (mmm) cc_final: 0.6300 (mmm) REVERT: H 11 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6567 (tp) REVERT: H 94 ARG cc_start: 0.6901 (ttp-170) cc_final: 0.6317 (ttp-170) REVERT: B 83 ASP cc_start: 0.5968 (p0) cc_final: 0.5607 (p0) REVERT: C 125 MET cc_start: 0.7233 (tpp) cc_final: 0.7004 (ttt) REVERT: C 191 GLU cc_start: 0.6462 (tp30) cc_final: 0.4947 (tp30) REVERT: C 384 ASP cc_start: 0.6645 (m-30) cc_final: 0.6265 (t0) REVERT: C 456 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8041 (mp) outliers start: 93 outliers final: 68 residues processed: 378 average time/residue: 0.2734 time to fit residues: 159.1768 Evaluate side-chains 379 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 309 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 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 213 VAL 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 A residue 495 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 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 274 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 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 E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 100 SER 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 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 456 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17196 Z= 0.371 Angle : 0.756 13.578 23304 Z= 0.390 Chirality : 0.050 0.864 2641 Planarity : 0.005 0.057 2942 Dihedral : 8.788 90.762 2513 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.09 % Favored : 88.78 % Rotamer: Outliers : 5.84 % Allowed : 18.90 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 2174 helix: -0.01 (0.25), residues: 465 sheet: 0.18 (0.20), residues: 676 loop : -2.44 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 400 HIS 0.007 0.001 HIS A 235 PHE 0.028 0.002 PHE E 37 TYR 0.014 0.002 TYR C 61 ARG 0.006 0.001 ARG B 164 *********************** 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 436 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 331 time to evaluate : 1.866 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: A 52 ASN cc_start: 0.7510 (p0) cc_final: 0.7230 (p0) REVERT: A 151 MET cc_start: 0.6666 (mmm) cc_final: 0.6411 (mmm) REVERT: D 25 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.5097 (p90) REVERT: H 11 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6586 (tp) REVERT: H 94 ARG cc_start: 0.7099 (ttp-170) cc_final: 0.6475 (ttp-170) REVERT: B 30 CYS cc_start: 0.7152 (p) cc_final: 0.6494 (p) REVERT: B 136 GLU cc_start: 0.6533 (tt0) cc_final: 0.6056 (tt0) REVERT: B 168 GLU cc_start: 0.6327 (mt-10) cc_final: 0.6086 (mt-10) REVERT: C 125 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6914 (ttt) REVERT: C 175 ARG cc_start: 0.5446 (ptt-90) cc_final: 0.4977 (ptp90) REVERT: C 384 ASP cc_start: 0.6699 (m-30) cc_final: 0.6434 (t0) outliers start: 105 outliers final: 80 residues processed: 402 average time/residue: 0.2671 time to fit residues: 167.1873 Evaluate side-chains 398 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 315 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 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 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 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 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS 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 265 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 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 E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 22 ASP 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 125 MET 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 295 MET Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 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 129 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** 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** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17196 Z= 0.309 Angle : 0.719 12.512 23304 Z= 0.371 Chirality : 0.048 0.602 2641 Planarity : 0.005 0.057 2942 Dihedral : 8.480 88.501 2512 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.76 % Favored : 89.05 % Rotamer: Outliers : 5.34 % Allowed : 20.29 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 2174 helix: 0.13 (0.25), residues: 459 sheet: 0.21 (0.20), residues: 672 loop : -2.44 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 400 HIS 0.008 0.001 HIS A 288 PHE 0.022 0.002 PHE E 37 TYR 0.012 0.002 TYR B 203 ARG 0.012 0.000 ARG B 283 *********************** 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 408 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 312 time to evaluate : 2.005 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: A 151 MET cc_start: 0.6589 (mmm) cc_final: 0.6355 (mmm) REVERT: A 316 LYS cc_start: 0.6594 (tttt) cc_final: 0.5817 (tttp) REVERT: D 25 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.4992 (p90) REVERT: H 94 ARG cc_start: 0.7136 (ttp-170) cc_final: 0.6517 (ttp-170) REVERT: B 168 GLU cc_start: 0.6403 (mt-10) cc_final: 0.6172 (mt-10) REVERT: l 47 MET cc_start: 0.5498 (mpp) cc_final: 0.5101 (ptp) REVERT: C 125 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6829 (ttt) REVERT: C 175 ARG cc_start: 0.5476 (ptt-90) cc_final: 0.5092 (ptt-90) REVERT: C 384 ASP cc_start: 0.6754 (m-30) cc_final: 0.6342 (t0) outliers start: 96 outliers final: 81 residues processed: 374 average time/residue: 0.2720 time to fit residues: 156.5191 Evaluate side-chains 389 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 306 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 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 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 375 MET 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 A residue 495 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 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 27 HIS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 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 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 22 ASP 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 72 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 152 ILE 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 405 SER 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 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 6.9990 chunk 200 optimal weight: 30.0000 chunk 182 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17196 Z= 0.320 Angle : 0.730 12.186 23304 Z= 0.377 Chirality : 0.048 0.620 2641 Planarity : 0.005 0.057 2942 Dihedral : 8.360 86.808 2512 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.18 % Favored : 88.64 % Rotamer: Outliers : 5.45 % Allowed : 20.79 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 2174 helix: 0.11 (0.25), residues: 459 sheet: 0.18 (0.20), residues: 672 loop : -2.44 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 400 HIS 0.007 0.001 HIS A 288 PHE 0.016 0.002 PHE F 42 TYR 0.013 0.002 TYR C 61 ARG 0.012 0.001 ARG B 283 *********************** 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 396 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 298 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6627 (mmm) cc_final: 0.6388 (mmm) REVERT: A 316 LYS cc_start: 0.6503 (tttt) cc_final: 0.5641 (tttp) REVERT: D 25 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.5033 (p90) REVERT: H 11 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6496 (tp) REVERT: H 94 ARG cc_start: 0.7148 (ttp-170) cc_final: 0.6544 (ttp-170) REVERT: B 27 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7269 (t-90) REVERT: B 317 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7949 (pt) REVERT: l 47 MET cc_start: 0.5472 (mpp) cc_final: 0.5129 (ptp) REVERT: C 87 ASP cc_start: 0.7521 (m-30) cc_final: 0.7312 (m-30) REVERT: C 125 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6757 (ttt) REVERT: C 175 ARG cc_start: 0.5529 (ptt-90) cc_final: 0.4498 (ptp90) outliers start: 98 outliers final: 84 residues processed: 365 average time/residue: 0.2674 time to fit residues: 152.6041 Evaluate side-chains 384 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 295 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 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 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain H residue 11 LEU 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 27 HIS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 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 274 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 22 ASP 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 72 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 152 ILE 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 349 MET Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 143 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 17 optimal weight: 0.0040 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17196 Z= 0.171 Angle : 0.666 13.642 23304 Z= 0.345 Chirality : 0.047 0.606 2641 Planarity : 0.005 0.052 2942 Dihedral : 7.933 82.974 2512 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.25 % Favored : 90.62 % Rotamer: Outliers : 3.06 % Allowed : 23.12 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2174 helix: 0.45 (0.26), residues: 459 sheet: 0.55 (0.20), residues: 677 loop : -2.58 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 33 HIS 0.010 0.001 HIS A 288 PHE 0.022 0.001 PHE F 42 TYR 0.010 0.001 TYR C 61 ARG 0.012 0.001 ARG B 283 ********************** 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 372 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 317 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6486 (mmm) cc_final: 0.6280 (mmm) REVERT: A 316 LYS cc_start: 0.6418 (tttt) cc_final: 0.5761 (tttt) REVERT: D 25 TYR cc_start: 0.5735 (OUTLIER) cc_final: 0.4667 (p90) REVERT: H 94 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6463 (ttp-170) REVERT: B 316 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7543 (mtpt) REVERT: B 317 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7938 (pt) REVERT: C 125 MET cc_start: 0.7085 (tpp) cc_final: 0.6527 (tpp) REVERT: C 175 ARG cc_start: 0.5676 (ptt-90) cc_final: 0.4637 (ptp90) REVERT: C 473 MET cc_start: 0.6826 (tpp) cc_final: 0.6349 (tpt) outliers start: 55 outliers final: 43 residues processed: 351 average time/residue: 0.3052 time to fit residues: 164.2067 Evaluate side-chains 343 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 298 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 158 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 72 optimal weight: 40.0000 chunk 177 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 151 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 465 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.185900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125020 restraints weight = 20216.219| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.21 r_work: 0.3215 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17196 Z= 0.305 Angle : 0.739 15.000 23304 Z= 0.377 Chirality : 0.048 0.597 2641 Planarity : 0.005 0.052 2942 Dihedral : 7.802 81.364 2512 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.63 % Favored : 89.24 % Rotamer: Outliers : 3.06 % Allowed : 23.90 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.18), residues: 2174 helix: 0.32 (0.25), residues: 459 sheet: 0.43 (0.20), residues: 685 loop : -2.54 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 400 HIS 0.007 0.001 HIS A 288 PHE 0.020 0.002 PHE B 245 TYR 0.016 0.002 TYR h 100N ARG 0.011 0.001 ARG B 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3917.68 seconds wall clock time: 72 minutes 34.19 seconds (4354.19 seconds total)