Starting phenix.real_space_refine on Sun Jun 29 20:17:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tra_26084/06_2025/7tra_26084.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tra_26084/06_2025/7tra_26084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tra_26084/06_2025/7tra_26084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tra_26084/06_2025/7tra_26084.map" model { file = "/net/cci-nas-00/data/ceres_data/7tra_26084/06_2025/7tra_26084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tra_26084/06_2025/7tra_26084.cif" } resolution = 3.3 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= -0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ni 2 6.56 5 P 112 5.49 5 S 80 5.16 5 C 21961 2.51 5 N 6004 2.21 5 O 6713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34872 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4315 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "H" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "Q" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1733 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 9, 'TRANS': 209} Chain: "R" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 890 Classifications: {'DNA': 25, 'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 11 Chain: "S" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 913 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "T" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 519 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 4 Chain: "E" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2494 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2134 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.89, per 1000 atoms: 0.54 Number of scatterers: 34872 At special positions: 0 Unit cell: (114.08, 147.56, 220.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 S 80 16.00 P 112 15.00 O 6713 8.00 N 6004 7.00 C 21961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 4.3 seconds 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7772 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 41 sheets defined 40.2% alpha, 9.7% beta 28 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 13.03 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 removed outlier: 3.631A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 44 through 59 removed outlier: 4.108A pdb=" N GLU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 74 through 93 Processing helix chain 'A' and resid 99 through 110 removed outlier: 4.160A pdb=" N ALA A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.667A pdb=" N THR A 120 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.814A pdb=" N ALA A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 209 removed outlier: 3.757A pdb=" N ARG A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.896A pdb=" N ILE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 297 through 304 removed outlier: 4.013A pdb=" N GLU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.814A pdb=" N ARG A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 371 through 389 removed outlier: 4.833A pdb=" N ALA A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 removed outlier: 3.875A pdb=" N GLU A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 403 " --> pdb=" O TYR A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.354A pdb=" N ARG A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 4.029A pdb=" N ALA A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 620 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 52 through 72 Processing helix chain 'B' and resid 98 through 114 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 193 through 204 removed outlier: 3.559A pdb=" N LYS B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 removed outlier: 3.512A pdb=" N ILE B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.770A pdb=" N HIS B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 removed outlier: 3.665A pdb=" N THR B 239 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 240 " --> pdb=" O LEU B 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 236 through 240' Processing helix chain 'B' and resid 265 through 278 Processing helix chain 'B' and resid 282 through 295 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 311 through 325 removed outlier: 4.235A pdb=" N PHE B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 3.980A pdb=" N VAL B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 24 through 33 removed outlier: 3.730A pdb=" N VAL C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 62 removed outlier: 3.698A pdb=" N LEU C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) Proline residue: C 52 - end of helix Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.519A pdb=" N ILE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 101 removed outlier: 3.860A pdb=" N LEU C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.707A pdb=" N ASN D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.855A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 62 removed outlier: 4.118A pdb=" N LEU D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.526A pdb=" N GLY H 22 " --> pdb=" O GLN H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 69 removed outlier: 4.191A pdb=" N LEU H 55 " --> pdb=" O THR H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 114 Processing helix chain 'H' and resid 116 through 121 Processing helix chain 'H' and resid 144 through 151 Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 227 through 248 removed outlier: 3.910A pdb=" N ILE H 243 " --> pdb=" O LEU H 239 " (cutoff:3.500A) Proline residue: H 244 - end of helix Processing helix chain 'H' and resid 286 through 298 Processing helix chain 'H' and resid 324 through 335 removed outlier: 3.926A pdb=" N MET H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 removed outlier: 3.610A pdb=" N LEU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 Processing helix chain 'I' and resid 107 through 114 removed outlier: 3.777A pdb=" N GLU I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 Processing helix chain 'I' and resid 144 through 151 Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 241 through 246 removed outlier: 4.360A pdb=" N MET I 245 " --> pdb=" O ALA I 241 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 246 " --> pdb=" O LEU I 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 241 through 246' Processing helix chain 'I' and resid 286 through 300 Processing helix chain 'I' and resid 324 through 335 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.608A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.890A pdb=" N LEU J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'J' and resid 107 through 115 Processing helix chain 'J' and resid 115 through 121 removed outlier: 3.669A pdb=" N ASP J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 152 Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 241 through 247 removed outlier: 3.735A pdb=" N MET J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 301 Processing helix chain 'J' and resid 324 through 335 removed outlier: 4.460A pdb=" N MET J 335 " --> pdb=" O ASN J 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 68 removed outlier: 3.808A pdb=" N LEU K 55 " --> pdb=" O THR K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 removed outlier: 4.129A pdb=" N ARG K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 242 through 243 No H-bonds generated for 'chain 'K' and resid 242 through 243' Processing helix chain 'K' and resid 244 through 248 removed outlier: 3.789A pdb=" N GLY K 248 " --> pdb=" O MET K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 301 Processing helix chain 'K' and resid 325 through 333 Processing helix chain 'O' and resid 30 through 46 Processing helix chain 'O' and resid 54 through 70 Processing helix chain 'O' and resid 129 through 141 removed outlier: 3.863A pdb=" N MET O 141 " --> pdb=" O LEU O 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 41 removed outlier: 5.503A pdb=" N ASN Q 27 " --> pdb=" O GLU Q 23 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) Proline residue: Q 31 - end of helix removed outlier: 3.687A pdb=" N GLY Q 41 " --> pdb=" O MET Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 59 removed outlier: 3.521A pdb=" N LEU Q 59 " --> pdb=" O THR Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 65 removed outlier: 5.921A pdb=" N GLY Q 63 " --> pdb=" O HIS Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 75 Processing helix chain 'Q' and resid 83 through 101 removed outlier: 4.287A pdb=" N VAL Q 87 " --> pdb=" O ARG Q 83 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET Q 99 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS Q 101 " --> pdb=" O LYS Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 115 removed outlier: 3.544A pdb=" N ALA Q 106 " --> pdb=" O ASP Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 128 Processing helix chain 'Q' and resid 134 through 140 removed outlier: 3.808A pdb=" N VAL Q 138 " --> pdb=" O THR Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 164 removed outlier: 3.501A pdb=" N GLU Q 153 " --> pdb=" O MET Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 191 removed outlier: 3.735A pdb=" N VAL Q 178 " --> pdb=" O THR Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 211 Proline residue: Q 208 - end of helix Processing helix chain 'Q' and resid 215 through 220 removed outlier: 3.805A pdb=" N ALA Q 219 " --> pdb=" O GLY Q 215 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA Q 220 " --> pdb=" O ALA Q 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 215 through 220' Processing helix chain 'E' and resid 5 through 16 removed outlier: 3.507A pdb=" N LEU E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 33 Processing helix chain 'E' and resid 39 through 61 Proline residue: E 52 - end of helix Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 86 through 100 removed outlier: 3.573A pdb=" N LEU E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 25 through 33 Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.732A pdb=" N LEU F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 59 removed outlier: 3.681A pdb=" N LEU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 removed outlier: 4.568A pdb=" N GLN F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 removed outlier: 3.800A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 14 removed outlier: 4.471A pdb=" N ILE G 8 " --> pdb=" O TRP G 4 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 33 removed outlier: 3.894A pdb=" N ASP G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 3.726A pdb=" N LEU G 40 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 62 Processing helix chain 'G' and resid 70 through 82 removed outlier: 4.252A pdb=" N ILE G 74 " --> pdb=" O SER G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 100 removed outlier: 4.159A pdb=" N LEU G 90 " --> pdb=" O ASN G 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 68 removed outlier: 3.746A pdb=" N LYS L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 76 removed outlier: 3.874A pdb=" N ASN L 75 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 82 removed outlier: 3.671A pdb=" N ARG L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 115 through 122 Processing helix chain 'L' and resid 144 through 152 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 241 through 248 removed outlier: 3.800A pdb=" N MET L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 298 removed outlier: 4.081A pdb=" N ARG L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 301 No H-bonds generated for 'chain 'L' and resid 299 through 301' Processing helix chain 'L' and resid 325 through 334 Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.736A pdb=" N LYS M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 Processing helix chain 'M' and resid 108 through 114 Processing helix chain 'M' and resid 115 through 122 Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 153 through 157 removed outlier: 3.973A pdb=" N ILE M 157 " --> pdb=" O GLU M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 247 Processing helix chain 'M' and resid 286 through 301 removed outlier: 3.682A pdb=" N GLY M 301 " --> pdb=" O ALA M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 336 Processing helix chain 'N' and resid 51 through 69 removed outlier: 3.527A pdb=" N LEU N 55 " --> pdb=" O THR N 51 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 3.899A pdb=" N ARG N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'N' and resid 116 through 121 Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.608A pdb=" N ILE N 148 " --> pdb=" O THR N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 205 No H-bonds generated for 'chain 'N' and resid 203 through 205' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 242 through 247 Processing helix chain 'N' and resid 285 through 301 removed outlier: 3.985A pdb=" N ALA N 289 " --> pdb=" O ASP N 285 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY N 301 " --> pdb=" O ALA N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 336 removed outlier: 3.709A pdb=" N VAL N 336 " --> pdb=" O LEU N 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.791A pdb=" N TYR A 70 " --> pdb=" O VAL A 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 235 removed outlier: 7.466A pdb=" N ARG A 234 " --> pdb=" O ILE A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 175 removed outlier: 4.412A pdb=" N SER B 261 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU B 251 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 259 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 14 current: chain 'H' and resid 182 through 201 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 182 through 201 current: chain 'H' and resid 304 through 309 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 32 through 37 Processing sheet with id=AB1, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=AB2, first strand: chain 'H' and resid 123 through 125 removed outlier: 6.715A pdb=" N PHE H 123 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG H 131 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA H 125 " --> pdb=" O GLY H 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 14 current: chain 'I' and resid 185 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 185 through 201 current: chain 'I' and resid 305 through 309 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 31 through 33 Processing sheet with id=AB5, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AB6, first strand: chain 'I' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'J' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 2 through 14 current: chain 'J' and resid 186 through 201 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 186 through 201 current: chain 'J' and resid 305 through 309 Processing sheet with id=AB8, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AB9, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AC1, first strand: chain 'J' and resid 123 through 124 removed outlier: 3.589A pdb=" N PHE J 123 " --> pdb=" O ARG J 132 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG J 132 " --> pdb=" O PHE J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 26 through 29 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 26 through 29 current: chain 'K' and resid 183 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 183 through 201 current: chain 'K' and resid 305 through 309 removed outlier: 6.772A pdb=" N VAL K 306 " --> pdb=" O THR K 320 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL K 322 " --> pdb=" O VAL K 306 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR K 308 " --> pdb=" O VAL K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AC4, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AC5, first strand: chain 'K' and resid 123 through 125 Processing sheet with id=AC6, first strand: chain 'O' and resid 77 through 80 removed outlier: 3.534A pdb=" N LEU O 119 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE O 3 " --> pdb=" O PHE O 160 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE O 160 " --> pdb=" O ILE O 3 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU O 5 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA O 158 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N CYS O 7 " --> pdb=" O VAL O 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 113 through 115 Processing sheet with id=AC8, first strand: chain 'O' and resid 90 through 94 Processing sheet with id=AC9, first strand: chain 'O' and resid 168 through 169 removed outlier: 3.621A pdb=" N ALA O 168 " --> pdb=" O VAL O 240 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL O 240 " --> pdb=" O ALA O 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'O' and resid 174 through 175 Processing sheet with id=AD2, first strand: chain 'O' and resid 244 through 246 Processing sheet with id=AD3, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 306 through 309 Processing sheet with id=AD4, first strand: chain 'L' and resid 26 through 27 removed outlier: 3.501A pdb=" N ILE L 160 " --> pdb=" O ARG L 187 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AD6, first strand: chain 'L' and resid 95 through 96 Processing sheet with id=AD7, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 185 through 201 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 185 through 201 current: chain 'M' and resid 305 through 309 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AE1, first strand: chain 'M' and resid 123 through 124 Processing sheet with id=AE2, first strand: chain 'N' and resid 2 through 10 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 10 current: chain 'N' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 193 through 201 current: chain 'N' and resid 305 through 309 removed outlier: 6.707A pdb=" N VAL N 306 " --> pdb=" O THR N 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'N' and resid 32 through 35 Processing sheet with id=AE4, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AE5, first strand: chain 'N' and resid 123 through 125 1124 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 12.59 Time building geometry restraints manager: 11.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10779 1.34 - 1.46: 6238 1.46 - 1.58: 18407 1.58 - 1.70: 219 1.70 - 1.82: 144 Bond restraints: 35787 Sorted by residual: bond pdb=" CB PRO Q 119 " pdb=" CG PRO Q 119 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.40e+00 bond pdb=" N ALA A 611 " pdb=" CA ALA A 611 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.32e-02 5.74e+03 2.93e+00 bond pdb=" CG PRO Q 119 " pdb=" CD PRO Q 119 " ideal model delta sigma weight residual 1.503 1.546 -0.043 3.40e-02 8.65e+02 1.57e+00 bond pdb=" CG GLU G 78 " pdb=" CD GLU G 78 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.48e+00 bond pdb=" CG LEU Q 128 " pdb=" CD1 LEU Q 128 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 35782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 48091 1.97 - 3.95: 731 3.95 - 5.92: 112 5.92 - 7.90: 26 7.90 - 9.87: 6 Bond angle restraints: 48966 Sorted by residual: angle pdb=" CA PRO Q 119 " pdb=" N PRO Q 119 " pdb=" CD PRO Q 119 " ideal model delta sigma weight residual 112.00 105.16 6.84 1.40e+00 5.10e-01 2.38e+01 angle pdb=" N GLU G 78 " pdb=" CA GLU G 78 " pdb=" CB GLU G 78 " ideal model delta sigma weight residual 110.07 116.21 -6.14 1.45e+00 4.76e-01 1.79e+01 angle pdb=" N ILE C 5 " pdb=" CA ILE C 5 " pdb=" C ILE C 5 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.59e+01 angle pdb=" C LEU G 77 " pdb=" N GLU G 78 " pdb=" CA GLU G 78 " ideal model delta sigma weight residual 120.44 115.43 5.01 1.36e+00 5.41e-01 1.36e+01 angle pdb=" C LEU N 242 " pdb=" N ILE N 243 " pdb=" CA ILE N 243 " ideal model delta sigma weight residual 120.33 123.09 -2.76 8.00e-01 1.56e+00 1.19e+01 ... (remaining 48961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20845 35.99 - 71.98: 571 71.98 - 107.98: 22 107.98 - 143.97: 1 143.97 - 179.96: 5 Dihedral angle restraints: 21444 sinusoidal: 9361 harmonic: 12083 Sorted by residual: dihedral pdb=" CB CYS F 63 " pdb=" SG CYS F 63 " pdb=" SG CYS F 108 " pdb=" CB CYS F 108 " ideal model delta sinusoidal sigma weight residual 93.00 -177.29 -89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" O4' U R 3 " pdb=" C1' U R 3 " pdb=" N1 U R 3 " pdb=" C2 U R 3 " ideal model delta sinusoidal sigma weight residual 200.00 42.74 157.26 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" CA THR Q 134 " pdb=" C THR Q 134 " pdb=" N PRO Q 135 " pdb=" CA PRO Q 135 " ideal model delta harmonic sigma weight residual 180.00 -142.02 -37.98 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 21441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4369 0.049 - 0.097: 988 0.097 - 0.146: 230 0.146 - 0.194: 10 0.194 - 0.243: 5 Chirality restraints: 5602 Sorted by residual: chirality pdb=" C3' U R 27 " pdb=" C4' U R 27 " pdb=" O3' U R 27 " pdb=" C2' U R 27 " both_signs ideal model delta sigma weight residual False -2.50 -2.26 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C1' U R 31 " pdb=" O4' U R 31 " pdb=" C2' U R 31 " pdb=" N1 U R 31 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO Q 119 " pdb=" N PRO Q 119 " pdb=" C PRO Q 119 " pdb=" CB PRO Q 119 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 5599 not shown) Planarity restraints: 5877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 610 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C LEU A 610 " -0.071 2.00e-02 2.50e+03 pdb=" O LEU A 610 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA A 611 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 100 " 0.026 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP F 100 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP F 100 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP F 100 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 100 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 100 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 100 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 100 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 100 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 100 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 118 " 0.063 5.00e-02 4.00e+02 9.17e-02 1.35e+01 pdb=" N PRO Q 119 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Q 119 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 119 " 0.051 5.00e-02 4.00e+02 ... (remaining 5874 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 456 2.59 - 3.17: 31064 3.17 - 3.75: 59812 3.75 - 4.32: 80362 4.32 - 4.90: 129441 Nonbonded interactions: 301135 Sorted by model distance: nonbonded pdb=" OD1 ASP Q 61 " pdb="NI NI Q 301 " model vdw 2.017 2.180 nonbonded pdb=" OH TYR E 11 " pdb=" O ALA E 47 " model vdw 2.129 3.040 nonbonded pdb=" OG SER A 203 " pdb=" OE2 GLU A 398 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASP A 219 " pdb=" N LYS A 220 " model vdw 2.138 3.120 nonbonded pdb=" O LEU A 77 " pdb=" NE2 GLN A 81 " model vdw 2.159 3.120 ... (remaining 301130 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 'C' selection = (chain 'D' and resid 3 through 109) selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 164 or resid 180 th \ rough 335)) selection = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 164 or resid 180 through 335)) selection = (chain 'J' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'K' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'L' and (resid 1 through 164 or resid 180 through 335)) selection = (chain 'M' and resid 1 through 335) } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.180 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 83.690 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.180 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:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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 : 0.003 0.092 35793 Z= 0.118 Angle : 0.605 9.873 48978 Z= 0.310 Chirality : 0.043 0.243 5602 Planarity : 0.004 0.092 5877 Dihedral : 15.665 179.961 13654 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.63 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.17 (0.13), residues: 4126 helix: 0.62 (0.14), residues: 1501 sheet: -0.58 (0.22), residues: 559 loop : -1.95 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.001 TRP F 100 HIS 0.005 0.001 HIS A 406 PHE 0.028 0.001 PHE I 67 TYR 0.034 0.001 TYR Q 90 ARG 0.007 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.14947 ( 1193) hydrogen bonds : angle 5.91466 ( 3360) SS BOND : bond 0.00108 ( 6) SS BOND : angle 0.49756 ( 12) covalent geometry : bond 0.00252 (35787) covalent geometry : angle 0.60499 (48966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 3.431 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 71 VAL cc_start: 0.7784 (m) cc_final: 0.7495 (p) REVERT: A 83 GLU cc_start: 0.8774 (tp30) cc_final: 0.8337 (tp30) REVERT: A 212 ASP cc_start: 0.7583 (p0) cc_final: 0.6901 (t0) REVERT: B 199 SER cc_start: 0.9344 (m) cc_final: 0.8977 (p) REVERT: C 89 ASP cc_start: 0.7566 (m-30) cc_final: 0.7343 (m-30) REVERT: D 25 TYR cc_start: 0.8788 (m-80) cc_final: 0.8241 (m-80) REVERT: D 26 ASP cc_start: 0.8125 (p0) cc_final: 0.7890 (p0) REVERT: J 1 MET cc_start: 0.6636 (mmt) cc_final: 0.6397 (mmt) REVERT: O 10 PHE cc_start: 0.8542 (p90) cc_final: 0.7633 (p90) REVERT: O 141 MET cc_start: 0.7653 (mpp) cc_final: 0.7097 (mpp) REVERT: Q 27 ASN cc_start: 0.8712 (t0) cc_final: 0.8511 (t0) REVERT: E 70 SER cc_start: 0.8643 (p) cc_final: 0.8358 (p) REVERT: F 38 GLU cc_start: 0.6434 (mt-10) cc_final: 0.5771 (pt0) REVERT: G 56 LYS cc_start: 0.8505 (ptmm) cc_final: 0.7669 (tptt) REVERT: L 182 GLN cc_start: 0.7742 (tt0) cc_final: 0.7491 (tm-30) REVERT: M 61 VAL cc_start: 0.8401 (t) cc_final: 0.7600 (t) REVERT: M 142 LEU cc_start: 0.7661 (mp) cc_final: 0.7409 (mp) REVERT: M 194 TYR cc_start: 0.7221 (m-80) cc_final: 0.6866 (m-80) REVERT: M 199 VAL cc_start: 0.7223 (t) cc_final: 0.6936 (t) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.4158 time to fit residues: 446.4085 Evaluate side-chains 479 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 0.8980 chunk 317 optimal weight: 8.9990 chunk 176 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 328 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 380 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 397 ASN A 406 HIS B 228 HIS H 17 ASN H 90 GLN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 290 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.123134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.102070 restraints weight = 106494.298| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.88 r_work: 0.3775 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35793 Z= 0.154 Angle : 0.629 11.769 48978 Z= 0.320 Chirality : 0.045 0.324 5602 Planarity : 0.004 0.048 5877 Dihedral : 15.623 179.952 5897 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.56 % Favored : 92.20 % Rotamer: Outliers : 1.22 % Allowed : 11.01 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.11 (0.13), residues: 4126 helix: 0.58 (0.14), residues: 1546 sheet: -0.55 (0.22), residues: 595 loop : -1.90 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 100 HIS 0.009 0.001 HIS A 406 PHE 0.016 0.002 PHE I 63 TYR 0.039 0.002 TYR A 399 ARG 0.007 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 1193) hydrogen bonds : angle 4.53266 ( 3360) SS BOND : bond 0.00163 ( 6) SS BOND : angle 0.47034 ( 12) covalent geometry : bond 0.00348 (35787) covalent geometry : angle 0.62922 (48966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 527 time to evaluate : 3.745 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 83 GLU cc_start: 0.8957 (tp30) cc_final: 0.8538 (tp30) REVERT: A 108 ARG cc_start: 0.6927 (tpt90) cc_final: 0.5832 (tpm170) REVERT: A 208 MET cc_start: 0.6805 (ppp) cc_final: 0.6001 (ppp) REVERT: A 212 ASP cc_start: 0.8036 (p0) cc_final: 0.7392 (t0) REVERT: B 185 GLN cc_start: 0.7715 (tt0) cc_final: 0.7316 (tt0) REVERT: B 200 LEU cc_start: 0.9359 (mt) cc_final: 0.9151 (mt) REVERT: C 89 ASP cc_start: 0.8212 (m-30) cc_final: 0.7960 (m-30) REVERT: D 25 TYR cc_start: 0.8955 (m-80) cc_final: 0.8579 (m-80) REVERT: D 26 ASP cc_start: 0.8605 (p0) cc_final: 0.8336 (p0) REVERT: D 75 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7862 (mt-10) REVERT: J 88 PHE cc_start: 0.6764 (m-80) cc_final: 0.6560 (m-80) REVERT: K 1 MET cc_start: 0.8466 (ppp) cc_final: 0.8123 (ppp) REVERT: K 83 TYR cc_start: 0.8563 (m-10) cc_final: 0.8304 (m-10) REVERT: O 5 LEU cc_start: 0.8765 (tp) cc_final: 0.8409 (tt) REVERT: O 141 MET cc_start: 0.8235 (mpp) cc_final: 0.7561 (mpp) REVERT: O 226 TYR cc_start: 0.7234 (t80) cc_final: 0.7027 (t80) REVERT: Q 10 THR cc_start: 0.8396 (m) cc_final: 0.7882 (p) REVERT: Q 179 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8069 (mt) REVERT: E 70 SER cc_start: 0.9015 (p) cc_final: 0.8620 (p) REVERT: F 18 ASP cc_start: 0.8516 (t0) cc_final: 0.8244 (m-30) REVERT: G 56 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8142 (ptmm) REVERT: L 65 ASP cc_start: 0.8344 (t0) cc_final: 0.8138 (t0) REVERT: L 66 TYR cc_start: 0.8361 (m-80) cc_final: 0.8050 (m-80) REVERT: L 236 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7699 (tm-30) REVERT: M 83 TYR cc_start: 0.7506 (m-10) cc_final: 0.7153 (m-10) REVERT: M 152 GLU cc_start: 0.8313 (mp0) cc_final: 0.7826 (mp0) REVERT: M 183 MET cc_start: 0.6112 (ppp) cc_final: 0.5816 (tmm) REVERT: M 194 TYR cc_start: 0.7710 (m-80) cc_final: 0.7286 (m-80) REVERT: M 245 MET cc_start: 0.8245 (mmp) cc_final: 0.7722 (mmp) outliers start: 42 outliers final: 27 residues processed: 552 average time/residue: 0.4313 time to fit residues: 405.5726 Evaluate side-chains 502 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 474 time to evaluate : 4.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 278 LEU Chi-restraints excluded: chain N residue 279 VAL Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 315 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 140 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 372 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 HIS Q 191 HIS ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.118488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.096647 restraints weight = 105207.893| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.82 r_work: 0.3686 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35793 Z= 0.166 Angle : 0.628 11.536 48978 Z= 0.320 Chirality : 0.045 0.349 5602 Planarity : 0.004 0.049 5877 Dihedral : 15.616 179.531 5897 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.68 % Favored : 92.10 % Rotamer: Outliers : 1.95 % Allowed : 14.74 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.17 (0.13), residues: 4126 helix: 0.47 (0.14), residues: 1537 sheet: -0.64 (0.21), residues: 633 loop : -1.88 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 100 HIS 0.010 0.001 HIS Q 191 PHE 0.019 0.002 PHE B 54 TYR 0.026 0.002 TYR F 45 ARG 0.008 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 1193) hydrogen bonds : angle 4.41567 ( 3360) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.51074 ( 12) covalent geometry : bond 0.00372 (35787) covalent geometry : angle 0.62753 (48966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 521 time to evaluate : 3.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7391 (mm-40) REVERT: A 126 TRP cc_start: 0.7953 (m-10) cc_final: 0.7750 (m-10) REVERT: A 212 ASP cc_start: 0.8055 (p0) cc_final: 0.7367 (t0) REVERT: B 185 GLN cc_start: 0.7917 (tt0) cc_final: 0.7559 (tt0) REVERT: B 200 LEU cc_start: 0.9340 (mt) cc_final: 0.9092 (mt) REVERT: B 219 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8296 (tp) REVERT: D 25 TYR cc_start: 0.8994 (m-80) cc_final: 0.8609 (m-80) REVERT: D 26 ASP cc_start: 0.8631 (p0) cc_final: 0.8351 (p0) REVERT: D 70 SER cc_start: 0.8422 (t) cc_final: 0.8212 (t) REVERT: H 54 MET cc_start: 0.7863 (mmp) cc_final: 0.7626 (mmp) REVERT: H 119 ASP cc_start: 0.6951 (m-30) cc_final: 0.6431 (m-30) REVERT: J 26 TYR cc_start: 0.8983 (t80) cc_final: 0.8451 (t80) REVERT: J 194 TYR cc_start: 0.8128 (m-80) cc_final: 0.7548 (m-80) REVERT: K 1 MET cc_start: 0.8519 (ppp) cc_final: 0.8100 (ppp) REVERT: K 198 ILE cc_start: 0.8764 (mm) cc_final: 0.8563 (mm) REVERT: K 265 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5846 (mm-30) REVERT: O 5 LEU cc_start: 0.8878 (tp) cc_final: 0.8586 (tt) REVERT: O 141 MET cc_start: 0.8233 (mpp) cc_final: 0.7507 (mpp) REVERT: Q 105 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8430 (mt) REVERT: Q 139 LEU cc_start: 0.6341 (tp) cc_final: 0.6062 (tt) REVERT: Q 179 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8128 (mt) REVERT: E 70 SER cc_start: 0.9021 (p) cc_final: 0.8576 (p) REVERT: F 18 ASP cc_start: 0.8614 (t0) cc_final: 0.8392 (m-30) REVERT: F 38 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6585 (pt0) REVERT: G 56 LYS cc_start: 0.8477 (ptmm) cc_final: 0.7951 (tptt) REVERT: G 75 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8529 (mt-10) REVERT: L 15 SER cc_start: 0.8434 (t) cc_final: 0.8142 (t) REVERT: L 54 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8662 (tmm) REVERT: L 65 ASP cc_start: 0.8510 (t0) cc_final: 0.8209 (t0) REVERT: L 66 TYR cc_start: 0.8590 (m-10) cc_final: 0.8300 (m-80) REVERT: L 81 LEU cc_start: 0.9222 (mt) cc_final: 0.9022 (mt) REVERT: L 303 ASN cc_start: 0.7512 (p0) cc_final: 0.7157 (t0) REVERT: M 83 TYR cc_start: 0.7770 (m-10) cc_final: 0.7399 (m-10) REVERT: M 152 GLU cc_start: 0.8414 (mp0) cc_final: 0.8041 (mp0) REVERT: M 183 MET cc_start: 0.6112 (ppp) cc_final: 0.5444 (ttm) REVERT: M 189 TYR cc_start: 0.5511 (m-10) cc_final: 0.5036 (m-10) REVERT: M 194 TYR cc_start: 0.7827 (m-80) cc_final: 0.6983 (m-80) REVERT: M 245 MET cc_start: 0.8314 (mmp) cc_final: 0.8023 (mmp) outliers start: 67 outliers final: 45 residues processed: 555 average time/residue: 0.4214 time to fit residues: 391.9984 Evaluate side-chains 511 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 461 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 265 GLU Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 249 TYR Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 LEU Chi-restraints excluded: chain N residue 279 VAL Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 287 ILE Chi-restraints excluded: chain N residue 315 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 326 optimal weight: 4.9990 chunk 374 optimal weight: 0.6980 chunk 395 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 383 optimal weight: 0.0470 chunk 274 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 0.0030 overall best weight: 0.9490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS B 256 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 HIS ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.117865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.095907 restraints weight = 105267.598| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.81 r_work: 0.3662 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35793 Z= 0.142 Angle : 0.618 12.174 48978 Z= 0.313 Chirality : 0.044 0.353 5602 Planarity : 0.004 0.046 5877 Dihedral : 15.562 179.028 5897 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.66 % Favored : 92.12 % Rotamer: Outliers : 1.86 % Allowed : 17.22 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.24 (0.13), residues: 4126 helix: 0.38 (0.13), residues: 1564 sheet: -0.69 (0.21), residues: 634 loop : -1.91 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 22 HIS 0.008 0.001 HIS Q 191 PHE 0.027 0.002 PHE L 140 TYR 0.025 0.001 TYR F 45 ARG 0.006 0.000 ARG L 187 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 1193) hydrogen bonds : angle 4.34465 ( 3360) SS BOND : bond 0.00255 ( 6) SS BOND : angle 2.96610 ( 12) covalent geometry : bond 0.00323 (35787) covalent geometry : angle 0.61676 (48966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 505 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8121 (p0) cc_final: 0.7415 (t0) REVERT: B 185 GLN cc_start: 0.7963 (tt0) cc_final: 0.7539 (tt0) REVERT: B 205 MET cc_start: 0.7768 (tpt) cc_final: 0.7190 (mmm) REVERT: C 89 ASP cc_start: 0.8302 (m-30) cc_final: 0.8083 (m-30) REVERT: D 25 TYR cc_start: 0.8995 (m-80) cc_final: 0.8619 (m-80) REVERT: D 26 ASP cc_start: 0.8557 (p0) cc_final: 0.8339 (p0) REVERT: H 31 LYS cc_start: 0.7340 (mtmm) cc_final: 0.6873 (mttt) REVERT: H 119 ASP cc_start: 0.6980 (m-30) cc_final: 0.6485 (m-30) REVERT: H 146 ASP cc_start: 0.8455 (p0) cc_final: 0.8219 (p0) REVERT: I 83 TYR cc_start: 0.8171 (m-10) cc_final: 0.7885 (m-10) REVERT: I 106 ASN cc_start: 0.8547 (m-40) cc_final: 0.8200 (p0) REVERT: I 194 TYR cc_start: 0.7587 (m-80) cc_final: 0.7126 (m-80) REVERT: J 17 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8303 (m110) REVERT: J 54 MET cc_start: 0.8206 (tpt) cc_final: 0.7901 (tpp) REVERT: K 1 MET cc_start: 0.8567 (ppp) cc_final: 0.8126 (ppp) REVERT: K 83 TYR cc_start: 0.8766 (m-10) cc_final: 0.8508 (m-10) REVERT: K 117 ASP cc_start: 0.7203 (t0) cc_final: 0.6978 (t0) REVERT: O 5 LEU cc_start: 0.8936 (tp) cc_final: 0.8664 (tt) REVERT: O 121 VAL cc_start: 0.8893 (t) cc_final: 0.8669 (t) REVERT: O 141 MET cc_start: 0.8206 (mpp) cc_final: 0.7450 (mpp) REVERT: Q 139 LEU cc_start: 0.6526 (tp) cc_final: 0.6206 (tt) REVERT: Q 179 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8023 (mt) REVERT: F 18 ASP cc_start: 0.8599 (t0) cc_final: 0.8356 (m-30) REVERT: F 59 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: F 70 SER cc_start: 0.7914 (t) cc_final: 0.7696 (t) REVERT: G 21 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7710 (tp30) REVERT: G 75 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8165 (tm-30) REVERT: G 79 GLU cc_start: 0.9045 (pp20) cc_final: 0.8626 (pp20) REVERT: L 15 SER cc_start: 0.8534 (t) cc_final: 0.8261 (t) REVERT: L 54 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8630 (tmm) REVERT: L 66 TYR cc_start: 0.8587 (m-10) cc_final: 0.8378 (m-80) REVERT: L 81 LEU cc_start: 0.9250 (mt) cc_final: 0.9036 (mt) REVERT: L 194 TYR cc_start: 0.8445 (m-80) cc_final: 0.8209 (m-80) REVERT: L 303 ASN cc_start: 0.7523 (p0) cc_final: 0.7216 (t0) REVERT: M 83 TYR cc_start: 0.7669 (m-10) cc_final: 0.7270 (m-10) REVERT: M 131 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8436 (ptm-80) REVERT: M 152 GLU cc_start: 0.8409 (mp0) cc_final: 0.8055 (mp0) REVERT: M 189 TYR cc_start: 0.5567 (m-10) cc_final: 0.5358 (m-10) REVERT: M 194 TYR cc_start: 0.7837 (m-80) cc_final: 0.6971 (m-80) REVERT: M 245 MET cc_start: 0.8280 (mmp) cc_final: 0.8058 (mmp) REVERT: N 61 VAL cc_start: 0.8484 (m) cc_final: 0.8262 (p) REVERT: N 81 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8875 (mm) outliers start: 64 outliers final: 41 residues processed: 540 average time/residue: 0.4621 time to fit residues: 420.5394 Evaluate side-chains 502 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 456 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 LEU Chi-restraints excluded: chain N residue 315 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 129 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 224 optimal weight: 0.3980 chunk 2 optimal weight: 20.0000 chunk 332 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 278 optimal weight: 9.9990 chunk 356 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS B 156 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 209 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 HIS ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.114255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.092030 restraints weight = 104681.806| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.77 r_work: 0.3599 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35793 Z= 0.167 Angle : 0.637 11.924 48978 Z= 0.323 Chirality : 0.045 0.358 5602 Planarity : 0.004 0.074 5877 Dihedral : 15.541 179.204 5897 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.76 % Favored : 92.03 % Rotamer: Outliers : 2.86 % Allowed : 18.15 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.28 (0.13), residues: 4126 helix: 0.31 (0.13), residues: 1587 sheet: -0.64 (0.21), residues: 634 loop : -1.95 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 22 HIS 0.011 0.001 HIS Q 116 PHE 0.025 0.002 PHE I 140 TYR 0.031 0.001 TYR F 45 ARG 0.005 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1193) hydrogen bonds : angle 4.41372 ( 3360) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.79246 ( 12) covalent geometry : bond 0.00377 (35787) covalent geometry : angle 0.63666 (48966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 500 time to evaluate : 3.741 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 30 MET cc_start: 0.7810 (tpp) cc_final: 0.7601 (tpp) REVERT: A 407 TYR cc_start: 0.6652 (m-10) cc_final: 0.6410 (m-10) REVERT: B 56 HIS cc_start: 0.7729 (m-70) cc_final: 0.7424 (t70) REVERT: B 205 MET cc_start: 0.7873 (tpt) cc_final: 0.7342 (mmm) REVERT: B 219 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8513 (tp) REVERT: D 25 TYR cc_start: 0.9049 (m-80) cc_final: 0.8611 (m-80) REVERT: H 119 ASP cc_start: 0.7248 (m-30) cc_final: 0.6719 (m-30) REVERT: H 146 ASP cc_start: 0.8525 (p0) cc_final: 0.8180 (p0) REVERT: H 284 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: I 51 THR cc_start: 0.8690 (p) cc_final: 0.8471 (p) REVERT: I 83 TYR cc_start: 0.8177 (m-10) cc_final: 0.7921 (m-10) REVERT: I 194 TYR cc_start: 0.7859 (m-80) cc_final: 0.7390 (m-80) REVERT: I 303 ASN cc_start: 0.7128 (p0) cc_final: 0.6851 (p0) REVERT: J 54 MET cc_start: 0.8391 (tpt) cc_final: 0.8054 (tpp) REVERT: K 1 MET cc_start: 0.8540 (ppp) cc_final: 0.8070 (ppp) REVERT: K 265 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6018 (mm-30) REVERT: O 1 MET cc_start: 0.6344 (tpt) cc_final: 0.5691 (tpp) REVERT: O 5 LEU cc_start: 0.9028 (tp) cc_final: 0.8790 (tt) REVERT: O 56 ASP cc_start: 0.7533 (m-30) cc_final: 0.7300 (m-30) REVERT: O 99 SER cc_start: 0.8575 (m) cc_final: 0.8308 (p) REVERT: O 121 VAL cc_start: 0.8977 (t) cc_final: 0.8774 (t) REVERT: O 141 MET cc_start: 0.8314 (mpp) cc_final: 0.7508 (mpp) REVERT: O 195 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7196 (ptp) REVERT: Q 12 ARG cc_start: 0.8575 (tpt90) cc_final: 0.8090 (tpt90) REVERT: Q 18 MET cc_start: 0.8897 (mmt) cc_final: 0.8431 (mmt) REVERT: Q 101 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8570 (mmmt) REVERT: Q 139 LEU cc_start: 0.6753 (tp) cc_final: 0.6445 (tt) REVERT: Q 179 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8119 (mt) REVERT: Q 184 ARG cc_start: 0.8583 (tmm-80) cc_final: 0.8340 (tmm-80) REVERT: F 38 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6680 (pt0) REVERT: F 59 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: G 21 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7646 (tp30) REVERT: G 25 TYR cc_start: 0.8753 (m-10) cc_final: 0.8498 (m-10) REVERT: G 56 LYS cc_start: 0.8653 (tmmt) cc_final: 0.8350 (tptt) REVERT: L 15 SER cc_start: 0.8609 (t) cc_final: 0.8337 (t) REVERT: L 81 LEU cc_start: 0.9335 (mt) cc_final: 0.9045 (mt) REVERT: L 194 TYR cc_start: 0.8487 (m-80) cc_final: 0.8270 (m-80) REVERT: L 249 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7089 (m-10) REVERT: L 303 ASN cc_start: 0.7461 (p0) cc_final: 0.7105 (t0) REVERT: M 83 TYR cc_start: 0.7823 (m-10) cc_final: 0.7433 (m-10) REVERT: M 131 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8480 (ptm-80) REVERT: M 152 GLU cc_start: 0.8409 (mp0) cc_final: 0.8058 (mp0) REVERT: M 194 TYR cc_start: 0.7851 (m-80) cc_final: 0.7180 (m-80) REVERT: M 211 LEU cc_start: 0.8033 (mt) cc_final: 0.7773 (pp) outliers start: 98 outliers final: 68 residues processed: 564 average time/residue: 0.4659 time to fit residues: 435.2428 Evaluate side-chains 537 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 462 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 284 GLU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 265 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 286 TYR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 195 MET Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 HIS Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 249 TYR Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 308 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 LEU Chi-restraints excluded: chain N residue 279 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 193 optimal weight: 10.0000 chunk 344 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 chunk 375 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 376 optimal weight: 6.9990 chunk 170 optimal weight: 0.3980 chunk 230 optimal weight: 0.0370 chunk 53 optimal weight: 0.1980 chunk 302 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 104 GLN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 HIS ** O 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 ASN M 14 HIS ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.116484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.094394 restraints weight = 104084.700| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.78 r_work: 0.3647 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35793 Z= 0.125 Angle : 0.633 14.545 48978 Z= 0.315 Chirality : 0.044 0.342 5602 Planarity : 0.004 0.054 5877 Dihedral : 15.523 177.922 5897 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.51 % Favored : 92.27 % Rotamer: Outliers : 2.51 % Allowed : 19.84 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.27 (0.13), residues: 4126 helix: 0.35 (0.13), residues: 1572 sheet: -0.73 (0.20), residues: 651 loop : -1.93 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 22 HIS 0.010 0.001 HIS Q 191 PHE 0.022 0.001 PHE I 140 TYR 0.026 0.001 TYR F 45 ARG 0.006 0.000 ARG O 110 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 1193) hydrogen bonds : angle 4.36988 ( 3360) SS BOND : bond 0.00164 ( 6) SS BOND : angle 1.86284 ( 12) covalent geometry : bond 0.00281 (35787) covalent geometry : angle 0.63210 (48966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 484 time to evaluate : 3.699 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 81 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7266 (mm-40) REVERT: A 212 ASP cc_start: 0.8123 (p0) cc_final: 0.7456 (t0) REVERT: A 407 TYR cc_start: 0.6816 (m-10) cc_final: 0.6564 (m-10) REVERT: B 58 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7178 (tt) REVERT: B 131 MET cc_start: 0.7874 (tpp) cc_final: 0.7480 (tpp) REVERT: B 205 MET cc_start: 0.7860 (tpt) cc_final: 0.7394 (mmm) REVERT: B 219 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8409 (tp) REVERT: C 100 TRP cc_start: 0.8334 (m100) cc_final: 0.8087 (m100) REVERT: D 13 SER cc_start: 0.7872 (m) cc_final: 0.7491 (p) REVERT: D 25 TYR cc_start: 0.9006 (m-80) cc_final: 0.8626 (m-80) REVERT: D 26 ASP cc_start: 0.8745 (p0) cc_final: 0.8452 (p0) REVERT: H 31 LYS cc_start: 0.7553 (mtmm) cc_final: 0.6870 (mttt) REVERT: H 119 ASP cc_start: 0.7245 (m-30) cc_final: 0.6903 (m-30) REVERT: H 146 ASP cc_start: 0.8427 (p0) cc_final: 0.8212 (p0) REVERT: H 188 GLU cc_start: 0.8009 (tt0) cc_final: 0.7693 (tt0) REVERT: I 83 TYR cc_start: 0.8227 (m-10) cc_final: 0.7910 (m-10) REVERT: I 107 ASP cc_start: 0.7763 (t0) cc_final: 0.7519 (t70) REVERT: I 177 LYS cc_start: 0.8024 (pttm) cc_final: 0.7699 (ptpp) REVERT: I 194 TYR cc_start: 0.7753 (m-80) cc_final: 0.7288 (m-80) REVERT: I 303 ASN cc_start: 0.7153 (p0) cc_final: 0.6868 (p0) REVERT: J 54 MET cc_start: 0.8186 (tpt) cc_final: 0.7912 (tpp) REVERT: K 1 MET cc_start: 0.8537 (ppp) cc_final: 0.8058 (ppp) REVERT: K 15 SER cc_start: 0.8710 (p) cc_final: 0.8350 (p) REVERT: K 265 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5821 (mm-30) REVERT: O 1 MET cc_start: 0.6343 (tpt) cc_final: 0.5651 (tpp) REVERT: O 5 LEU cc_start: 0.8993 (tp) cc_final: 0.8754 (tt) REVERT: O 10 PHE cc_start: 0.8843 (p90) cc_final: 0.7817 (p90) REVERT: O 56 ASP cc_start: 0.7459 (m-30) cc_final: 0.7227 (m-30) REVERT: O 99 SER cc_start: 0.8597 (m) cc_final: 0.8289 (t) REVERT: O 141 MET cc_start: 0.8283 (mpp) cc_final: 0.7451 (mpp) REVERT: Q 18 MET cc_start: 0.8829 (mmt) cc_final: 0.8409 (mmt) REVERT: Q 101 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8658 (mmmt) REVERT: Q 140 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7595 (t0) REVERT: Q 179 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.7936 (mt) REVERT: E 38 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7256 (mm-30) REVERT: F 38 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6523 (pt0) REVERT: F 59 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: F 67 ARG cc_start: 0.8356 (mmp-170) cc_final: 0.8096 (mmp-170) REVERT: G 21 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7629 (tp30) REVERT: G 25 TYR cc_start: 0.8649 (m-80) cc_final: 0.8403 (m-10) REVERT: G 56 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8176 (tptt) REVERT: L 15 SER cc_start: 0.8501 (t) cc_final: 0.8213 (t) REVERT: L 81 LEU cc_start: 0.9267 (mt) cc_final: 0.8994 (mt) REVERT: L 303 ASN cc_start: 0.7469 (p0) cc_final: 0.7091 (t0) REVERT: M 83 TYR cc_start: 0.7568 (m-10) cc_final: 0.7141 (m-10) REVERT: M 131 ARG cc_start: 0.8894 (ttp80) cc_final: 0.8456 (ptm-80) REVERT: M 152 GLU cc_start: 0.8329 (mp0) cc_final: 0.7983 (mp0) REVERT: M 194 TYR cc_start: 0.7754 (m-80) cc_final: 0.6963 (m-80) REVERT: M 211 LEU cc_start: 0.8011 (mt) cc_final: 0.7712 (pp) outliers start: 86 outliers final: 59 residues processed: 543 average time/residue: 0.4901 time to fit residues: 451.5770 Evaluate side-chains 505 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 440 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 265 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 286 TYR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 HIS Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 117 HIS Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 138 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 290 optimal weight: 4.9990 chunk 320 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 279 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 340 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 302 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 104 GLN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 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 = 0.4159 r_free = 0.4159 target = 0.116015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.093927 restraints weight = 104952.047| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.84 r_work: 0.3651 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35793 Z= 0.127 Angle : 0.632 12.809 48978 Z= 0.315 Chirality : 0.044 0.329 5602 Planarity : 0.004 0.051 5877 Dihedral : 15.503 179.688 5897 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.49 % Favored : 92.29 % Rotamer: Outliers : 2.62 % Allowed : 20.34 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.24 (0.13), residues: 4126 helix: 0.36 (0.13), residues: 1574 sheet: -0.67 (0.21), residues: 646 loop : -1.91 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 58 HIS 0.010 0.001 HIS Q 191 PHE 0.019 0.001 PHE I 140 TYR 0.026 0.001 TYR F 45 ARG 0.005 0.000 ARG A 431 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 1193) hydrogen bonds : angle 4.34363 ( 3360) SS BOND : bond 0.00114 ( 6) SS BOND : angle 1.19344 ( 12) covalent geometry : bond 0.00288 (35787) covalent geometry : angle 0.63201 (48966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 476 time to evaluate : 3.972 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 81 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7139 (mm-40) REVERT: A 212 ASP cc_start: 0.7941 (p0) cc_final: 0.7350 (t0) REVERT: A 407 TYR cc_start: 0.6660 (m-10) cc_final: 0.6434 (m-10) REVERT: B 56 HIS cc_start: 0.7700 (m-70) cc_final: 0.7390 (t70) REVERT: B 58 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7597 (tp) REVERT: B 205 MET cc_start: 0.7810 (tpt) cc_final: 0.7432 (mmm) REVERT: B 219 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8327 (tp) REVERT: C 100 TRP cc_start: 0.8338 (m100) cc_final: 0.8063 (m100) REVERT: D 13 SER cc_start: 0.7826 (m) cc_final: 0.7330 (p) REVERT: D 25 TYR cc_start: 0.8990 (m-80) cc_final: 0.8498 (m-80) REVERT: H 31 LYS cc_start: 0.7507 (mtmm) cc_final: 0.6803 (mttt) REVERT: H 119 ASP cc_start: 0.7377 (m-30) cc_final: 0.7020 (m-30) REVERT: H 188 GLU cc_start: 0.8033 (tt0) cc_final: 0.7680 (tt0) REVERT: I 83 TYR cc_start: 0.8254 (m-10) cc_final: 0.7943 (m-10) REVERT: I 194 TYR cc_start: 0.7779 (m-80) cc_final: 0.7305 (m-80) REVERT: I 303 ASN cc_start: 0.7116 (p0) cc_final: 0.6814 (p0) REVERT: J 17 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: J 54 MET cc_start: 0.8298 (tpt) cc_final: 0.8006 (tpp) REVERT: K 1 MET cc_start: 0.8528 (ppp) cc_final: 0.8007 (ppp) REVERT: K 15 SER cc_start: 0.8724 (p) cc_final: 0.8379 (p) REVERT: K 117 ASP cc_start: 0.7440 (t0) cc_final: 0.7192 (t0) REVERT: K 265 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5816 (mm-30) REVERT: O 1 MET cc_start: 0.6329 (tpt) cc_final: 0.5639 (tpp) REVERT: O 5 LEU cc_start: 0.9011 (tp) cc_final: 0.8774 (tt) REVERT: O 10 PHE cc_start: 0.8695 (p90) cc_final: 0.8317 (p90) REVERT: O 28 LEU cc_start: 0.9464 (mt) cc_final: 0.9263 (mt) REVERT: O 56 ASP cc_start: 0.7483 (m-30) cc_final: 0.7261 (m-30) REVERT: O 99 SER cc_start: 0.8642 (m) cc_final: 0.8336 (t) REVERT: O 141 MET cc_start: 0.8400 (mpp) cc_final: 0.7518 (mpp) REVERT: Q 18 MET cc_start: 0.8862 (mmt) cc_final: 0.8465 (mmt) REVERT: Q 101 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8667 (mmmt) REVERT: Q 140 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7505 (t0) REVERT: Q 179 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7894 (mt) REVERT: E 26 ASP cc_start: 0.8631 (p0) cc_final: 0.8295 (p0) REVERT: E 38 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7423 (mm-30) REVERT: F 38 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6524 (pt0) REVERT: F 59 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: F 67 ARG cc_start: 0.8453 (mmp-170) cc_final: 0.8169 (mmp-170) REVERT: G 21 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7618 (tp30) REVERT: G 25 TYR cc_start: 0.8739 (m-80) cc_final: 0.8383 (m-10) REVERT: G 56 LYS cc_start: 0.8695 (tmmt) cc_final: 0.8294 (tptt) REVERT: L 15 SER cc_start: 0.8541 (t) cc_final: 0.8213 (t) REVERT: L 28 GLU cc_start: 0.7665 (tp30) cc_final: 0.7454 (mm-30) REVERT: L 81 LEU cc_start: 0.9275 (mt) cc_final: 0.9035 (mt) REVERT: L 188 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7727 (mt-10) REVERT: L 303 ASN cc_start: 0.7378 (p0) cc_final: 0.6992 (t0) REVERT: M 83 TYR cc_start: 0.7482 (m-10) cc_final: 0.7067 (m-10) REVERT: M 131 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8378 (ptm-80) REVERT: M 152 GLU cc_start: 0.8335 (mp0) cc_final: 0.7992 (mp0) REVERT: M 194 TYR cc_start: 0.7740 (m-80) cc_final: 0.6803 (m-80) REVERT: M 211 LEU cc_start: 0.8078 (mt) cc_final: 0.7746 (pp) REVERT: N 104 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7463 (mm-40) outliers start: 90 outliers final: 62 residues processed: 539 average time/residue: 0.4517 time to fit residues: 408.6663 Evaluate side-chains 524 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 455 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 265 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 286 TYR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 HIS Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 117 HIS Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 361 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 396 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 414 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 411 optimal weight: 0.0670 chunk 357 optimal weight: 0.8980 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS M 162 HIS ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 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 = 0.109435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.086684 restraints weight = 104320.385| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.64 r_work: 0.3499 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35793 Z= 0.207 Angle : 0.703 17.360 48978 Z= 0.354 Chirality : 0.047 0.319 5602 Planarity : 0.005 0.053 5877 Dihedral : 15.555 179.524 5897 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.07 % Favored : 91.71 % Rotamer: Outliers : 2.83 % Allowed : 20.86 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.41 (0.13), residues: 4126 helix: 0.12 (0.13), residues: 1583 sheet: -0.64 (0.21), residues: 625 loop : -1.95 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 100 HIS 0.009 0.002 HIS Q 191 PHE 0.024 0.002 PHE I 258 TYR 0.031 0.002 TYR F 45 ARG 0.007 0.001 ARG Q 126 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 1193) hydrogen bonds : angle 4.50568 ( 3360) SS BOND : bond 0.00246 ( 6) SS BOND : angle 0.78534 ( 12) covalent geometry : bond 0.00472 (35787) covalent geometry : angle 0.70277 (48966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 474 time to evaluate : 3.668 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 407 TYR cc_start: 0.6588 (m-10) cc_final: 0.6388 (m-10) REVERT: B 138 MET cc_start: 0.6283 (tpp) cc_final: 0.5989 (tpp) REVERT: B 205 MET cc_start: 0.7845 (tpt) cc_final: 0.7506 (mmm) REVERT: B 219 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8556 (tp) REVERT: H 31 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7706 (mtmt) REVERT: H 119 ASP cc_start: 0.7683 (m-30) cc_final: 0.7237 (m-30) REVERT: I 303 ASN cc_start: 0.7120 (p0) cc_final: 0.6776 (p0) REVERT: J 312 ASP cc_start: 0.8361 (p0) cc_final: 0.8151 (p0) REVERT: K 1 MET cc_start: 0.8629 (ppp) cc_final: 0.8082 (ppp) REVERT: K 15 SER cc_start: 0.8867 (p) cc_final: 0.8556 (p) REVERT: K 183 MET cc_start: 0.8735 (tpp) cc_final: 0.8502 (tpp) REVERT: K 265 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6715 (mm-30) REVERT: O 1 MET cc_start: 0.6115 (tpt) cc_final: 0.5493 (tpp) REVERT: O 10 PHE cc_start: 0.8750 (p90) cc_final: 0.8127 (p90) REVERT: O 99 SER cc_start: 0.8666 (m) cc_final: 0.8429 (p) REVERT: O 141 MET cc_start: 0.8366 (mpp) cc_final: 0.7607 (mpp) REVERT: Q 50 ASP cc_start: 0.8686 (m-30) cc_final: 0.8292 (p0) REVERT: Q 101 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8566 (mmpt) REVERT: Q 126 ARG cc_start: 0.8752 (mmm160) cc_final: 0.6840 (mtt180) REVERT: Q 140 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7642 (t0) REVERT: Q 179 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7721 (mt) REVERT: E 26 ASP cc_start: 0.8709 (p0) cc_final: 0.8448 (p0) REVERT: E 79 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8543 (mm-30) REVERT: F 59 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: F 67 ARG cc_start: 0.8214 (mmp-170) cc_final: 0.7904 (mmp-170) REVERT: G 21 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7708 (tp30) REVERT: G 56 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8375 (tptt) REVERT: G 75 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8711 (mt-10) REVERT: L 81 LEU cc_start: 0.9442 (mt) cc_final: 0.9208 (mt) REVERT: L 249 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: L 303 ASN cc_start: 0.7534 (p0) cc_final: 0.7116 (t0) REVERT: M 83 TYR cc_start: 0.7920 (m-10) cc_final: 0.7566 (m-10) REVERT: M 194 TYR cc_start: 0.8084 (m-80) cc_final: 0.7167 (m-80) REVERT: M 211 LEU cc_start: 0.8090 (mt) cc_final: 0.7720 (pp) REVERT: N 112 ILE cc_start: 0.9016 (mm) cc_final: 0.8558 (tt) outliers start: 97 outliers final: 70 residues processed: 542 average time/residue: 0.4350 time to fit residues: 396.2141 Evaluate side-chains 516 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 440 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 265 GLU Chi-restraints excluded: chain K residue 283 TYR Chi-restraints excluded: chain K residue 286 TYR Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 HIS Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 249 TYR Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 308 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 225 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 278 LEU Chi-restraints excluded: chain N residue 279 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 121 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 351 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 HIS ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.110094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.086980 restraints weight = 102512.858| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.62 r_work: 0.3458 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35793 Z= 0.162 Angle : 0.683 17.125 48978 Z= 0.341 Chirality : 0.046 0.320 5602 Planarity : 0.004 0.053 5877 Dihedral : 15.581 179.579 5897 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.66 % Favored : 92.15 % Rotamer: Outliers : 2.53 % Allowed : 21.82 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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 (0.13), residues: 4126 helix: 0.12 (0.13), residues: 1575 sheet: -0.72 (0.21), residues: 626 loop : -1.96 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 22 HIS 0.010 0.001 HIS Q 116 PHE 0.029 0.002 PHE I 258 TYR 0.029 0.002 TYR F 45 ARG 0.009 0.000 ARG K 164 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 1193) hydrogen bonds : angle 4.48531 ( 3360) SS BOND : bond 0.00200 ( 6) SS BOND : angle 1.30168 ( 12) covalent geometry : bond 0.00372 (35787) covalent geometry : angle 0.68311 (48966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 459 time to evaluate : 3.724 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 407 TYR cc_start: 0.6647 (m-10) cc_final: 0.6430 (m-10) REVERT: B 205 MET cc_start: 0.7916 (tpt) cc_final: 0.7515 (mmm) REVERT: B 219 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (tp) REVERT: C 100 TRP cc_start: 0.8530 (m100) cc_final: 0.8329 (m100) REVERT: H 119 ASP cc_start: 0.7712 (m-30) cc_final: 0.7278 (m-30) REVERT: H 189 TYR cc_start: 0.8240 (m-80) cc_final: 0.7817 (m-80) REVERT: I 303 ASN cc_start: 0.7098 (p0) cc_final: 0.6761 (p0) REVERT: J 17 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8555 (t0) REVERT: J 312 ASP cc_start: 0.8391 (p0) cc_final: 0.8145 (p0) REVERT: K 1 MET cc_start: 0.8488 (ppp) cc_final: 0.8002 (ppp) REVERT: K 15 SER cc_start: 0.8790 (p) cc_final: 0.8462 (p) REVERT: K 117 ASP cc_start: 0.7856 (t0) cc_final: 0.7608 (t0) REVERT: K 183 MET cc_start: 0.8715 (tpp) cc_final: 0.8387 (tpp) REVERT: K 265 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6310 (mm-30) REVERT: O 1 MET cc_start: 0.6145 (tpt) cc_final: 0.5669 (tpp) REVERT: O 10 PHE cc_start: 0.8696 (p90) cc_final: 0.8265 (p90) REVERT: O 99 SER cc_start: 0.8721 (m) cc_final: 0.8517 (p) REVERT: O 141 MET cc_start: 0.8329 (mpp) cc_final: 0.7554 (mpp) REVERT: Q 50 ASP cc_start: 0.8694 (m-30) cc_final: 0.8301 (p0) REVERT: Q 101 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8558 (mmpt) REVERT: Q 140 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7557 (t0) REVERT: Q 179 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7965 (mt) REVERT: E 26 ASP cc_start: 0.8743 (p0) cc_final: 0.8502 (p0) REVERT: E 38 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7267 (mm-30) REVERT: F 38 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7068 (pt0) REVERT: F 59 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: F 67 ARG cc_start: 0.8206 (mmp-170) cc_final: 0.7898 (mmp-170) REVERT: G 21 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7700 (tp30) REVERT: G 56 LYS cc_start: 0.8777 (tmmt) cc_final: 0.8401 (tptt) REVERT: L 54 MET cc_start: 0.8978 (tmm) cc_final: 0.8458 (tpp) REVERT: L 81 LEU cc_start: 0.9367 (mt) cc_final: 0.9159 (mt) REVERT: L 119 ASP cc_start: 0.8110 (t0) cc_final: 0.7874 (t0) REVERT: L 249 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: L 278 LEU cc_start: 0.8475 (tp) cc_final: 0.8007 (tp) REVERT: M 83 TYR cc_start: 0.7816 (m-10) cc_final: 0.7440 (m-10) REVERT: M 194 TYR cc_start: 0.7980 (m-80) cc_final: 0.6927 (m-80) REVERT: M 211 LEU cc_start: 0.8085 (mt) cc_final: 0.7726 (pp) REVERT: N 112 ILE cc_start: 0.9195 (mm) cc_final: 0.8659 (tt) REVERT: N 119 ASP cc_start: 0.8675 (m-30) cc_final: 0.8173 (m-30) outliers start: 87 outliers final: 67 residues processed: 522 average time/residue: 0.4489 time to fit residues: 398.7274 Evaluate side-chains 501 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 427 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 265 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 283 TYR Chi-restraints excluded: chain K residue 286 TYR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 HIS Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 116 HIS Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 249 TYR Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 308 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 311 VAL Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 336 optimal weight: 3.9990 chunk 350 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 211 optimal weight: 0.0980 chunk 133 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 167 optimal weight: 0.3980 chunk 239 optimal weight: 3.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 ASN ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.111500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.088587 restraints weight = 102269.561| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.63 r_work: 0.3491 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35793 Z= 0.141 Angle : 0.693 17.136 48978 Z= 0.344 Chirality : 0.046 0.310 5602 Planarity : 0.004 0.053 5877 Dihedral : 15.585 179.325 5897 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.00 % Favored : 91.81 % Rotamer: Outliers : 2.33 % Allowed : 22.47 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.42 (0.13), residues: 4126 helix: 0.13 (0.13), residues: 1572 sheet: -0.77 (0.21), residues: 622 loop : -1.92 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 22 HIS 0.016 0.001 HIS Q 116 PHE 0.026 0.002 PHE I 258 TYR 0.029 0.001 TYR F 45 ARG 0.009 0.000 ARG K 164 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 1193) hydrogen bonds : angle 4.46968 ( 3360) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.90721 ( 12) covalent geometry : bond 0.00323 (35787) covalent geometry : angle 0.69286 (48966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8252 Ramachandran restraints generated. 4126 Oldfield, 0 Emsley, 4126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 448 time to evaluate : 3.704 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: symmetry clash REVERT: A 407 TYR cc_start: 0.6660 (m-10) cc_final: 0.6447 (m-10) REVERT: B 131 MET cc_start: 0.8093 (tpp) cc_final: 0.7642 (tpp) REVERT: B 205 MET cc_start: 0.7850 (tpt) cc_final: 0.7440 (mmm) REVERT: B 219 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8465 (tp) REVERT: H 189 TYR cc_start: 0.8258 (m-80) cc_final: 0.7763 (m-80) REVERT: I 194 TYR cc_start: 0.7765 (m-80) cc_final: 0.7240 (m-80) REVERT: I 303 ASN cc_start: 0.7115 (p0) cc_final: 0.6789 (p0) REVERT: J 312 ASP cc_start: 0.8384 (p0) cc_final: 0.8133 (p0) REVERT: K 1 MET cc_start: 0.8474 (ppp) cc_final: 0.8008 (ppp) REVERT: K 15 SER cc_start: 0.8719 (p) cc_final: 0.8405 (p) REVERT: K 117 ASP cc_start: 0.7784 (t0) cc_final: 0.7529 (t0) REVERT: K 265 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.5935 (mm-30) REVERT: O 1 MET cc_start: 0.6381 (tpt) cc_final: 0.6039 (tpp) REVERT: O 10 PHE cc_start: 0.8635 (p90) cc_final: 0.8281 (p90) REVERT: O 99 SER cc_start: 0.8722 (m) cc_final: 0.8510 (p) REVERT: O 107 ASP cc_start: 0.7735 (t0) cc_final: 0.7499 (m-30) REVERT: O 141 MET cc_start: 0.8419 (mpp) cc_final: 0.7615 (mpp) REVERT: Q 50 ASP cc_start: 0.8668 (m-30) cc_final: 0.8267 (p0) REVERT: Q 101 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8568 (mmpt) REVERT: Q 117 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.7533 (m-70) REVERT: Q 140 ASP cc_start: 0.8004 (t70) cc_final: 0.7406 (t0) REVERT: Q 179 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7934 (mt) REVERT: E 26 ASP cc_start: 0.8704 (p0) cc_final: 0.8481 (p0) REVERT: F 25 TYR cc_start: 0.9087 (m-80) cc_final: 0.8760 (m-80) REVERT: F 38 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6905 (pt0) REVERT: F 59 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: F 67 ARG cc_start: 0.8242 (mmp-170) cc_final: 0.7948 (mmp-170) REVERT: G 21 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7683 (tp30) REVERT: G 25 TYR cc_start: 0.8844 (m-10) cc_final: 0.8323 (m-10) REVERT: G 56 LYS cc_start: 0.8802 (tmmt) cc_final: 0.8420 (tptt) REVERT: G 75 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8513 (tm-30) REVERT: L 54 MET cc_start: 0.8837 (tmm) cc_final: 0.8451 (tpp) REVERT: L 245 MET cc_start: 0.8738 (mmm) cc_final: 0.8420 (mmm) REVERT: L 249 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: M 83 TYR cc_start: 0.7644 (m-10) cc_final: 0.7258 (m-10) REVERT: M 131 ARG cc_start: 0.8764 (ttp80) cc_final: 0.8326 (ptm-80) REVERT: M 194 TYR cc_start: 0.7863 (m-80) cc_final: 0.6836 (m-80) REVERT: M 211 LEU cc_start: 0.8024 (mt) cc_final: 0.7655 (pp) REVERT: N 112 ILE cc_start: 0.9148 (mm) cc_final: 0.8642 (tt) REVERT: N 119 ASP cc_start: 0.8689 (m-30) cc_final: 0.8255 (m-30) outliers start: 80 outliers final: 65 residues processed: 507 average time/residue: 0.4352 time to fit residues: 369.9028 Evaluate side-chains 503 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 432 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 265 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 283 TYR Chi-restraints excluded: chain K residue 286 TYR Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 60 HIS Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 117 HIS Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 179 LEU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 249 TYR Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 308 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 311 VAL Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 142 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 30.0000 chunk 285 optimal weight: 9.9990 chunk 315 optimal weight: 1.9990 chunk 357 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.111404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088506 restraints weight = 102615.342| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.65 r_work: 0.3489 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.286 35793 Z= 0.174 Angle : 0.783 59.200 48978 Z= 0.417 Chirality : 0.046 0.312 5602 Planarity : 0.004 0.053 5877 Dihedral : 15.583 179.333 5897 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 2.36 % Allowed : 22.49 % Favored : 75.15 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -1.42 (0.13), residues: 4126 helix: 0.13 (0.13), residues: 1572 sheet: -0.77 (0.21), residues: 622 loop : -1.92 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 100 HIS 0.011 0.001 HIS Q 116 PHE 0.069 0.002 PHE A 13 TYR 0.026 0.001 TYR K 309 ARG 0.009 0.000 ARG Q 126 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 1193) hydrogen bonds : angle 4.46923 ( 3360) SS BOND : bond 0.00139 ( 6) SS BOND : angle 1.04166 ( 12) covalent geometry : bond 0.00404 (35787) covalent geometry : angle 0.78317 (48966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18226.09 seconds wall clock time: 313 minutes 57.56 seconds (18837.56 seconds total)