Starting phenix.real_space_refine on Tue Sep 15 01:50:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tra_26084/09_2026/7tra_26084.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tra_26084/09_2026/7tra_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_26084/09_2026/7tra_26084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tra_26084/09_2026/7tra_26084.map" model { file = "/net/cci-nas-00/data/ceres_data/7tra_26084/09_2026/7tra_26084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tra_26084/09_2026/7tra_26084.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tra_26084/09_2026/7tra_26084.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tra_26084/09_2026/7tra_26084.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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, 'RNAv2': 19} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 40} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 12 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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: 7.31, per 1000 atoms: 0.21 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: 3.17 Conformation dependent library (CDL) restraints added in 1.6 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: 4.03 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: 7.10 Time building geometry restraints manager: 4.19 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=" C3' DG S 37 " pdb=" C2' DG S 37 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.48e+00 bond pdb=" C3' DT S 38 " pdb=" C2' DT S 38 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.36e+00 bond pdb=" C1' C R 23 " pdb=" N1 C R 23 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.24e+00 bond pdb=" C1' DC S 35 " pdb=" N1 DC S 35 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.52e+00 bond pdb=" C3' C R 25 " pdb=" C2' C R 25 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.35e+00 ... (remaining 35782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 47921 1.97 - 3.95: 852 3.95 - 5.92: 119 5.92 - 7.90: 26 7.90 - 9.87: 6 Bond angle restraints: 48924 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=" N3 DT S 29 " pdb=" C4 DT S 29 " pdb=" O4 DT S 29 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT T 24 " pdb=" C4 DT T 24 " pdb=" O4 DT T 24 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT S 21 " pdb=" C4 DT S 21 " pdb=" O4 DT S 21 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 48919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20773 35.99 - 71.98: 551 71.98 - 107.98: 23 107.98 - 143.97: 1 143.97 - 179.96: 4 Dihedral angle restraints: 21352 sinusoidal: 9269 harmonic: 12083 Sorted by residual: dihedral pdb=" C4' G R 8 " pdb=" C3' G R 8 " pdb=" C2' G R 8 " pdb=" C1' G R 8 " ideal model delta sinusoidal sigma weight residual 36.34 -36.14 72.49 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' U R 2 " pdb=" C3' U R 2 " pdb=" C2' U R 2 " pdb=" C1' U R 2 " ideal model delta sinusoidal sigma weight residual 36.35 -35.26 71.61 1 3.10e+00 1.04e-01 6.84e+02 dihedral pdb=" C4' A R 7 " pdb=" C3' A R 7 " pdb=" C2' A R 7 " pdb=" C1' A R 7 " ideal model delta sinusoidal sigma weight residual 36.34 -34.06 70.40 1 3.10e+00 1.04e-01 6.64e+02 ... (remaining 21349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4561 0.057 - 0.113: 929 0.113 - 0.170: 90 0.170 - 0.226: 8 0.226 - 0.283: 14 Chirality restraints: 5602 Sorted by residual: chirality pdb=" C2' G R 8 " pdb=" C3' G R 8 " pdb=" O2' G R 8 " pdb=" C1' G R 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' A R 7 " pdb=" C3' A R 7 " pdb=" O2' A R 7 " pdb=" C1' A R 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' U R 2 " pdb=" C3' U R 2 " pdb=" O2' U R 2 " pdb=" C1' U R 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.85e+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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.830 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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= 0.197 Angle : 0.631 9.873 48936 Z= 0.362 Chirality : 0.046 0.283 5602 Planarity : 0.004 0.092 5877 Dihedral : 15.525 179.961 13562 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (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 ARG 0.007 0.000 ARG C 49 TYR 0.034 0.001 TYR Q 90 PHE 0.028 0.001 PHE I 67 TRP 0.065 0.001 TRP F 100 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.20 (35787) covalent geometry : angle 0.63106 / 0.36 (48924) SS BOND : bond 0.00108 / 0.06 ( 6) SS BOND : angle 0.49756 / 0.28 ( 12) hydrogen bonds : bond 0.14947 / 9.75 ( 1193) hydrogen bonds : angle 5.91466 / 4.15 ( 3360) *********************** 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 : 1.390 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: 0.8976 (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: 0.8240 (m-80) REVERT: D 26 ASP cc_start: 0.8125 (p0) cc_final: 0.7889 (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: 0.7599 (t) REVERT: M 142 LEU cc_start: 0.7661 (mp) cc_final: 0.7415 (mp) REVERT: M 194 TYR cc_start: 0.7221 (m-80) cc_final: 0.6870 (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: 0.2028 time to fit residues: 220.3596 Evaluate side-chains 480 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0040 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN A 406 HIS B 228 HIS H 17 ASN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN J 53 ASN J 229 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 ASN ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 310 ASN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 ASN N 290 ASN N 331 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.124843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.104100 restraints weight = 106688.100| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.87 r_work: 0.3812 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35793 Z= 0.156 Angle : 0.671 11.993 48936 Z= 0.338 Chirality : 0.048 0.694 5602 Planarity : 0.004 0.048 5877 Dihedral : 15.279 178.127 5805 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.71 % Favored : 92.03 % Rotamer: Outliers : 1.08 % Allowed : 10.64 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 4126 helix: 0.51 (0.14), residues: 1555 sheet: -0.58 (0.22), residues: 595 loop : -1.94 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 187 TYR 0.035 0.002 TYR A 399 PHE 0.017 0.002 PHE I 63 TRP 0.034 0.002 TRP H 42 HIS 0.008 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (35787) covalent geometry : angle 0.67080 / 0.34 (48924) SS BOND : bond 0.00178 / 0.09 ( 6) SS BOND : angle 0.42424 / 0.21 ( 12) hydrogen bonds : bond 0.04432 / 3.04 ( 1193) hydrogen bonds : angle 4.69122 / 3.28 ( 3360) *********************** 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 564 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 527 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8966 (tp30) cc_final: 0.8549 (tp30) REVERT: A 108 ARG cc_start: 0.6930 (tpt90) cc_final: 0.5841 (tpm170) REVERT: A 207 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7988 (pp20) REVERT: A 212 ASP cc_start: 0.7995 (p0) cc_final: 0.7373 (t0) REVERT: B 185 GLN cc_start: 0.7655 (tt0) cc_final: 0.7243 (tt0) REVERT: C 89 ASP cc_start: 0.8150 (m-30) cc_final: 0.7855 (m-30) REVERT: D 25 TYR cc_start: 0.8920 (m-80) cc_final: 0.8495 (m-80) REVERT: D 26 ASP cc_start: 0.8599 (p0) cc_final: 0.8315 (p0) REVERT: D 75 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7786 (mt-10) REVERT: J 1 MET cc_start: 0.7226 (mmt) cc_final: 0.7003 (mmt) REVERT: J 88 PHE cc_start: 0.6669 (m-80) cc_final: 0.6417 (m-80) REVERT: K 1 MET cc_start: 0.8404 (ppp) cc_final: 0.8125 (ppp) REVERT: K 83 TYR cc_start: 0.8405 (m-10) cc_final: 0.8144 (m-10) REVERT: O 5 LEU cc_start: 0.8696 (tp) cc_final: 0.8279 (tt) REVERT: O 87 ASN cc_start: 0.8174 (p0) cc_final: 0.7896 (p0) REVERT: O 141 MET cc_start: 0.8188 (mpp) cc_final: 0.7543 (mpp) REVERT: Q 10 THR cc_start: 0.8341 (m) cc_final: 0.7843 (p) REVERT: E 70 SER cc_start: 0.9002 (p) cc_final: 0.8631 (p) REVERT: G 56 LYS cc_start: 0.8550 (ptmm) cc_final: 0.8134 (ptmm) REVERT: G 75 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8516 (tm-30) REVERT: L 66 TYR cc_start: 0.8312 (m-10) cc_final: 0.8081 (m-80) REVERT: L 182 GLN cc_start: 0.8244 (tt0) cc_final: 0.7587 (tm-30) REVERT: L 236 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7758 (tm-30) REVERT: M 83 TYR cc_start: 0.7434 (m-10) cc_final: 0.7070 (m-10) REVERT: M 152 GLU cc_start: 0.8302 (mp0) cc_final: 0.7815 (mp0) REVERT: M 183 MET cc_start: 0.6162 (ppp) cc_final: 0.5684 (tmm) REVERT: M 194 TYR cc_start: 0.7627 (m-80) cc_final: 0.7172 (m-80) REVERT: M 245 MET cc_start: 0.8279 (mmp) cc_final: 0.7746 (mmp) outliers start: 37 outliers final: 24 residues processed: 547 average time/residue: 0.1985 time to fit residues: 185.6549 Evaluate side-chains 497 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 472 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU 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 H residue 47 VAL 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 F residue 33 LYS Chi-restraints excluded: chain F residue 89 ASP 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 81 LEU Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 278 LEU 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 263 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 354 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 394 optimal weight: 4.9990 chunk 295 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 412 optimal weight: 2.9990 chunk 393 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 406 HIS B 231 HIS H 90 GLN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 GLN I 253 ASN ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 ASN K 12 ASN Q 94 ASN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 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** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.113541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.090766 restraints weight = 104171.429| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.73 r_work: 0.3567 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 35793 Z= 0.263 Angle : 0.762 15.911 48936 Z= 0.393 Chirality : 0.050 0.346 5602 Planarity : 0.006 0.130 5877 Dihedral : 15.423 177.567 5805 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.02 % Favored : 91.74 % Rotamer: Outliers : 2.39 % Allowed : 14.28 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4126 helix: 0.07 (0.13), residues: 1572 sheet: -0.98 (0.20), residues: 676 loop : -1.92 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 55 TYR 0.038 0.002 TYR F 45 PHE 0.034 0.003 PHE I 88 TRP 0.031 0.003 TRP F 100 HIS 0.014 0.002 HIS Q 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.26 (35787) covalent geometry : angle 0.76210 / 0.39 (48924) SS BOND : bond 0.00277 / 0.13 ( 6) SS BOND : angle 0.74015 / 0.40 ( 12) hydrogen bonds : bond 0.04771 / 3.24 ( 1193) hydrogen bonds : angle 4.68888 / 3.27 ( 3360) *********************** 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 610 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 528 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TRP cc_start: 0.7911 (m100) cc_final: 0.6898 (m-10) REVERT: A 81 GLN cc_start: 0.7800 (mm110) cc_final: 0.7574 (mm-40) REVERT: A 207 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8235 (pp20) REVERT: A 208 MET cc_start: 0.7353 (ppp) cc_final: 0.6539 (ppp) REVERT: A 212 ASP cc_start: 0.8110 (p0) cc_final: 0.7387 (t0) REVERT: B 170 TYR cc_start: 0.8966 (p90) cc_final: 0.8711 (p90) REVERT: B 185 GLN cc_start: 0.8036 (tt0) cc_final: 0.7468 (tt0) REVERT: B 200 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9175 (mt) REVERT: C 89 ASP cc_start: 0.8569 (m-30) cc_final: 0.8253 (m-30) REVERT: D 25 TYR cc_start: 0.9032 (m-80) cc_final: 0.8737 (m-80) REVERT: D 26 ASP cc_start: 0.8615 (p0) cc_final: 0.8318 (p0) REVERT: D 70 SER cc_start: 0.8611 (t) cc_final: 0.8339 (t) REVERT: H 119 ASP cc_start: 0.7344 (m-30) cc_final: 0.6729 (m-30) REVERT: H 146 ASP cc_start: 0.8551 (p0) cc_final: 0.8300 (p0) REVERT: H 188 GLU cc_start: 0.8462 (tt0) cc_final: 0.8193 (tt0) REVERT: H 312 ASP cc_start: 0.8181 (p0) cc_final: 0.7952 (p0) REVERT: I 263 VAL cc_start: 0.7717 (t) cc_final: 0.7403 (m) REVERT: J 1 MET cc_start: 0.7757 (mmt) cc_final: 0.7486 (mmt) REVERT: J 54 MET cc_start: 0.8480 (tpt) cc_final: 0.8066 (tpp) REVERT: J 194 TYR cc_start: 0.8323 (m-80) cc_final: 0.7712 (m-80) REVERT: K 1 MET cc_start: 0.8529 (ppp) cc_final: 0.8223 (ppp) REVERT: K 65 ASP cc_start: 0.8363 (m-30) cc_final: 0.8103 (m-30) REVERT: K 198 ILE cc_start: 0.8956 (mm) cc_final: 0.8740 (mm) REVERT: K 265 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: O 5 LEU cc_start: 0.9065 (tp) cc_final: 0.8756 (tt) REVERT: O 141 MET cc_start: 0.8357 (mpp) cc_final: 0.7701 (mpp) REVERT: O 195 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7738 (ptm) REVERT: Q 139 LEU cc_start: 0.6471 (tp) cc_final: 0.6170 (tt) REVERT: Q 179 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8236 (mt) REVERT: E 38 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7795 (mm-30) REVERT: E 55 LYS cc_start: 0.9204 (mttm) cc_final: 0.8879 (mttm) REVERT: G 21 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8012 (mm-30) REVERT: G 56 LYS cc_start: 0.8575 (ptmm) cc_final: 0.8101 (tptt) REVERT: G 75 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8718 (mt-10) REVERT: L 15 SER cc_start: 0.8485 (t) cc_final: 0.8198 (t) REVERT: L 81 LEU cc_start: 0.9351 (mt) cc_final: 0.9012 (mt) REVERT: L 194 TYR cc_start: 0.8603 (m-80) cc_final: 0.8312 (m-80) REVERT: L 236 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7968 (tm-30) REVERT: L 303 ASN cc_start: 0.7344 (p0) cc_final: 0.7111 (t0) REVERT: M 152 GLU cc_start: 0.8386 (mp0) cc_final: 0.8033 (mp0) REVERT: M 183 MET cc_start: 0.6110 (ppp) cc_final: 0.5535 (ttm) REVERT: M 194 TYR cc_start: 0.8152 (m-80) cc_final: 0.7576 (m-80) REVERT: N 194 TYR cc_start: 0.8494 (m-80) cc_final: 0.8135 (m-80) outliers start: 82 outliers final: 53 residues processed: 574 average time/residue: 0.1979 time to fit residues: 192.0596 Evaluate side-chains 505 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 447 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 207 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 66 LEU 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 200 LEU 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 I residue 27 ILE Chi-restraints excluded: chain I residue 111 ILE 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 133 VAL 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 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 104 THR Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 172 SER 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 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 86 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 200 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 81 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 240 optimal weight: 0.6980 chunk 373 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 311 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 295 optimal weight: 30.0000 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 HIS B 256 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN J 17 ASN J 229 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 191 HIS ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.115881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.093597 restraints weight = 103528.295| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.72 r_work: 0.3620 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35793 Z= 0.144 Angle : 0.644 12.135 48936 Z= 0.330 Chirality : 0.046 0.339 5602 Planarity : 0.004 0.053 5877 Dihedral : 15.299 178.908 5805 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.44 % Favored : 92.34 % Rotamer: Outliers : 2.30 % Allowed : 18.04 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 4126 helix: 0.24 (0.13), residues: 1556 sheet: -0.69 (0.20), residues: 642 loop : -1.91 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 55 TYR 0.051 0.002 TYR A 399 PHE 0.033 0.002 PHE B 54 TRP 0.023 0.002 TRP Q 22 HIS 0.007 0.001 HIS K 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (35787) covalent geometry : angle 0.64304 / 0.33 (48924) SS BOND : bond 0.00329 / 0.22 ( 6) SS BOND : angle 2.20723 / 1.33 ( 12) hydrogen bonds : bond 0.03736 / 2.53 ( 1193) hydrogen bonds : angle 4.49797 / 3.14 ( 3360) *********************** 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 563 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 484 time to evaluate : 1.936 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 207 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8250 (pp20) REVERT: A 208 MET cc_start: 0.7202 (ppp) cc_final: 0.6460 (ppp) REVERT: A 212 ASP cc_start: 0.8099 (p0) cc_final: 0.7352 (t0) REVERT: B 200 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9091 (mt) REVERT: B 205 MET cc_start: 0.7798 (tpt) cc_final: 0.7248 (mmm) REVERT: C 89 ASP cc_start: 0.8511 (m-30) cc_final: 0.8288 (m-30) REVERT: D 25 TYR cc_start: 0.8963 (m-80) cc_final: 0.8579 (m-80) REVERT: D 26 ASP cc_start: 0.8604 (p0) cc_final: 0.8349 (p0) REVERT: D 70 SER cc_start: 0.8578 (t) cc_final: 0.8362 (t) REVERT: H 119 ASP cc_start: 0.7178 (m-30) cc_final: 0.6621 (m-30) REVERT: H 146 ASP cc_start: 0.8416 (p0) cc_final: 0.8056 (p0) REVERT: H 312 ASP cc_start: 0.8300 (p0) cc_final: 0.8052 (p0) REVERT: I 83 TYR cc_start: 0.8300 (m-10) cc_final: 0.8003 (m-10) REVERT: J 1 MET cc_start: 0.7564 (mmt) cc_final: 0.7140 (mmt) REVERT: J 54 MET cc_start: 0.8169 (tpt) cc_final: 0.7879 (tpp) REVERT: J 194 TYR cc_start: 0.8163 (m-80) cc_final: 0.7657 (m-80) REVERT: J 202 LEU cc_start: 0.8412 (mp) cc_final: 0.8191 (mp) REVERT: J 312 ASP cc_start: 0.8398 (p0) cc_final: 0.8124 (p0) REVERT: K 1 MET cc_start: 0.8560 (ppp) cc_final: 0.8153 (ppp) REVERT: K 117 ASP cc_start: 0.7246 (t0) cc_final: 0.7015 (t0) REVERT: K 265 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6125 (mm-30) REVERT: O 5 LEU cc_start: 0.9017 (tp) cc_final: 0.8717 (tt) REVERT: O 99 SER cc_start: 0.8532 (m) cc_final: 0.8220 (t) REVERT: O 141 MET cc_start: 0.8278 (mpp) cc_final: 0.7592 (mpp) REVERT: O 195 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7372 (ptm) REVERT: Q 139 LEU cc_start: 0.6429 (tp) cc_final: 0.6126 (tt) REVERT: Q 179 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8207 (mt) REVERT: F 18 ASP cc_start: 0.8620 (m-30) cc_final: 0.8317 (m-30) REVERT: G 56 LYS cc_start: 0.8528 (ptmm) cc_final: 0.8313 (tmmt) REVERT: G 75 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8527 (tm-30) REVERT: G 78 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8800 (mt-10) REVERT: G 79 GLU cc_start: 0.8719 (pp20) cc_final: 0.8334 (pp20) REVERT: L 15 SER cc_start: 0.8252 (t) cc_final: 0.7925 (t) REVERT: L 81 LEU cc_start: 0.9297 (mt) cc_final: 0.9062 (mt) REVERT: L 278 LEU cc_start: 0.8748 (tp) cc_final: 0.8487 (tp) REVERT: L 303 ASN cc_start: 0.7491 (p0) cc_final: 0.7212 (t0) REVERT: M 83 TYR cc_start: 0.7801 (m-10) cc_final: 0.7421 (m-10) REVERT: M 152 GLU cc_start: 0.8347 (mp0) cc_final: 0.8000 (mp0) REVERT: M 183 MET cc_start: 0.5802 (ppp) cc_final: 0.5415 (ttm) REVERT: M 194 TYR cc_start: 0.8034 (m-80) cc_final: 0.7186 (m-80) REVERT: M 211 LEU cc_start: 0.8015 (mt) cc_final: 0.7775 (pp) outliers start: 79 outliers final: 53 residues processed: 533 average time/residue: 0.2047 time to fit residues: 185.2543 Evaluate side-chains 499 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 441 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 207 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 182 GLN 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 111 ILE Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 265 GLU 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 20 TYR Chi-restraints excluded: chain O residue 195 MET Chi-restraints excluded: chain O residue 196 TYR 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 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 G residue 16 VAL 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 242 LEU Chi-restraints excluded: chain L residue 243 ILE 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 286 TYR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 278 LEU Chi-restraints excluded: chain N residue 279 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 113 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 385 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 48 optimal weight: 0.0570 chunk 112 optimal weight: 0.9980 chunk 292 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 HIS B 156 ASN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 229 ASN Q 191 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.114968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.093062 restraints weight = 104222.631| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.65 r_work: 0.3612 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35793 Z= 0.156 Angle : 0.638 11.950 48936 Z= 0.326 Chirality : 0.046 0.348 5602 Planarity : 0.004 0.053 5877 Dihedral : 15.273 179.594 5805 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.78 % Favored : 92.00 % Rotamer: Outliers : 2.80 % Allowed : 18.94 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 4126 helix: 0.27 (0.13), residues: 1564 sheet: -0.67 (0.21), residues: 632 loop : -1.91 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 4 TYR 0.043 0.002 TYR A 399 PHE 0.021 0.002 PHE I 140 TRP 0.022 0.002 TRP O 254 HIS 0.010 0.001 HIS Q 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (35787) covalent geometry : angle 0.63757 / 0.33 (48924) SS BOND : bond 0.00431 / 0.31 ( 6) SS BOND : angle 1.74831 / 1.08 ( 12) hydrogen bonds : bond 0.03705 / 2.51 ( 1193) hydrogen bonds : angle 4.48700 / 3.14 ( 3360) *********************** 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 568 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 472 time to evaluate : 1.198 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 55 PHE cc_start: 0.8906 (m-80) cc_final: 0.8639 (m-80) REVERT: A 207 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: A 208 MET cc_start: 0.7025 (ppp) cc_final: 0.6274 (ppp) REVERT: A 212 ASP cc_start: 0.8189 (p0) cc_final: 0.7445 (t0) REVERT: B 200 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9096 (mt) REVERT: B 205 MET cc_start: 0.7857 (tpt) cc_final: 0.7299 (mmm) REVERT: C 89 ASP cc_start: 0.8572 (m-30) cc_final: 0.8348 (m-30) REVERT: C 100 TRP cc_start: 0.8381 (m100) cc_final: 0.8156 (m100) REVERT: D 25 TYR cc_start: 0.9016 (m-80) cc_final: 0.8580 (m-80) REVERT: D 26 ASP cc_start: 0.8650 (p0) cc_final: 0.8432 (p0) REVERT: H 31 LYS cc_start: 0.7790 (mtmm) cc_final: 0.7352 (mttt) REVERT: H 119 ASP cc_start: 0.7257 (m-30) cc_final: 0.6691 (m-30) REVERT: H 146 ASP cc_start: 0.8479 (p0) cc_final: 0.8248 (p0) REVERT: H 312 ASP cc_start: 0.8300 (p0) cc_final: 0.8069 (p0) REVERT: I 83 TYR cc_start: 0.8183 (m-10) cc_final: 0.7914 (m-10) REVERT: I 107 ASP cc_start: 0.7663 (t0) cc_final: 0.7417 (t0) REVERT: I 303 ASN cc_start: 0.7111 (p0) cc_final: 0.6809 (p0) REVERT: J 1 MET cc_start: 0.7592 (mmt) cc_final: 0.7116 (mmt) REVERT: K 1 MET cc_start: 0.8658 (ppp) cc_final: 0.8151 (ppp) REVERT: K 117 ASP cc_start: 0.7437 (t0) cc_final: 0.7214 (t0) REVERT: K 183 MET cc_start: 0.8640 (tpp) cc_final: 0.8276 (tpt) REVERT: O 5 LEU cc_start: 0.9055 (tp) cc_final: 0.8805 (tt) REVERT: O 56 ASP cc_start: 0.7430 (m-30) cc_final: 0.7202 (m-30) REVERT: O 99 SER cc_start: 0.8549 (m) cc_final: 0.8281 (p) REVERT: O 121 VAL cc_start: 0.8980 (t) cc_final: 0.8771 (t) REVERT: O 141 MET cc_start: 0.8391 (mpp) cc_final: 0.7654 (mpp) REVERT: O 195 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7342 (ptm) REVERT: Q 18 MET cc_start: 0.8825 (mmt) cc_final: 0.8312 (mmt) REVERT: Q 139 LEU cc_start: 0.6659 (tp) cc_final: 0.6370 (tt) REVERT: Q 179 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8187 (mt) REVERT: F 18 ASP cc_start: 0.8707 (m-30) cc_final: 0.8383 (m-30) REVERT: F 67 ARG cc_start: 0.8500 (mmp-170) cc_final: 0.8214 (mmp-170) REVERT: F 81 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.9038 (p) REVERT: G 75 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8448 (tm-30) REVERT: G 78 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8779 (mt-10) REVERT: G 79 GLU cc_start: 0.8882 (pp20) cc_final: 0.8403 (pp20) REVERT: L 15 SER cc_start: 0.8319 (t) cc_final: 0.7973 (t) REVERT: L 81 LEU cc_start: 0.9336 (mt) cc_final: 0.9020 (mt) REVERT: L 194 TYR cc_start: 0.8537 (m-80) cc_final: 0.8224 (m-80) REVERT: L 278 LEU cc_start: 0.8750 (tp) cc_final: 0.8521 (tp) REVERT: L 303 ASN cc_start: 0.7364 (p0) cc_final: 0.7129 (t0) REVERT: M 83 TYR cc_start: 0.7836 (m-10) cc_final: 0.7425 (m-10) REVERT: M 131 ARG cc_start: 0.8896 (ttp80) cc_final: 0.8504 (ptm-80) REVERT: M 152 GLU cc_start: 0.8375 (mp0) cc_final: 0.7966 (mp0) REVERT: M 194 TYR cc_start: 0.8054 (m-80) cc_final: 0.6955 (m-80) REVERT: M 211 LEU cc_start: 0.8064 (mt) cc_final: 0.7806 (pp) REVERT: N 194 TYR cc_start: 0.7940 (m-80) cc_final: 0.7615 (m-80) outliers start: 96 outliers final: 66 residues processed: 532 average time/residue: 0.2038 time to fit residues: 183.2751 Evaluate side-chains 516 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 445 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 426 VAL 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 195 ILE Chi-restraints excluded: chain B residue 200 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 36 VAL Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 335 MET 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 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 254 LEU 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 20 TYR Chi-restraints excluded: chain O residue 195 MET 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 179 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 81 VAL 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 11 LEU Chi-restraints excluded: chain L residue 86 THR 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 242 LEU Chi-restraints excluded: chain L residue 243 ILE Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 269 ILE 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 286 TYR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain M residue 325 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 278 LEU Chi-restraints excluded: chain N residue 279 VAL Chi-restraints excluded: chain N residue 315 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 325 optimal weight: 1.9990 chunk 411 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 354 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN H 84 ASN I 209 GLN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN Q 175 GLN ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS M 53 ASN M 162 HIS M 209 GLN ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 296 ASN ** M 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 ASN ** N 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.099240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.075307 restraints weight = 101894.345| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.41 r_work: 0.3214 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.230 35793 Z= 0.452 Angle : 0.997 12.641 48936 Z= 0.511 Chirality : 0.057 0.399 5602 Planarity : 0.007 0.076 5877 Dihedral : 15.689 173.936 5805 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 29.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.57 % Favored : 90.18 % Rotamer: Outliers : 4.78 % Allowed : 18.30 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 4126 helix: -0.56 (0.12), residues: 1553 sheet: -1.24 (0.20), residues: 682 loop : -2.23 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG M 187 TYR 0.054 0.003 TYR F 45 PHE 0.048 0.004 PHE L 88 TRP 0.039 0.004 TRP F 4 HIS 0.018 0.003 HIS M 280 Details of bonding type rmsd/Z covalent geometry : bond 0.01018 / 0.45 (35787) covalent geometry : angle 0.99603 / 0.51 (48924) SS BOND : bond 0.00561 / 0.27 ( 6) SS BOND : angle 2.21868 / 1.33 ( 12) hydrogen bonds : bond 0.05770 / 3.88 ( 1193) hydrogen bonds : angle 5.25844 / 3.68 ( 3360) *********************** 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 623 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 459 time to evaluate : 1.213 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 55 PHE cc_start: 0.8957 (m-80) cc_final: 0.8749 (m-80) REVERT: A 81 GLN cc_start: 0.7938 (mm110) cc_final: 0.7718 (mm-40) REVERT: A 176 MET cc_start: 0.8858 (mmp) cc_final: 0.8574 (mmp) REVERT: A 505 GLU cc_start: 0.7596 (mp0) cc_final: 0.6961 (tp30) REVERT: B 9 GLN cc_start: 0.7761 (tp40) cc_final: 0.7554 (tp-100) REVERT: B 159 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8530 (tp) REVERT: D 83 GLN cc_start: 0.9004 (pt0) cc_final: 0.8569 (pp30) REVERT: H 166 ASP cc_start: 0.7012 (t0) cc_final: 0.6717 (t0) REVERT: H 183 MET cc_start: 0.8940 (ppp) cc_final: 0.8643 (ppp) REVERT: H 312 ASP cc_start: 0.8635 (p0) cc_final: 0.8417 (p0) REVERT: I 1 MET cc_start: 0.8483 (tmm) cc_final: 0.7761 (ttm) REVERT: I 303 ASN cc_start: 0.7211 (p0) cc_final: 0.6957 (p0) REVERT: I 335 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5634 (ppp) REVERT: J 54 MET cc_start: 0.8642 (tpt) cc_final: 0.8213 (tpp) REVERT: J 86 THR cc_start: 0.8065 (m) cc_final: 0.7599 (p) REVERT: J 312 ASP cc_start: 0.8451 (p0) cc_final: 0.8197 (p0) REVERT: K 83 TYR cc_start: 0.9339 (m-10) cc_final: 0.9125 (m-10) REVERT: K 167 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8681 (m) REVERT: K 249 TYR cc_start: 0.8333 (m-80) cc_final: 0.8114 (m-80) REVERT: K 261 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: K 265 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: K 303 ASN cc_start: 0.8185 (p0) cc_final: 0.7792 (p0) REVERT: K 318 GLU cc_start: 0.7733 (pp20) cc_final: 0.7437 (pp20) REVERT: O 1 MET cc_start: 0.6581 (tpt) cc_final: 0.5858 (tpp) REVERT: O 15 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7932 (t) REVERT: Q 139 LEU cc_start: 0.7609 (tp) cc_final: 0.7348 (tt) REVERT: E 83 GLN cc_start: 0.9184 (mt0) cc_final: 0.8981 (mt0) REVERT: F 67 ARG cc_start: 0.8129 (mmp-170) cc_final: 0.7873 (mmp-170) REVERT: G 21 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8331 (mm-30) REVERT: G 27 VAL cc_start: 0.9570 (m) cc_final: 0.9238 (m) REVERT: G 31 ILE cc_start: 0.9250 (mm) cc_final: 0.9002 (mm) REVERT: G 56 LYS cc_start: 0.8663 (tmmt) cc_final: 0.8371 (tptt) REVERT: G 75 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8578 (tm-30) REVERT: G 78 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8805 (mt-10) REVERT: G 79 GLU cc_start: 0.8906 (pp20) cc_final: 0.8464 (pp20) REVERT: G 80 LYS cc_start: 0.7613 (pttm) cc_final: 0.7195 (pttm) REVERT: L 81 LEU cc_start: 0.9610 (mt) cc_final: 0.9293 (mt) REVERT: L 119 ASP cc_start: 0.8533 (t0) cc_final: 0.8273 (t0) REVERT: M 194 TYR cc_start: 0.8457 (m-80) cc_final: 0.8117 (m-80) REVERT: M 211 LEU cc_start: 0.8213 (mt) cc_final: 0.7895 (pp) REVERT: N 46 GLU cc_start: 0.8085 (tt0) cc_final: 0.7641 (tp30) REVERT: N 112 ILE cc_start: 0.9262 (mm) cc_final: 0.9054 (mm) REVERT: N 141 ILE cc_start: 0.9334 (mp) cc_final: 0.9051 (mm) REVERT: N 194 TYR cc_start: 0.8375 (m-80) cc_final: 0.7873 (m-80) outliers start: 164 outliers final: 104 residues processed: 577 average time/residue: 0.2055 time to fit residues: 197.7825 Evaluate side-chains 520 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 410 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 ILE 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 C residue 16 VAL 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 47 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 304 ILE Chi-restraints excluded: chain H residue 335 MET Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 335 MET Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 111 ILE 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 50 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 261 PHE Chi-restraints excluded: chain K residue 265 GLU Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 283 TYR Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 308 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 20 TYR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 195 MET Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 247 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 211 CYS Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 198 ILE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 286 TYR Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 279 VAL Chi-restraints excluded: chain N residue 313 LEU Chi-restraints excluded: chain N residue 315 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 235 optimal weight: 4.9990 chunk 355 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 418 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 347 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** J 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Q 116 HIS ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 GLN ** M 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 296 ASN ** M 331 ASN ** 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 = 0.3925 r_free = 0.3925 target = 0.104608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.080981 restraints weight = 101473.732| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.50 r_work: 0.3337 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35793 Z= 0.180 Angle : 0.742 12.445 48936 Z= 0.379 Chirality : 0.049 0.332 5602 Planarity : 0.005 0.073 5877 Dihedral : 15.500 176.261 5805 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.73 % Favored : 92.05 % Rotamer: Outliers : 3.18 % Allowed : 21.56 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.13), residues: 4126 helix: -0.34 (0.13), residues: 1571 sheet: -0.97 (0.21), residues: 608 loop : -2.16 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 298 TYR 0.035 0.002 TYR F 45 PHE 0.036 0.002 PHE L 261 TRP 0.019 0.002 TRP Q 22 HIS 0.010 0.002 HIS Q 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (35787) covalent geometry : angle 0.74215 / 0.38 (48924) SS BOND : bond 0.00464 / 0.30 ( 6) SS BOND : angle 1.41705 / 0.85 ( 12) hydrogen bonds : bond 0.04044 / 2.72 ( 1193) hydrogen bonds : angle 4.85039 / 3.41 ( 3360) *********************** 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 568 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 459 time to evaluate : 1.302 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 55 PHE cc_start: 0.8875 (m-80) cc_final: 0.8659 (m-80) REVERT: A 176 MET cc_start: 0.8857 (mmp) cc_final: 0.8564 (mmp) REVERT: A 208 MET cc_start: 0.6760 (ppp) cc_final: 0.6537 (ppp) REVERT: B 131 MET cc_start: 0.7958 (tpp) cc_final: 0.6852 (tmm) REVERT: B 205 MET cc_start: 0.7947 (tpt) cc_final: 0.7411 (mmm) REVERT: C 89 ASP cc_start: 0.8793 (m-30) cc_final: 0.8509 (m-30) REVERT: H 31 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8289 (mtmt) REVERT: H 54 MET cc_start: 0.8465 (mmp) cc_final: 0.8184 (mmp) REVERT: H 166 ASP cc_start: 0.6826 (t0) cc_final: 0.6482 (t0) REVERT: H 312 ASP cc_start: 0.8772 (p0) cc_final: 0.8453 (p0) REVERT: I 303 ASN cc_start: 0.7178 (p0) cc_final: 0.6863 (p0) REVERT: I 335 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5627 (ppp) REVERT: J 54 MET cc_start: 0.8380 (tpt) cc_final: 0.8032 (tpp) REVERT: J 312 ASP cc_start: 0.8452 (p0) cc_final: 0.8230 (p0) REVERT: K 303 ASN cc_start: 0.8106 (p0) cc_final: 0.7716 (p0) REVERT: K 318 GLU cc_start: 0.7592 (pp20) cc_final: 0.7285 (pp20) REVERT: O 1 MET cc_start: 0.6507 (tpt) cc_final: 0.6152 (tpp) REVERT: O 10 PHE cc_start: 0.8687 (p90) cc_final: 0.8222 (p90) REVERT: Q 52 PHE cc_start: 0.8901 (t80) cc_final: 0.8634 (t80) REVERT: Q 139 LEU cc_start: 0.6773 (tp) cc_final: 0.6351 (tt) REVERT: Q 140 ASP cc_start: 0.8226 (t70) cc_final: 0.7705 (t70) REVERT: F 7 ASN cc_start: 0.2577 (OUTLIER) cc_final: 0.2355 (p0) REVERT: F 25 TYR cc_start: 0.9099 (m-80) cc_final: 0.8857 (m-80) REVERT: F 38 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7207 (pt0) REVERT: F 67 ARG cc_start: 0.8081 (mmp-170) cc_final: 0.7805 (mmp-170) REVERT: G 27 VAL cc_start: 0.9538 (m) cc_final: 0.9274 (m) REVERT: G 56 LYS cc_start: 0.8729 (tmmt) cc_final: 0.8384 (tptt) REVERT: L 81 LEU cc_start: 0.9486 (mt) cc_final: 0.9168 (mt) REVERT: L 119 ASP cc_start: 0.8410 (t0) cc_final: 0.8142 (t0) REVERT: M 8 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8165 (mtm-85) REVERT: M 83 TYR cc_start: 0.8038 (m-10) cc_final: 0.7686 (m-10) REVERT: M 194 TYR cc_start: 0.8301 (m-80) cc_final: 0.7426 (m-80) REVERT: M 211 LEU cc_start: 0.8163 (mt) cc_final: 0.7794 (pp) REVERT: N 46 GLU cc_start: 0.7956 (tt0) cc_final: 0.7317 (tp30) REVERT: N 54 MET cc_start: 0.8385 (mmp) cc_final: 0.8115 (mmm) REVERT: N 112 ILE cc_start: 0.9204 (mm) cc_final: 0.8997 (mm) REVERT: N 194 TYR cc_start: 0.8366 (m-80) cc_final: 0.7773 (m-80) outliers start: 109 outliers final: 69 residues processed: 534 average time/residue: 0.2145 time to fit residues: 193.4554 Evaluate side-chains 498 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 426 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 56 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 246 HIS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain H residue 5 ILE 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 72 TYR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain I residue 335 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 111 ILE 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 184 LEU Chi-restraints excluded: chain K residue 246 LEU 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 O residue 6 VAL Chi-restraints excluded: chain O residue 20 TYR Chi-restraints excluded: chain O residue 195 MET 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 117 HIS Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 201 ASP Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 286 TYR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 369 optimal weight: 0.8980 chunk 385 optimal weight: 0.9980 chunk 240 optimal weight: 0.0570 chunk 234 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 368 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 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 ** 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 = 0.3939 r_free = 0.3939 target = 0.105332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081909 restraints weight = 101342.286| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.48 r_work: 0.3359 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35793 Z= 0.171 Angle : 0.723 12.763 48936 Z= 0.365 Chirality : 0.048 0.346 5602 Planarity : 0.005 0.072 5877 Dihedral : 15.431 177.774 5805 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.24 % Favored : 91.54 % Rotamer: Outliers : 2.59 % Allowed : 22.67 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 4126 helix: -0.21 (0.13), residues: 1569 sheet: -1.14 (0.21), residues: 570 loop : -2.00 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 164 TYR 0.031 0.002 TYR F 45 PHE 0.025 0.002 PHE K 258 TRP 0.017 0.002 TRP Q 22 HIS 0.051 0.002 HIS Q 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (35787) covalent geometry : angle 0.72264 / 0.37 (48924) SS BOND : bond 0.00366 / 0.25 ( 6) SS BOND : angle 0.93017 / 0.53 ( 12) hydrogen bonds : bond 0.03923 / 2.65 ( 1193) hydrogen bonds : angle 4.73791 / 3.31 ( 3360) *********************** 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 533 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 444 time to evaluate : 1.351 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: symmetry clash REVERT: A 52 MET cc_start: 0.7956 (tpt) cc_final: 0.7125 (mtt) REVERT: A 55 PHE cc_start: 0.8877 (m-80) cc_final: 0.8676 (m-80) REVERT: A 176 MET cc_start: 0.8861 (mmp) cc_final: 0.8609 (mmp) REVERT: A 208 MET cc_start: 0.6745 (ppp) cc_final: 0.6505 (ppp) REVERT: B 131 MET cc_start: 0.7884 (tpp) cc_final: 0.6789 (tmm) REVERT: B 205 MET cc_start: 0.8010 (tpt) cc_final: 0.7405 (mmm) REVERT: C 89 ASP cc_start: 0.8773 (m-30) cc_final: 0.8491 (m-30) REVERT: H 31 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8332 (mtmt) REVERT: H 119 ASP cc_start: 0.8250 (m-30) cc_final: 0.8042 (m-30) REVERT: H 166 ASP cc_start: 0.6702 (t0) cc_final: 0.6424 (t0) REVERT: H 312 ASP cc_start: 0.8719 (p0) cc_final: 0.8403 (p0) REVERT: I 303 ASN cc_start: 0.7280 (p0) cc_final: 0.6964 (p0) REVERT: J 54 MET cc_start: 0.8338 (tpt) cc_final: 0.8016 (tpp) REVERT: K 303 ASN cc_start: 0.8072 (p0) cc_final: 0.7688 (p0) REVERT: K 318 GLU cc_start: 0.7548 (pp20) cc_final: 0.7245 (pp20) REVERT: O 1 MET cc_start: 0.6602 (tpt) cc_final: 0.6384 (tpp) REVERT: O 10 PHE cc_start: 0.8726 (p90) cc_final: 0.7943 (p90) REVERT: Q 52 PHE cc_start: 0.8919 (t80) cc_final: 0.8693 (t80) REVERT: Q 117 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7420 (m90) REVERT: Q 139 LEU cc_start: 0.6568 (tp) cc_final: 0.6190 (tt) REVERT: Q 140 ASP cc_start: 0.8239 (t70) cc_final: 0.7697 (t70) REVERT: F 25 TYR cc_start: 0.9061 (m-80) cc_final: 0.8765 (m-80) REVERT: F 38 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7183 (pt0) REVERT: G 36 THR cc_start: 0.7970 (m) cc_final: 0.7738 (p) REVERT: G 56 LYS cc_start: 0.8715 (tmmt) cc_final: 0.8348 (tptt) REVERT: G 61 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8503 (mmmt) REVERT: L 81 LEU cc_start: 0.9492 (mt) cc_final: 0.9169 (mt) REVERT: L 119 ASP cc_start: 0.8322 (t0) cc_final: 0.8054 (t0) REVERT: L 245 MET cc_start: 0.8652 (mmm) cc_final: 0.8434 (mmm) REVERT: M 8 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8136 (mtm-85) REVERT: M 83 TYR cc_start: 0.7943 (m-10) cc_final: 0.7582 (m-10) REVERT: M 194 TYR cc_start: 0.8178 (m-80) cc_final: 0.7972 (m-80) REVERT: M 211 LEU cc_start: 0.8232 (mt) cc_final: 0.7827 (pp) REVERT: N 54 MET cc_start: 0.8546 (mmp) cc_final: 0.8252 (mmm) REVERT: N 194 TYR cc_start: 0.8222 (m-80) cc_final: 0.7818 (m-80) outliers start: 89 outliers final: 67 residues processed: 504 average time/residue: 0.2172 time to fit residues: 184.1296 Evaluate side-chains 487 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 418 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 TYR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 116 LYS 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 C residue 40 LEU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain J residue 3 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 246 LEU Chi-restraints excluded: chain K residue 261 PHE 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 O residue 6 VAL Chi-restraints excluded: chain O residue 20 TYR Chi-restraints excluded: chain O residue 114 THR Chi-restraints excluded: chain O residue 195 MET Chi-restraints excluded: chain Q residue 40 VAL 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 211 CYS Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 201 ASP Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 271 SER Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 286 TYR Chi-restraints excluded: chain M residue 322 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 348 optimal weight: 5.9990 chunk 391 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 363 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 358 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 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** ** L 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** M 121 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.081490 restraints weight = 100994.878| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.46 r_work: 0.3351 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35793 Z= 0.188 Angle : 0.725 13.051 48936 Z= 0.367 Chirality : 0.048 0.340 5602 Planarity : 0.005 0.073 5877 Dihedral : 15.421 179.158 5805 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.22 % Favored : 91.57 % Rotamer: Outliers : 2.65 % Allowed : 23.57 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.13), residues: 4126 helix: -0.14 (0.13), residues: 1559 sheet: -1.15 (0.21), residues: 584 loop : -2.00 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 79 TYR 0.039 0.002 TYR F 45 PHE 0.024 0.002 PHE I 258 TRP 0.018 0.002 TRP I 58 HIS 0.007 0.002 HIS H 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (35787) covalent geometry : angle 0.72492 / 0.37 (48924) SS BOND : bond 0.00264 / 0.14 ( 6) SS BOND : angle 0.90990 / 0.52 ( 12) hydrogen bonds : bond 0.03889 / 2.63 ( 1193) hydrogen bonds : angle 4.69685 / 3.29 ( 3360) *********************** 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 528 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 437 time to evaluate : 1.239 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: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.7924 (tpt) cc_final: 0.7110 (mtt) REVERT: A 55 PHE cc_start: 0.8905 (m-80) cc_final: 0.8701 (m-80) REVERT: A 81 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7328 (mm-40) REVERT: A 176 MET cc_start: 0.8877 (mmp) cc_final: 0.8585 (mmp) REVERT: A 208 MET cc_start: 0.6747 (ppp) cc_final: 0.6510 (ppp) REVERT: A 272 GLN cc_start: 0.6755 (mm-40) cc_final: 0.6369 (mm-40) REVERT: A 505 GLU cc_start: 0.7710 (mp0) cc_final: 0.7078 (tp30) REVERT: B 131 MET cc_start: 0.7945 (tpp) cc_final: 0.6918 (tmm) REVERT: C 89 ASP cc_start: 0.8801 (m-30) cc_final: 0.8526 (m-30) REVERT: D 26 ASP cc_start: 0.8673 (p0) cc_final: 0.8313 (p0) REVERT: H 26 TYR cc_start: 0.9420 (t80) cc_final: 0.9011 (t80) REVERT: H 31 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8326 (mtmt) REVERT: H 166 ASP cc_start: 0.6684 (t0) cc_final: 0.6413 (t0) REVERT: H 312 ASP cc_start: 0.8749 (p0) cc_final: 0.8426 (p0) REVERT: I 194 TYR cc_start: 0.8143 (m-80) cc_final: 0.7702 (m-80) REVERT: I 232 LYS cc_start: 0.7644 (mmtt) cc_final: 0.7328 (tptt) REVERT: I 303 ASN cc_start: 0.7342 (p0) cc_final: 0.7037 (p0) REVERT: I 335 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5607 (ppp) REVERT: J 54 MET cc_start: 0.8422 (tpt) cc_final: 0.8089 (tpp) REVERT: K 67 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: K 167 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8412 (m) REVERT: K 183 MET cc_start: 0.8874 (tpp) cc_final: 0.8542 (tpt) REVERT: K 194 TYR cc_start: 0.8216 (m-80) cc_final: 0.7926 (m-80) REVERT: K 303 ASN cc_start: 0.8082 (p0) cc_final: 0.7698 (p0) REVERT: K 318 GLU cc_start: 0.7542 (pp20) cc_final: 0.7226 (pp20) REVERT: O 1 MET cc_start: 0.6499 (tpt) cc_final: 0.6269 (tpp) REVERT: O 10 PHE cc_start: 0.8617 (p90) cc_final: 0.8091 (p90) REVERT: O 107 ASP cc_start: 0.7664 (t0) cc_final: 0.7422 (m-30) REVERT: Q 52 PHE cc_start: 0.8938 (t80) cc_final: 0.8697 (t80) REVERT: Q 117 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7499 (m90) REVERT: Q 139 LEU cc_start: 0.6691 (tp) cc_final: 0.6363 (tt) REVERT: Q 140 ASP cc_start: 0.8285 (t70) cc_final: 0.7722 (t0) REVERT: F 25 TYR cc_start: 0.9008 (m-80) cc_final: 0.8796 (m-80) REVERT: F 38 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7216 (pt0) REVERT: G 56 LYS cc_start: 0.8747 (tmmt) cc_final: 0.8365 (tptt) REVERT: G 61 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8525 (mmmt) REVERT: L 54 MET cc_start: 0.8881 (tpt) cc_final: 0.8653 (tpt) REVERT: L 81 LEU cc_start: 0.9508 (mt) cc_final: 0.9191 (mt) REVERT: L 119 ASP cc_start: 0.8337 (t0) cc_final: 0.8051 (t0) REVERT: L 227 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8307 (p0) REVERT: L 278 LEU cc_start: 0.8846 (tp) cc_final: 0.8608 (tp) REVERT: M 8 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8123 (mtm-85) REVERT: M 83 TYR cc_start: 0.7960 (m-10) cc_final: 0.7638 (m-10) REVERT: M 194 TYR cc_start: 0.8138 (m-80) cc_final: 0.7199 (m-80) REVERT: M 211 LEU cc_start: 0.8255 (mt) cc_final: 0.7833 (pp) REVERT: N 46 GLU cc_start: 0.7826 (tt0) cc_final: 0.7124 (tp30) REVERT: N 54 MET cc_start: 0.8611 (mmp) cc_final: 0.8240 (mmm) REVERT: N 194 TYR cc_start: 0.8138 (m-80) cc_final: 0.7742 (m-80) outliers start: 91 outliers final: 70 residues processed: 505 average time/residue: 0.2112 time to fit residues: 179.7144 Evaluate side-chains 505 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 429 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 116 LYS 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 C residue 40 LEU 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 72 TYR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 67 PHE Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 182 GLN Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 335 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 45 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 67 PHE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 261 PHE 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 20 TYR Chi-restraints excluded: chain O residue 114 THR Chi-restraints excluded: chain O residue 195 MET Chi-restraints excluded: chain Q residue 40 VAL 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 211 CYS Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 227 ASP Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 271 SER Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 286 TYR Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain N residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 128 optimal weight: 0.9980 chunk 314 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 413 optimal weight: 0.9990 chunk 354 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 ASN ** Q 60 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.107045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.084004 restraints weight = 101574.282| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.49 r_work: 0.3400 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 35793 Z= 0.150 Angle : 0.724 13.495 48936 Z= 0.365 Chirality : 0.047 0.331 5602 Planarity : 0.005 0.072 5877 Dihedral : 15.376 179.679 5805 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.14 % Favored : 91.66 % Rotamer: Outliers : 2.19 % Allowed : 24.18 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 4126 helix: -0.05 (0.13), residues: 1558 sheet: -1.16 (0.21), residues: 585 loop : -1.98 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 35 TYR 0.044 0.002 TYR A 399 PHE 0.025 0.002 PHE K 258 TRP 0.021 0.002 TRP Q 22 HIS 0.012 0.001 HIS Q 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (35787) covalent geometry : angle 0.72411 / 0.36 (48924) SS BOND : bond 0.00176 / 0.09 ( 6) SS BOND : angle 0.76056 / 0.43 ( 12) hydrogen bonds : bond 0.03732 / 2.52 ( 1193) hydrogen bonds : angle 4.65023 / 3.26 ( 3360) ********************** 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: 75 poor density : 453 time to evaluate : 1.342 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: symmetry clash REVERT: A 52 MET cc_start: 0.7641 (tpt) cc_final: 0.6944 (mtt) REVERT: A 55 PHE cc_start: 0.8894 (m-80) cc_final: 0.8691 (m-80) REVERT: A 79 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9027 (mm-30) REVERT: A 81 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7270 (mm-40) REVERT: A 176 MET cc_start: 0.8847 (mmp) cc_final: 0.8600 (mmp) REVERT: A 207 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8302 (pp20) REVERT: A 208 MET cc_start: 0.6762 (ppp) cc_final: 0.5923 (ppp) REVERT: A 272 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6581 (mm-40) REVERT: A 505 GLU cc_start: 0.7585 (mp0) cc_final: 0.6831 (tp30) REVERT: B 131 MET cc_start: 0.7899 (tpp) cc_final: 0.6833 (tmm) REVERT: C 89 ASP cc_start: 0.8738 (m-30) cc_final: 0.8490 (m-30) REVERT: C 100 TRP cc_start: 0.8546 (m100) cc_final: 0.8333 (m100) REVERT: D 25 TYR cc_start: 0.8925 (m-80) cc_final: 0.8243 (m-80) REVERT: H 119 ASP cc_start: 0.8052 (m-30) cc_final: 0.7591 (m-30) REVERT: H 312 ASP cc_start: 0.8697 (p0) cc_final: 0.8373 (p0) REVERT: I 83 TYR cc_start: 0.8432 (m-10) cc_final: 0.8208 (m-10) REVERT: I 194 TYR cc_start: 0.8053 (m-80) cc_final: 0.7640 (m-80) REVERT: I 232 LYS cc_start: 0.7437 (mmtt) cc_final: 0.7129 (tptt) REVERT: I 303 ASN cc_start: 0.7365 (p0) cc_final: 0.7097 (p0) REVERT: J 54 MET cc_start: 0.8348 (tpt) cc_final: 0.8068 (tpp) REVERT: K 15 SER cc_start: 0.8707 (p) cc_final: 0.8425 (p) REVERT: K 67 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: K 167 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8328 (m) REVERT: K 194 TYR cc_start: 0.8147 (m-80) cc_final: 0.7823 (m-80) REVERT: K 303 ASN cc_start: 0.8030 (p0) cc_final: 0.7634 (p0) REVERT: O 10 PHE cc_start: 0.8553 (p90) cc_final: 0.8165 (p90) REVERT: O 130 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8863 (tp-100) REVERT: O 195 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7488 (ptm) REVERT: Q 50 ASP cc_start: 0.8781 (m-30) cc_final: 0.8401 (p0) REVERT: Q 52 PHE cc_start: 0.8906 (t80) cc_final: 0.8654 (t80) REVERT: Q 139 LEU cc_start: 0.6621 (tp) cc_final: 0.6336 (tt) REVERT: Q 140 ASP cc_start: 0.8214 (t70) cc_final: 0.7625 (t0) REVERT: E 35 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7856 (mmt180) REVERT: F 25 TYR cc_start: 0.8985 (m-80) cc_final: 0.8781 (m-80) REVERT: F 38 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7166 (pt0) REVERT: F 67 ARG cc_start: 0.8187 (mmp-170) cc_final: 0.7939 (mmp-170) REVERT: G 42 GLU cc_start: 0.8329 (tp30) cc_final: 0.8044 (tp30) REVERT: G 56 LYS cc_start: 0.8766 (tmmt) cc_final: 0.8389 (tptt) REVERT: L 81 LEU cc_start: 0.9423 (mt) cc_final: 0.9070 (mt) REVERT: L 119 ASP cc_start: 0.8222 (t0) cc_final: 0.7949 (t0) REVERT: L 227 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8190 (p0) REVERT: L 278 LEU cc_start: 0.8697 (tp) cc_final: 0.8385 (tp) REVERT: M 8 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8140 (ttm-80) REVERT: M 83 TYR cc_start: 0.7808 (m-10) cc_final: 0.7571 (m-10) REVERT: M 194 TYR cc_start: 0.8004 (m-80) cc_final: 0.7082 (m-80) REVERT: M 211 LEU cc_start: 0.8228 (mt) cc_final: 0.7817 (pp) REVERT: N 54 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8187 (mmm) REVERT: N 194 TYR cc_start: 0.8112 (m-80) cc_final: 0.7855 (m-80) outliers start: 75 outliers final: 60 residues processed: 508 average time/residue: 0.2209 time to fit residues: 187.7037 Evaluate side-chains 500 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 434 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 116 LYS 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 C residue 40 LEU 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 I residue 5 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 67 PHE 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 36 VAL Chi-restraints excluded: chain J residue 45 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 67 PHE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 261 PHE 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 20 TYR Chi-restraints excluded: chain O residue 114 THR Chi-restraints excluded: chain O residue 195 MET Chi-restraints excluded: chain Q residue 40 VAL 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 211 CYS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 196 PHE Chi-restraints excluded: chain L residue 227 ASP Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 261 PHE Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 271 SER Chi-restraints excluded: chain M residue 286 TYR Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain N residue 54 MET Chi-restraints excluded: chain N residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 96 optimal weight: 0.0030 chunk 238 optimal weight: 0.9980 chunk 277 optimal weight: 6.9990 chunk 178 optimal weight: 0.5980 chunk 315 optimal weight: 0.7980 chunk 300 optimal weight: 0.6980 chunk 301 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 0.0050 chunk 226 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN ** Q 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 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** N 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.107990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085084 restraints weight = 101440.783| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.50 r_work: 0.3420 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 35793 Z= 0.147 Angle : 0.716 13.420 48936 Z= 0.360 Chirality : 0.047 0.320 5602 Planarity : 0.005 0.071 5877 Dihedral : 15.355 179.052 5805 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.22 % Favored : 91.61 % Rotamer: Outliers : 2.39 % Allowed : 24.53 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 4126 helix: -0.02 (0.13), residues: 1566 sheet: -1.16 (0.21), residues: 594 loop : -1.95 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 260 TYR 0.038 0.002 TYR A 399 PHE 0.024 0.002 PHE K 258 TRP 0.024 0.002 TRP D 4 HIS 0.010 0.001 HIS Q 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (35787) covalent geometry : angle 0.71611 / 0.36 (48924) SS BOND : bond 0.00137 / 0.07 ( 6) SS BOND : angle 0.69736 / 0.39 ( 12) hydrogen bonds : bond 0.03667 / 2.48 ( 1193) hydrogen bonds : angle 4.60748 / 3.23 ( 3360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8587.00 seconds wall clock time: 148 minutes 47.50 seconds (8927.50 seconds total)