Starting phenix.real_space_refine on Sun Jun 15 17:54:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4l_42972/06_2025/8v4l_42972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4l_42972/06_2025/8v4l_42972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v4l_42972/06_2025/8v4l_42972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4l_42972/06_2025/8v4l_42972.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4l_42972/06_2025/8v4l_42972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4l_42972/06_2025/8v4l_42972.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 12 5.49 5 Mg 4 5.21 5 S 117 5.16 5 C 11002 2.51 5 N 3007 2.21 5 O 3320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17463 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3373 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3345 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3363 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3303 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3908 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 35, 'TRANS': 465} Chain breaks: 3 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 14, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 115 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.72, per 1000 atoms: 0.67 Number of scatterers: 17463 At special positions: 0 Unit cell: (134.46, 124.5, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 117 16.00 P 12 15.00 Mg 4 11.99 O 3320 8.00 N 3007 7.00 C 11002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 434 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 252 " 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4146 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 14 sheets defined 48.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.946A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.891A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.718A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.902A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.986A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.718A pdb=" N GLU A 284 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.683A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.545A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.910A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.027A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.126A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.235A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.562A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.879A pdb=" N ILE B 84 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 85' Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.755A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.883A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.525A pdb=" N VAL B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 176 " --> pdb=" O PRO B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.284A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.893A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.545A pdb=" N ARG B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.557A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 299' Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.633A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.541A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.872A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.135A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.961A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.931A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.008A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 85 removed outlier: 4.614A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 127 removed outlier: 4.267A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.479A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.528A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.760A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.988A pdb=" N TYR C 282 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.786A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.550A pdb=" N GLY C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.818A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.999A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.902A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 435 removed outlier: 4.169A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.038A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.587A pdb=" N SER D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.877A pdb=" N GLU D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.640A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.903A pdb=" N SER D 176 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.577A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.856A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.720A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.682A pdb=" N ASN D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 299 " --> pdb=" O ALA D 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 295 through 299' Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.656A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.568A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.900A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.037A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 425 removed outlier: 3.837A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 104 removed outlier: 3.741A pdb=" N GLN E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 256 through 270 removed outlier: 4.023A pdb=" N PHE E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.541A pdb=" N GLN E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 340 removed outlier: 3.543A pdb=" N SER E 340 " --> pdb=" O HIS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 467 removed outlier: 4.558A pdb=" N TYR E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Proline residue: E 462 - end of helix Processing helix chain 'E' and resid 480 through 485 Processing helix chain 'E' and resid 494 through 497 removed outlier: 3.638A pdb=" N GLY E 497 " --> pdb=" O SER E 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 494 through 497' Processing helix chain 'E' and resid 498 through 508 Processing helix chain 'E' and resid 551 through 570 removed outlier: 3.555A pdb=" N MET E 569 " --> pdb=" O ALA E 565 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.930A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.559A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.255A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.708A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.940A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU C 3 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU C 136 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 5 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N SER C 140 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL C 9 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.077A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.552A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.532A pdb=" N ARG E 111 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR E 112 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG E 118 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.463A pdb=" N TYR E 52 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASN E 91 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE E 54 " --> pdb=" O ASN E 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 189 through 198 removed outlier: 7.160A pdb=" N VAL E 205 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE E 245 " --> pdb=" O LYS E 287 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE E 289 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 247 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR E 429 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 216 through 220 removed outlier: 5.236A pdb=" N ARG E 238 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2907 1.31 - 1.44: 4955 1.44 - 1.57: 9811 1.57 - 1.69: 22 1.69 - 1.82: 187 Bond restraints: 17882 Sorted by residual: bond pdb=" O3B G2P B 602 " pdb=" PG G2P B 602 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O3B G2P D 502 " pdb=" PG G2P D 502 " ideal model delta sigma weight residual 1.716 1.613 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C PHE D 260 " pdb=" N PRO D 261 " ideal model delta sigma weight residual 1.334 1.393 -0.058 1.51e-02 4.39e+03 1.50e+01 bond pdb=" CA VAL D 286 " pdb=" C VAL D 286 " ideal model delta sigma weight residual 1.520 1.552 -0.032 8.80e-03 1.29e+04 1.34e+01 bond pdb=" O5' G2P B 602 " pdb=" PA G2P B 602 " ideal model delta sigma weight residual 1.656 1.587 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 17877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 23539 2.65 - 5.31: 678 5.31 - 7.96: 76 7.96 - 10.62: 21 10.62 - 13.27: 7 Bond angle restraints: 24321 Sorted by residual: angle pdb=" N THR E 256 " pdb=" CA THR E 256 " pdb=" C THR E 256 " ideal model delta sigma weight residual 109.81 120.78 -10.97 2.21e+00 2.05e-01 2.46e+01 angle pdb=" C ASP E 534 " pdb=" N ASN E 535 " pdb=" CA ASN E 535 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 angle pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " pdb=" PB GTP A 502 " ideal model delta sigma weight residual 120.50 133.77 -13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" PA GTP C 502 " pdb=" O3A GTP C 502 " pdb=" PB GTP C 502 " ideal model delta sigma weight residual 120.50 133.63 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" C ASN E 178 " pdb=" N HIS E 179 " pdb=" CA HIS E 179 " ideal model delta sigma weight residual 121.80 132.28 -10.48 2.44e+00 1.68e-01 1.84e+01 ... (remaining 24316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.02: 10275 28.02 - 56.04: 301 56.04 - 84.06: 33 84.06 - 112.08: 4 112.08 - 140.11: 8 Dihedral angle restraints: 10621 sinusoidal: 4164 harmonic: 6457 Sorted by residual: dihedral pdb=" C8 GTP C 502 " pdb=" C1' GTP C 502 " pdb=" N9 GTP C 502 " pdb=" O4' GTP C 502 " ideal model delta sinusoidal sigma weight residual 104.59 -35.51 140.11 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C8 GTP A 502 " pdb=" C1' GTP A 502 " pdb=" N9 GTP A 502 " pdb=" O4' GTP A 502 " ideal model delta sinusoidal sigma weight residual 104.59 -34.82 139.41 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" C5' GTP A 502 " pdb=" O5' GTP A 502 " pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " ideal model delta sinusoidal sigma weight residual 69.27 -158.51 -132.22 1 2.00e+01 2.50e-03 4.01e+01 ... (remaining 10618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2332 0.093 - 0.185: 304 0.185 - 0.278: 19 0.278 - 0.371: 1 0.371 - 0.463: 1 Chirality restraints: 2657 Sorted by residual: chirality pdb=" CB ILE E 289 " pdb=" CA ILE E 289 " pdb=" CG1 ILE E 289 " pdb=" CG2 ILE E 289 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA GLU B1001 " pdb=" N GLU B1001 " pdb=" C GLU B1001 " pdb=" CB GLU B1001 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB VAL E 597 " pdb=" CA VAL E 597 " pdb=" CG1 VAL E 597 " pdb=" CG2 VAL E 597 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2654 not shown) Planarity restraints: 3175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 267 " -0.049 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO D 268 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 268 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 268 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 432 " -0.017 2.00e-02 2.50e+03 1.98e-02 7.88e+00 pdb=" CG TYR A 432 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 432 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 432 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 432 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 432 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 432 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 432 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 221 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO E 222 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 222 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 222 " 0.036 5.00e-02 4.00e+02 ... (remaining 3172 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 323 2.69 - 3.24: 15944 3.24 - 3.80: 28904 3.80 - 4.35: 38552 4.35 - 4.90: 64400 Nonbonded interactions: 148123 Sorted by model distance: nonbonded pdb=" OE2 GLU E 255 " pdb="ZN ZN E 701 " model vdw 2.140 2.230 nonbonded pdb="MG MG A 501 " pdb=" O2B GTP A 502 " model vdw 2.233 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G G2P B 602 " model vdw 2.257 2.170 nonbonded pdb="MG MG D 501 " pdb=" O2G G2P D 502 " model vdw 2.303 2.170 nonbonded pdb=" OG SER A 178 " pdb=" OE1 GLU A 183 " model vdw 2.323 3.040 ... (remaining 148118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 325 or (resid 326 and (name N or \ name CA or name C or name O or name CB )) or resid 327 through 413 or (resid 41 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 415 through \ 439 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 439 or resid 501 throu \ gh 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 281 or (resid 282 through 284 an \ d (name N or name CA or name C or name O or name CB )) or resid 285 through 287 \ or (resid 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 through 327 or (resid 328 and (name N or name CA or name C or name O or name \ CB )) or resid 329 through 360 or (resid 361 through 362 and (name N or name CA \ or name C or name O or name CB )) or resid 363 through 389 or (resid 390 and (n \ ame N or name CA or name C or name O or name CB )) or resid 391 through 428 or r \ esid 601 through 602)) selection = (chain 'D' and (resid 1 through 278 or (resid 279 and (name N or name CA or name \ C or name O or name CB )) or resid 280 through 428 or resid 501 through 502)) } 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: 9.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 44.200 Find NCS groups from input model: 0.820 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.006 0.106 17885 Z= 0.315 Angle : 1.052 13.274 24321 Z= 0.568 Chirality : 0.061 0.463 2657 Planarity : 0.009 0.102 3175 Dihedral : 14.216 140.105 6475 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 2208 helix: -1.63 (0.13), residues: 892 sheet: 0.34 (0.28), residues: 358 loop : -1.12 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 344 HIS 0.009 0.002 HIS A 197 PHE 0.031 0.003 PHE C 255 TYR 0.044 0.003 TYR A 432 ARG 0.014 0.001 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.16943 ( 784) hydrogen bonds : angle 7.31356 ( 2268) metal coordination : bond 0.00568 ( 2) covalent geometry : bond 0.00641 (17882) covalent geometry : angle 1.05202 (24321) Misc. bond : bond 0.04547 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 595 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7935 (p90) cc_final: 0.7520 (p90) REVERT: A 55 GLU cc_start: 0.7832 (tt0) cc_final: 0.7231 (tm-30) REVERT: A 83 TYR cc_start: 0.8300 (m-80) cc_final: 0.8035 (m-80) REVERT: A 110 ILE cc_start: 0.8283 (mm) cc_final: 0.8027 (mp) REVERT: A 117 LEU cc_start: 0.6935 (tp) cc_final: 0.6573 (tt) REVERT: A 120 ASP cc_start: 0.7308 (m-30) cc_final: 0.6875 (m-30) REVERT: A 124 LYS cc_start: 0.7498 (mttt) cc_final: 0.7247 (mtmm) REVERT: A 133 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8134 (mm-40) REVERT: A 158 SER cc_start: 0.8720 (t) cc_final: 0.8504 (t) REVERT: A 166 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8106 (mtmm) REVERT: A 199 ASP cc_start: 0.7346 (m-30) cc_final: 0.7124 (m-30) REVERT: A 256 GLN cc_start: 0.7629 (mt0) cc_final: 0.5913 (tm-30) REVERT: A 282 TYR cc_start: 0.8338 (m-80) cc_final: 0.8050 (m-80) REVERT: A 284 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7508 (mt-10) REVERT: A 290 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7318 (mt-10) REVERT: A 304 LYS cc_start: 0.8368 (tptp) cc_final: 0.7918 (ttmt) REVERT: A 322 ASP cc_start: 0.7715 (t0) cc_final: 0.7454 (t0) REVERT: A 324 VAL cc_start: 0.8081 (m) cc_final: 0.7158 (t) REVERT: A 326 LYS cc_start: 0.7735 (pttp) cc_final: 0.7226 (ptpt) REVERT: A 345 ASP cc_start: 0.8340 (p0) cc_final: 0.8121 (p0) REVERT: A 367 ASP cc_start: 0.7728 (p0) cc_final: 0.7280 (p0) REVERT: A 370 LYS cc_start: 0.8373 (tptt) cc_final: 0.8049 (tptt) REVERT: A 388 TRP cc_start: 0.7973 (m-10) cc_final: 0.7721 (m-10) REVERT: A 414 GLU cc_start: 0.7641 (mp0) cc_final: 0.7010 (pm20) REVERT: A 420 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 423 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 434 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7164 (pp20) REVERT: B 19 LYS cc_start: 0.8588 (tptm) cc_final: 0.8263 (tppp) REVERT: B 41 ASP cc_start: 0.8431 (m-30) cc_final: 0.8052 (t0) REVERT: B 48 ASN cc_start: 0.8256 (p0) cc_final: 0.7948 (p0) REVERT: B 53 GLU cc_start: 0.7832 (tt0) cc_final: 0.7531 (pm20) REVERT: B 58 LYS cc_start: 0.7195 (tttt) cc_final: 0.6973 (tttt) REVERT: B 69 GLU cc_start: 0.7732 (tt0) cc_final: 0.7333 (pt0) REVERT: B 103 LYS cc_start: 0.8556 (ttmm) cc_final: 0.7884 (ttmm) REVERT: B 107 THR cc_start: 0.8042 (m) cc_final: 0.7606 (p) REVERT: B 118 ASP cc_start: 0.7409 (m-30) cc_final: 0.6977 (m-30) REVERT: B 123 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7342 (tp30) REVERT: B 127 CYS cc_start: 0.6983 (m) cc_final: 0.6301 (m) REVERT: B 134 GLN cc_start: 0.7990 (mt0) cc_final: 0.7624 (mt0) REVERT: B 164 MET cc_start: 0.8599 (tpp) cc_final: 0.8345 (tpt) REVERT: B 174 LYS cc_start: 0.8377 (mmpt) cc_final: 0.7911 (mmpt) REVERT: B 191 GLN cc_start: 0.8032 (mm110) cc_final: 0.7767 (mp-120) REVERT: B 201 CYS cc_start: 0.8634 (m) cc_final: 0.8282 (m) REVERT: B 203 ASP cc_start: 0.8218 (t70) cc_final: 0.7641 (t0) REVERT: B 205 GLU cc_start: 0.7850 (tt0) cc_final: 0.7629 (tt0) REVERT: B 216 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8187 (mmmm) REVERT: B 252 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8191 (ttpt) REVERT: B 278 SER cc_start: 0.8408 (m) cc_final: 0.7674 (p) REVERT: B 289 LEU cc_start: 0.7435 (mt) cc_final: 0.7127 (mp) REVERT: B 291 GLN cc_start: 0.8152 (pp30) cc_final: 0.7946 (pp30) REVERT: B 309 ARG cc_start: 0.7216 (mtt-85) cc_final: 0.6999 (mtt-85) REVERT: B 328 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6853 (tp30) REVERT: B 361 LEU cc_start: 0.8147 (tp) cc_final: 0.7878 (tt) REVERT: B 362 LYS cc_start: 0.8192 (tttp) cc_final: 0.7944 (tttp) REVERT: B 380 ARG cc_start: 0.7563 (mtt90) cc_final: 0.7064 (mtm-85) REVERT: B 390 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7483 (ptp90) REVERT: B 407 GLU cc_start: 0.7863 (tt0) cc_final: 0.7506 (mt-10) REVERT: B 410 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7083 (mm-30) REVERT: B 412 GLU cc_start: 0.7800 (tp30) cc_final: 0.7527 (tp30) REVERT: B 414 ASN cc_start: 0.7425 (m110) cc_final: 0.7028 (m110) REVERT: B 417 ASP cc_start: 0.7524 (m-30) cc_final: 0.7201 (m-30) REVERT: B 421 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 3 GLU cc_start: 0.7415 (mp0) cc_final: 0.6179 (mp0) REVERT: C 60 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7528 (ttmm) REVERT: C 71 GLU cc_start: 0.7007 (pt0) cc_final: 0.6546 (pm20) REVERT: C 90 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8020 (tp30) REVERT: C 91 GLN cc_start: 0.7991 (mt0) cc_final: 0.7740 (mt0) REVERT: C 112 LYS cc_start: 0.7987 (pttp) cc_final: 0.7777 (pttp) REVERT: C 116 ASP cc_start: 0.7479 (p0) cc_final: 0.7219 (p0) REVERT: C 117 LEU cc_start: 0.7839 (tp) cc_final: 0.7599 (tt) REVERT: C 120 ASP cc_start: 0.7648 (m-30) cc_final: 0.7410 (m-30) REVERT: C 123 ARG cc_start: 0.7347 (tpp-160) cc_final: 0.7016 (tpp80) REVERT: C 155 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7440 (tp30) REVERT: C 158 SER cc_start: 0.8658 (t) cc_final: 0.8435 (t) REVERT: C 245 ASP cc_start: 0.8008 (p0) cc_final: 0.7584 (p0) REVERT: C 280 LYS cc_start: 0.8397 (mttp) cc_final: 0.7314 (mmtt) REVERT: C 308 ARG cc_start: 0.5105 (tpt170) cc_final: 0.3968 (mpp80) REVERT: C 322 ASP cc_start: 0.8028 (t70) cc_final: 0.7708 (t70) REVERT: C 386 GLU cc_start: 0.7714 (mp0) cc_final: 0.6990 (mp0) REVERT: C 411 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7869 (mm-30) REVERT: C 420 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7227 (mp0) REVERT: C 424 ASP cc_start: 0.7723 (m-30) cc_final: 0.7496 (t70) REVERT: C 429 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7803 (mt-10) REVERT: C 433 GLU cc_start: 0.7735 (pt0) cc_final: 0.7062 (tp30) REVERT: C 434 GLU cc_start: 0.7698 (pp20) cc_final: 0.7339 (pp20) REVERT: D 3 GLU cc_start: 0.7571 (mp0) cc_final: 0.6658 (mp0) REVERT: D 19 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8126 (tppp) REVERT: D 22 GLU cc_start: 0.8359 (tt0) cc_final: 0.7403 (tp30) REVERT: D 45 GLU cc_start: 0.8643 (tt0) cc_final: 0.7891 (tm-30) REVERT: D 58 LYS cc_start: 0.8056 (tttt) cc_final: 0.7346 (tttt) REVERT: D 69 GLU cc_start: 0.7568 (pp20) cc_final: 0.7221 (pm20) REVERT: D 88 ASP cc_start: 0.8394 (t70) cc_final: 0.7879 (t0) REVERT: D 108 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 121 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7537 (mtm-85) REVERT: D 123 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7721 (mm-30) REVERT: D 158 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7542 (mm-30) REVERT: D 159 TYR cc_start: 0.7792 (m-80) cc_final: 0.7322 (m-80) REVERT: D 174 LYS cc_start: 0.8346 (mptt) cc_final: 0.8080 (mptt) REVERT: D 175 VAL cc_start: 0.8429 (m) cc_final: 0.7537 (t) REVERT: D 181 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7399 (mt-10) REVERT: D 198 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7962 (mt-10) REVERT: D 203 ASP cc_start: 0.8200 (t0) cc_final: 0.7166 (t70) REVERT: D 205 GLU cc_start: 0.7943 (tt0) cc_final: 0.7386 (mp0) REVERT: D 209 ASP cc_start: 0.7469 (t0) cc_final: 0.7225 (t0) REVERT: D 213 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7887 (mtm-85) REVERT: D 216 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8513 (mmmm) REVERT: D 221 THR cc_start: 0.8638 (p) cc_final: 0.8429 (t) REVERT: D 281 TYR cc_start: 0.7968 (m-80) cc_final: 0.7715 (m-80) REVERT: D 291 GLN cc_start: 0.8104 (pp30) cc_final: 0.7811 (pp30) REVERT: D 325 GLU cc_start: 0.7952 (tp30) cc_final: 0.7508 (tp30) REVERT: D 383 GLU cc_start: 0.8032 (tp30) cc_final: 0.7417 (tp30) REVERT: D 391 ARG cc_start: 0.8335 (mmm160) cc_final: 0.6666 (ptm-80) REVERT: D 404 ASP cc_start: 0.8422 (m-30) cc_final: 0.7705 (m-30) REVERT: D 405 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8085 (tm-30) REVERT: D 407 GLU cc_start: 0.7766 (mp0) cc_final: 0.7106 (mp0) REVERT: D 410 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7433 (tm-30) REVERT: D 417 ASP cc_start: 0.8025 (m-30) cc_final: 0.7785 (m-30) REVERT: D 424 GLN cc_start: 0.8119 (tt0) cc_final: 0.7878 (tt0) REVERT: E 9 LEU cc_start: 0.7928 (tt) cc_final: 0.7480 (tm) REVERT: E 53 GLU cc_start: 0.6580 (mp0) cc_final: 0.6327 (mp0) REVERT: E 69 ASN cc_start: 0.7998 (t0) cc_final: 0.7388 (t0) REVERT: E 93 MET cc_start: 0.8118 (mmp) cc_final: 0.7704 (mmm) REVERT: E 104 GLN cc_start: 0.7333 (mt0) cc_final: 0.7058 (mt0) REVERT: E 120 GLU cc_start: 0.7517 (mp0) cc_final: 0.6947 (mp0) REVERT: E 129 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6812 (tm-30) REVERT: E 187 ASP cc_start: 0.8121 (t0) cc_final: 0.7510 (t0) REVERT: E 193 ARG cc_start: 0.7972 (ttt-90) cc_final: 0.7503 (ttt-90) REVERT: E 278 GLN cc_start: 0.8242 (mt0) cc_final: 0.7984 (mt0) REVERT: E 311 LEU cc_start: 0.7379 (mt) cc_final: 0.7174 (mp) REVERT: E 322 LEU cc_start: 0.8313 (mp) cc_final: 0.8102 (mp) REVERT: E 340 SER cc_start: 0.7772 (t) cc_final: 0.7550 (t) REVERT: E 458 ASN cc_start: 0.8596 (t0) cc_final: 0.8374 (t0) REVERT: E 473 ASP cc_start: 0.7613 (p0) cc_final: 0.7371 (p0) REVERT: E 478 ASN cc_start: 0.7546 (t0) cc_final: 0.7167 (t0) REVERT: E 534 ASP cc_start: 0.7943 (p0) cc_final: 0.7556 (p0) REVERT: E 550 TYR cc_start: 0.8562 (m-80) cc_final: 0.8073 (m-10) REVERT: E 578 ILE cc_start: 0.7834 (tp) cc_final: 0.7534 (tt) outliers start: 1 outliers final: 1 residues processed: 596 average time/residue: 1.5259 time to fit residues: 997.7001 Evaluate side-chains 466 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 465 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 6.9990 chunk 167 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 173 optimal weight: 0.3980 chunk 67 optimal weight: 0.1980 chunk 105 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 35 GLN A 176 GLN A 285 GLN B 227 HIS B 280 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 292 GLN D 348 ASN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 214 HIS E 226 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094556 restraints weight = 29688.858| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.94 r_work: 0.3291 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17885 Z= 0.128 Angle : 0.584 9.638 24321 Z= 0.303 Chirality : 0.044 0.183 2657 Planarity : 0.005 0.061 3175 Dihedral : 10.645 141.244 2522 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.55 % Allowed : 12.74 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2208 helix: 0.08 (0.16), residues: 921 sheet: 0.42 (0.27), residues: 368 loop : -0.81 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 592 HIS 0.007 0.001 HIS D 190 PHE 0.026 0.002 PHE A 255 TYR 0.011 0.001 TYR A 172 ARG 0.008 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 784) hydrogen bonds : angle 4.91953 ( 2268) metal coordination : bond 0.00316 ( 2) covalent geometry : bond 0.00284 (17882) covalent geometry : angle 0.58401 (24321) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 476 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8501 (p90) cc_final: 0.8070 (p90) REVERT: A 50 ASN cc_start: 0.8481 (t0) cc_final: 0.7998 (t0) REVERT: A 83 TYR cc_start: 0.8600 (m-80) cc_final: 0.8347 (m-80) REVERT: A 116 ASP cc_start: 0.7676 (m-30) cc_final: 0.6953 (p0) REVERT: A 117 LEU cc_start: 0.7958 (tp) cc_final: 0.7655 (tt) REVERT: A 120 ASP cc_start: 0.7754 (m-30) cc_final: 0.7418 (m-30) REVERT: A 290 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8251 (mm-30) REVERT: A 367 ASP cc_start: 0.7818 (p0) cc_final: 0.7540 (p0) REVERT: A 370 LYS cc_start: 0.8488 (tptt) cc_final: 0.8234 (tptt) REVERT: A 414 GLU cc_start: 0.7964 (mp0) cc_final: 0.7645 (pm20) REVERT: A 423 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7924 (mm-30) REVERT: B 19 LYS cc_start: 0.9037 (tptm) cc_final: 0.8599 (tppp) REVERT: B 81 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7429 (t80) REVERT: B 103 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8434 (mtpm) REVERT: B 118 ASP cc_start: 0.7983 (m-30) cc_final: 0.7697 (m-30) REVERT: B 123 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7661 (tp30) REVERT: B 127 CYS cc_start: 0.7616 (m) cc_final: 0.7076 (m) REVERT: B 158 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: B 203 ASP cc_start: 0.7895 (t70) cc_final: 0.7642 (t0) REVERT: B 216 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8711 (mmmm) REVERT: B 278 SER cc_start: 0.8606 (m) cc_final: 0.8195 (p) REVERT: B 291 GLN cc_start: 0.8301 (pp30) cc_final: 0.8013 (pp30) REVERT: B 324 LYS cc_start: 0.8492 (tptm) cc_final: 0.8083 (tppp) REVERT: B 328 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7353 (tp30) REVERT: B 391 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.7226 (mtp-110) REVERT: B 407 GLU cc_start: 0.7996 (tt0) cc_final: 0.7790 (mt-10) REVERT: B 412 GLU cc_start: 0.8228 (tp30) cc_final: 0.7815 (tp30) REVERT: B 414 ASN cc_start: 0.8054 (m110) cc_final: 0.7689 (m110) REVERT: B 417 ASP cc_start: 0.8164 (m-30) cc_final: 0.7629 (m-30) REVERT: B 421 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7450 (mt-10) REVERT: C 50 ASN cc_start: 0.8632 (t0) cc_final: 0.8233 (t0) REVERT: C 82 THR cc_start: 0.9130 (m) cc_final: 0.8930 (p) REVERT: C 123 ARG cc_start: 0.8029 (tpp-160) cc_final: 0.7635 (tpp80) REVERT: C 158 SER cc_start: 0.8887 (t) cc_final: 0.8658 (t) REVERT: C 280 LYS cc_start: 0.8872 (mttp) cc_final: 0.7436 (mmtt) REVERT: C 284 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7023 (mp0) REVERT: C 322 ASP cc_start: 0.8037 (t70) cc_final: 0.7819 (OUTLIER) REVERT: C 337 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8642 (p) REVERT: C 386 GLU cc_start: 0.7728 (mp0) cc_final: 0.7459 (mp0) REVERT: C 392 ASP cc_start: 0.7860 (m-30) cc_final: 0.7561 (m-30) REVERT: C 423 GLU cc_start: 0.8003 (tp30) cc_final: 0.7719 (mm-30) REVERT: D 3 GLU cc_start: 0.7799 (mp0) cc_final: 0.7178 (mp0) REVERT: D 19 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8673 (tppp) REVERT: D 22 GLU cc_start: 0.8579 (tt0) cc_final: 0.7993 (tp30) REVERT: D 45 GLU cc_start: 0.8290 (tt0) cc_final: 0.8020 (tm-30) REVERT: D 88 ASP cc_start: 0.8255 (t70) cc_final: 0.7829 (t0) REVERT: D 103 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8701 (mtpm) REVERT: D 123 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7978 (mm-30) REVERT: D 158 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 159 TYR cc_start: 0.8335 (m-80) cc_final: 0.8078 (m-80) REVERT: D 174 LYS cc_start: 0.8386 (mptt) cc_final: 0.8160 (mptt) REVERT: D 181 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7676 (mt-10) REVERT: D 198 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8045 (mt-10) REVERT: D 203 ASP cc_start: 0.8144 (t0) cc_final: 0.7858 (t70) REVERT: D 257 MET cc_start: 0.8414 (mmm) cc_final: 0.8078 (mtp) REVERT: D 291 GLN cc_start: 0.8620 (pp30) cc_final: 0.8387 (pp30) REVERT: D 323 MET cc_start: 0.8376 (mmm) cc_final: 0.8096 (mmm) REVERT: D 325 GLU cc_start: 0.7956 (tp30) cc_final: 0.7703 (tp30) REVERT: D 383 GLU cc_start: 0.8163 (tp30) cc_final: 0.7744 (tp30) REVERT: D 391 ARG cc_start: 0.8343 (mmm160) cc_final: 0.6844 (ptm-80) REVERT: D 404 ASP cc_start: 0.8293 (m-30) cc_final: 0.7551 (m-30) REVERT: D 407 GLU cc_start: 0.8031 (mp0) cc_final: 0.7650 (mp0) REVERT: D 410 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7792 (tm-30) REVERT: D 412 GLU cc_start: 0.7910 (tp30) cc_final: 0.7696 (mm-30) REVERT: D 413 SER cc_start: 0.8557 (t) cc_final: 0.7858 (p) REVERT: D 417 ASP cc_start: 0.8200 (m-30) cc_final: 0.7988 (m-30) REVERT: E 59 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8236 (mtp180) REVERT: E 69 ASN cc_start: 0.8123 (t0) cc_final: 0.7745 (t0) REVERT: E 98 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7879 (mp10) REVERT: E 120 GLU cc_start: 0.7514 (mp0) cc_final: 0.7235 (mp0) REVERT: E 129 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7650 (tm-30) REVERT: E 187 ASP cc_start: 0.7963 (t0) cc_final: 0.7289 (t0) REVERT: E 278 GLN cc_start: 0.8498 (mt0) cc_final: 0.8295 (mt0) REVERT: E 291 MET cc_start: 0.8694 (mtm) cc_final: 0.8364 (mtm) REVERT: E 432 ASP cc_start: 0.7515 (m-30) cc_final: 0.7307 (m-30) REVERT: E 439 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8278 (ttpp) REVERT: E 457 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7855 (mm-30) REVERT: E 478 ASN cc_start: 0.8280 (t0) cc_final: 0.7927 (t0) REVERT: E 519 TYR cc_start: 0.8666 (m-80) cc_final: 0.8466 (m-10) REVERT: E 578 ILE cc_start: 0.8492 (tp) cc_final: 0.8245 (tt) outliers start: 47 outliers final: 16 residues processed: 496 average time/residue: 1.6210 time to fit residues: 880.2011 Evaluate side-chains 455 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 436 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 533 HIS Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 597 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 66 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 52 optimal weight: 0.0570 chunk 213 optimal weight: 0.0030 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 153 optimal weight: 0.0570 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.3026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 170 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094062 restraints weight = 29563.503| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.94 r_work: 0.3283 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17885 Z= 0.112 Angle : 0.557 8.307 24321 Z= 0.284 Chirality : 0.043 0.168 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.296 151.496 2522 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.44 % Allowed : 16.32 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2208 helix: 0.78 (0.17), residues: 922 sheet: 0.49 (0.27), residues: 362 loop : -0.64 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.009 0.001 HIS D 190 PHE 0.020 0.001 PHE E 75 TYR 0.014 0.001 TYR B 340 ARG 0.010 0.001 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 784) hydrogen bonds : angle 4.53844 ( 2268) metal coordination : bond 0.00201 ( 2) covalent geometry : bond 0.00250 (17882) covalent geometry : angle 0.55734 (24321) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 443 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8530 (p90) cc_final: 0.8174 (p90) REVERT: A 50 ASN cc_start: 0.8455 (t0) cc_final: 0.7962 (t0) REVERT: A 77 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 83 TYR cc_start: 0.8636 (m-80) cc_final: 0.8340 (m-80) REVERT: A 116 ASP cc_start: 0.7768 (m-30) cc_final: 0.7031 (p0) REVERT: A 117 LEU cc_start: 0.7979 (tp) cc_final: 0.7590 (tt) REVERT: A 120 ASP cc_start: 0.7783 (m-30) cc_final: 0.7463 (m-30) REVERT: A 251 ASP cc_start: 0.7572 (m-30) cc_final: 0.7275 (p0) REVERT: A 290 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8258 (mm-30) REVERT: A 338 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8440 (ttpp) REVERT: A 367 ASP cc_start: 0.7951 (p0) cc_final: 0.7673 (p0) REVERT: A 370 LYS cc_start: 0.8477 (tptt) cc_final: 0.8220 (tptt) REVERT: A 414 GLU cc_start: 0.8000 (mp0) cc_final: 0.7522 (mp0) REVERT: A 417 GLU cc_start: 0.7894 (tt0) cc_final: 0.7673 (mt-10) REVERT: A 420 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 423 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7904 (mm-30) REVERT: A 438 ASP cc_start: 0.7970 (m-30) cc_final: 0.7651 (m-30) REVERT: B 19 LYS cc_start: 0.9003 (tptm) cc_final: 0.8540 (tppp) REVERT: B 103 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8423 (mtpm) REVERT: B 118 ASP cc_start: 0.7901 (m-30) cc_final: 0.7604 (m-30) REVERT: B 123 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7738 (tp30) REVERT: B 127 CYS cc_start: 0.7759 (m) cc_final: 0.7178 (m) REVERT: B 158 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: B 174 LYS cc_start: 0.8482 (mmpt) cc_final: 0.8229 (mmpt) REVERT: B 203 ASP cc_start: 0.7687 (t70) cc_final: 0.7428 (t0) REVERT: B 216 LYS cc_start: 0.9063 (mmtm) cc_final: 0.8731 (mmmm) REVERT: B 274 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8372 (p) REVERT: B 278 SER cc_start: 0.8585 (m) cc_final: 0.8174 (p) REVERT: B 291 GLN cc_start: 0.8334 (pp30) cc_final: 0.8027 (pp30) REVERT: B 328 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7330 (tp30) REVERT: B 407 GLU cc_start: 0.7959 (tt0) cc_final: 0.7702 (mt-10) REVERT: B 410 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7151 (mm-30) REVERT: B 412 GLU cc_start: 0.8164 (tp30) cc_final: 0.7701 (tp30) REVERT: B 414 ASN cc_start: 0.8184 (m110) cc_final: 0.7766 (m110) REVERT: B 417 ASP cc_start: 0.8140 (m-30) cc_final: 0.7746 (m-30) REVERT: C 3 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: C 50 ASN cc_start: 0.8748 (t0) cc_final: 0.8346 (t0) REVERT: C 71 GLU cc_start: 0.7389 (pt0) cc_final: 0.7147 (pm20) REVERT: C 123 ARG cc_start: 0.8013 (tpp-160) cc_final: 0.7588 (tpp80) REVERT: C 158 SER cc_start: 0.8920 (t) cc_final: 0.8697 (t) REVERT: C 196 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: C 280 LYS cc_start: 0.8918 (mttp) cc_final: 0.7471 (mmtt) REVERT: C 284 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7138 (mp0) REVERT: C 308 ARG cc_start: 0.6578 (tpt170) cc_final: 0.5629 (tpt170) REVERT: C 322 ASP cc_start: 0.8017 (t70) cc_final: 0.7796 (t0) REVERT: C 386 GLU cc_start: 0.7673 (mp0) cc_final: 0.7391 (mp0) REVERT: C 413 MET cc_start: 0.8637 (ttm) cc_final: 0.8407 (ttp) REVERT: C 420 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7432 (mm-30) REVERT: C 423 GLU cc_start: 0.7901 (tp30) cc_final: 0.7669 (mm-30) REVERT: C 431 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: D 3 GLU cc_start: 0.7915 (mp0) cc_final: 0.7363 (mp0) REVERT: D 22 GLU cc_start: 0.8612 (tt0) cc_final: 0.8010 (tp30) REVERT: D 45 GLU cc_start: 0.8295 (tt0) cc_final: 0.7933 (tm-30) REVERT: D 69 GLU cc_start: 0.7590 (pm20) cc_final: 0.7386 (pm20) REVERT: D 88 ASP cc_start: 0.8319 (t70) cc_final: 0.7856 (t0) REVERT: D 103 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8763 (mtpm) REVERT: D 123 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7933 (mm-30) REVERT: D 159 TYR cc_start: 0.8492 (m-80) cc_final: 0.8250 (m-80) REVERT: D 181 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7678 (mt-10) REVERT: D 198 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 203 ASP cc_start: 0.8109 (t0) cc_final: 0.7802 (t70) REVERT: D 216 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8726 (mmmm) REVERT: D 251 ARG cc_start: 0.8732 (tpp-160) cc_final: 0.8362 (ttm110) REVERT: D 291 GLN cc_start: 0.8593 (pp30) cc_final: 0.8291 (pp30) REVERT: D 325 GLU cc_start: 0.7928 (tp30) cc_final: 0.7727 (tp30) REVERT: D 376 GLU cc_start: 0.7714 (mp0) cc_final: 0.7193 (mp0) REVERT: D 383 GLU cc_start: 0.8201 (tp30) cc_final: 0.7744 (tp30) REVERT: D 391 ARG cc_start: 0.8410 (mmm160) cc_final: 0.7785 (mtm110) REVERT: D 404 ASP cc_start: 0.8307 (m-30) cc_final: 0.7514 (m-30) REVERT: D 407 GLU cc_start: 0.8050 (mp0) cc_final: 0.7688 (mp0) REVERT: D 412 GLU cc_start: 0.7975 (tp30) cc_final: 0.7687 (mm-30) REVERT: E 61 ASP cc_start: 0.7444 (m-30) cc_final: 0.7209 (m-30) REVERT: E 69 ASN cc_start: 0.8133 (t0) cc_final: 0.7775 (t0) REVERT: E 93 MET cc_start: 0.8025 (mmm) cc_final: 0.7815 (mmp) REVERT: E 120 GLU cc_start: 0.7373 (mp0) cc_final: 0.7101 (mp0) REVERT: E 129 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7575 (tm-30) REVERT: E 187 ASP cc_start: 0.8007 (t0) cc_final: 0.7369 (t0) REVERT: E 278 GLN cc_start: 0.8535 (mt0) cc_final: 0.8309 (mt0) REVERT: E 322 LEU cc_start: 0.8634 (mp) cc_final: 0.8419 (mm) REVERT: E 444 MET cc_start: 0.8483 (mtm) cc_final: 0.8209 (mtp) REVERT: E 478 ASN cc_start: 0.8313 (t0) cc_final: 0.7904 (t0) REVERT: E 534 ASP cc_start: 0.7632 (p0) cc_final: 0.7328 (p0) REVERT: E 556 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7568 (mm-30) REVERT: E 569 MET cc_start: 0.7786 (mtp) cc_final: 0.7456 (mtm) REVERT: E 578 ILE cc_start: 0.8536 (tp) cc_final: 0.8312 (tt) outliers start: 45 outliers final: 10 residues processed: 466 average time/residue: 1.5612 time to fit residues: 797.0142 Evaluate side-chains 444 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 429 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 136 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS B 190 HIS B 227 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS C 101 ASN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 292 GLN E 98 GLN E 165 GLN E 170 GLN ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086084 restraints weight = 28918.499| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.86 r_work: 0.3133 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17885 Z= 0.275 Angle : 0.666 8.749 24321 Z= 0.345 Chirality : 0.049 0.175 2657 Planarity : 0.005 0.059 3175 Dihedral : 11.112 176.797 2519 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.52 % Allowed : 16.00 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2208 helix: 1.00 (0.17), residues: 911 sheet: 0.32 (0.28), residues: 355 loop : -0.65 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.013 0.002 HIS E 323 PHE 0.025 0.002 PHE E 75 TYR 0.018 0.002 TYR A 432 ARG 0.011 0.001 ARG E 590 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 784) hydrogen bonds : angle 4.77740 ( 2268) metal coordination : bond 0.00892 ( 2) covalent geometry : bond 0.00630 (17882) covalent geometry : angle 0.66600 (24321) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 452 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8597 (p90) cc_final: 0.8315 (p90) REVERT: A 77 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 83 TYR cc_start: 0.8790 (m-80) cc_final: 0.8436 (m-80) REVERT: A 116 ASP cc_start: 0.8117 (m-30) cc_final: 0.7458 (m-30) REVERT: A 117 LEU cc_start: 0.8438 (tp) cc_final: 0.7973 (tt) REVERT: A 120 ASP cc_start: 0.8040 (m-30) cc_final: 0.7714 (m-30) REVERT: A 211 ASP cc_start: 0.8103 (m-30) cc_final: 0.7777 (m-30) REVERT: A 214 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.7878 (ttp-110) REVERT: A 254 GLU cc_start: 0.5262 (mm-30) cc_final: 0.4056 (mm-30) REVERT: A 277 SER cc_start: 0.8917 (t) cc_final: 0.8611 (p) REVERT: A 290 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 338 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8486 (ttpp) REVERT: A 367 ASP cc_start: 0.8030 (p0) cc_final: 0.7678 (p0) REVERT: A 370 LYS cc_start: 0.8519 (tptt) cc_final: 0.8305 (tptt) REVERT: A 388 TRP cc_start: 0.8825 (m-10) cc_final: 0.8230 (m-10) REVERT: A 392 ASP cc_start: 0.8258 (m-30) cc_final: 0.7809 (m-30) REVERT: A 414 GLU cc_start: 0.8057 (mp0) cc_final: 0.7518 (mp0) REVERT: A 417 GLU cc_start: 0.8113 (tt0) cc_final: 0.7818 (mt-10) REVERT: A 423 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 19 LYS cc_start: 0.8978 (tptm) cc_final: 0.8561 (mmmt) REVERT: B 53 GLU cc_start: 0.8164 (tt0) cc_final: 0.7725 (tp30) REVERT: B 74 ASP cc_start: 0.8219 (t0) cc_final: 0.7849 (t0) REVERT: B 103 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8541 (mtpm) REVERT: B 114 ASP cc_start: 0.8208 (m-30) cc_final: 0.7981 (m-30) REVERT: B 118 ASP cc_start: 0.7922 (m-30) cc_final: 0.7618 (m-30) REVERT: B 123 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7809 (tp30) REVERT: B 127 CYS cc_start: 0.7900 (m) cc_final: 0.7382 (m) REVERT: B 147 MET cc_start: 0.8711 (ttt) cc_final: 0.8507 (ttt) REVERT: B 154 LYS cc_start: 0.8948 (mmtp) cc_final: 0.8473 (mtpp) REVERT: B 158 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: B 174 LYS cc_start: 0.8552 (mmpt) cc_final: 0.8324 (mmpt) REVERT: B 216 LYS cc_start: 0.9086 (mmtm) cc_final: 0.8831 (mmmm) REVERT: B 274 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 278 SER cc_start: 0.8557 (m) cc_final: 0.8244 (p) REVERT: B 291 GLN cc_start: 0.8317 (pp30) cc_final: 0.8067 (pp30) REVERT: B 325 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7399 (mm-30) REVERT: B 328 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7518 (OUTLIER) REVERT: B 377 LEU cc_start: 0.8430 (mt) cc_final: 0.8201 (mp) REVERT: B 407 GLU cc_start: 0.8246 (tt0) cc_final: 0.7917 (mt-10) REVERT: B 410 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 414 ASN cc_start: 0.8460 (m110) cc_final: 0.8113 (m110) REVERT: C 3 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6963 (pm20) REVERT: C 120 ASP cc_start: 0.7912 (m-30) cc_final: 0.7708 (m-30) REVERT: C 123 ARG cc_start: 0.7997 (tpp-160) cc_final: 0.7607 (tpp80) REVERT: C 154 MET cc_start: 0.9040 (mmm) cc_final: 0.8640 (mtm) REVERT: C 196 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: C 245 ASP cc_start: 0.7941 (p0) cc_final: 0.7669 (p0) REVERT: C 277 SER cc_start: 0.8677 (t) cc_final: 0.8468 (p) REVERT: C 280 LYS cc_start: 0.8969 (mttp) cc_final: 0.8411 (mtpt) REVERT: C 308 ARG cc_start: 0.6679 (tpt170) cc_final: 0.6165 (tpt170) REVERT: C 322 ASP cc_start: 0.8280 (t70) cc_final: 0.7986 (t0) REVERT: C 386 GLU cc_start: 0.8071 (mp0) cc_final: 0.7669 (mp0) REVERT: C 420 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7543 (mm-30) REVERT: C 423 GLU cc_start: 0.8117 (tp30) cc_final: 0.7863 (mm-30) REVERT: C 424 ASP cc_start: 0.8101 (t70) cc_final: 0.7866 (t0) REVERT: C 434 GLU cc_start: 0.7895 (pp20) cc_final: 0.7684 (pp20) REVERT: D 1 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8248 (ttp) REVERT: D 3 GLU cc_start: 0.7986 (mp0) cc_final: 0.7632 (mp0) REVERT: D 22 GLU cc_start: 0.8727 (tt0) cc_final: 0.8338 (tm-30) REVERT: D 26 ASP cc_start: 0.7781 (m-30) cc_final: 0.7456 (t0) REVERT: D 45 GLU cc_start: 0.8485 (tt0) cc_final: 0.8184 (tm-30) REVERT: D 57 ASN cc_start: 0.7181 (t0) cc_final: 0.6409 (t0) REVERT: D 64 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8977 (mt) REVERT: D 69 GLU cc_start: 0.7549 (pm20) cc_final: 0.7217 (pm20) REVERT: D 88 ASP cc_start: 0.8407 (t70) cc_final: 0.7899 (t0) REVERT: D 103 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8484 (mtpm) REVERT: D 161 ASP cc_start: 0.8596 (p0) cc_final: 0.8353 (p0) REVERT: D 174 LYS cc_start: 0.8715 (mptt) cc_final: 0.8499 (mptt) REVERT: D 181 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7814 (mt-10) REVERT: D 198 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8203 (mt-10) REVERT: D 291 GLN cc_start: 0.8617 (pp30) cc_final: 0.8391 (pp30) REVERT: D 325 GLU cc_start: 0.8158 (tp30) cc_final: 0.7840 (tp30) REVERT: D 376 GLU cc_start: 0.7852 (mp0) cc_final: 0.7596 (mp0) REVERT: D 383 GLU cc_start: 0.8327 (tp30) cc_final: 0.8004 (tp30) REVERT: D 391 ARG cc_start: 0.8806 (mmm160) cc_final: 0.8015 (mtm110) REVERT: D 404 ASP cc_start: 0.8359 (m-30) cc_final: 0.7599 (m-30) REVERT: D 407 GLU cc_start: 0.8066 (mp0) cc_final: 0.7400 (mp0) REVERT: D 412 GLU cc_start: 0.7875 (tp30) cc_final: 0.7517 (tm-30) REVERT: D 416 ASN cc_start: 0.8329 (m-40) cc_final: 0.7450 (m-40) REVERT: E 61 ASP cc_start: 0.7627 (m-30) cc_final: 0.7299 (m-30) REVERT: E 69 ASN cc_start: 0.8223 (t0) cc_final: 0.7844 (t0) REVERT: E 120 GLU cc_start: 0.7537 (mp0) cc_final: 0.7323 (mp0) REVERT: E 129 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7734 (tm-30) REVERT: E 152 PHE cc_start: 0.8571 (m-10) cc_final: 0.8358 (m-10) REVERT: E 181 THR cc_start: 0.6569 (OUTLIER) cc_final: 0.6348 (p) REVERT: E 187 ASP cc_start: 0.8352 (t0) cc_final: 0.7522 (t0) REVERT: E 243 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8404 (mmt90) REVERT: E 334 LEU cc_start: 0.8201 (mt) cc_final: 0.7778 (mp) REVERT: E 340 SER cc_start: 0.8147 (t) cc_final: 0.7926 (t) REVERT: E 440 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8036 (mpp80) REVERT: E 444 MET cc_start: 0.8718 (mtm) cc_final: 0.8239 (mtt) REVERT: E 457 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7867 (mm-30) REVERT: E 478 ASN cc_start: 0.8395 (t0) cc_final: 0.8056 (t0) REVERT: E 528 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7834 (mm) REVERT: E 556 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7569 (mm-30) REVERT: E 562 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8136 (ttp) REVERT: E 569 MET cc_start: 0.7803 (mtp) cc_final: 0.7522 (mtm) REVERT: E 588 ASN cc_start: 0.8784 (m-40) cc_final: 0.8519 (m-40) REVERT: E 593 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7976 (tpp) outliers start: 65 outliers final: 21 residues processed: 483 average time/residue: 1.5596 time to fit residues: 824.9159 Evaluate side-chains 448 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 418 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 440 ARG Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 562 MET Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 593 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 210 optimal weight: 5.9990 chunk 203 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN A 256 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 128 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087951 restraints weight = 28839.511| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.89 r_work: 0.3159 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17885 Z= 0.148 Angle : 0.578 8.426 24321 Z= 0.294 Chirality : 0.044 0.156 2657 Planarity : 0.004 0.055 3175 Dihedral : 10.939 175.017 2519 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.66 % Allowed : 18.22 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2208 helix: 1.23 (0.17), residues: 916 sheet: 0.37 (0.28), residues: 355 loop : -0.64 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 21 HIS 0.006 0.001 HIS D 190 PHE 0.025 0.002 PHE E 75 TYR 0.020 0.001 TYR D 159 ARG 0.008 0.000 ARG C 221 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 784) hydrogen bonds : angle 4.57019 ( 2268) metal coordination : bond 0.00422 ( 2) covalent geometry : bond 0.00342 (17882) covalent geometry : angle 0.57821 (24321) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 432 time to evaluate : 1.843 Fit side-chains REVERT: A 49 PHE cc_start: 0.8575 (p90) cc_final: 0.8301 (p90) REVERT: A 77 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 83 TYR cc_start: 0.8842 (m-80) cc_final: 0.8514 (m-80) REVERT: A 103 TYR cc_start: 0.8719 (t80) cc_final: 0.8514 (t80) REVERT: A 116 ASP cc_start: 0.8097 (m-30) cc_final: 0.7470 (m-30) REVERT: A 117 LEU cc_start: 0.8391 (tp) cc_final: 0.7911 (tt) REVERT: A 120 ASP cc_start: 0.8053 (m-30) cc_final: 0.7713 (m-30) REVERT: A 154 MET cc_start: 0.8793 (mmp) cc_final: 0.8545 (mmm) REVERT: A 214 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8036 (ttp-110) REVERT: A 251 ASP cc_start: 0.7826 (m-30) cc_final: 0.7559 (t0) REVERT: A 254 GLU cc_start: 0.5226 (mm-30) cc_final: 0.4152 (mm-30) REVERT: A 277 SER cc_start: 0.8859 (t) cc_final: 0.8649 (p) REVERT: A 290 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 338 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8497 (mtpp) REVERT: A 367 ASP cc_start: 0.8091 (p0) cc_final: 0.7718 (p0) REVERT: A 370 LYS cc_start: 0.8533 (tptt) cc_final: 0.8298 (tptt) REVERT: A 388 TRP cc_start: 0.8726 (m-10) cc_final: 0.8046 (m-10) REVERT: A 392 ASP cc_start: 0.8075 (m-30) cc_final: 0.7605 (m-30) REVERT: A 414 GLU cc_start: 0.8122 (mp0) cc_final: 0.7551 (mp0) REVERT: A 417 GLU cc_start: 0.7997 (tt0) cc_final: 0.7694 (mt-10) REVERT: A 420 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 423 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 1 MET cc_start: 0.8526 (mtt) cc_final: 0.8135 (mtm) REVERT: B 19 LYS cc_start: 0.8923 (tptm) cc_final: 0.8529 (mmmt) REVERT: B 36 TYR cc_start: 0.8732 (t80) cc_final: 0.8285 (t80) REVERT: B 53 GLU cc_start: 0.8204 (tt0) cc_final: 0.7792 (tp30) REVERT: B 114 ASP cc_start: 0.8180 (m-30) cc_final: 0.7936 (m-30) REVERT: B 118 ASP cc_start: 0.7919 (m-30) cc_final: 0.7599 (m-30) REVERT: B 123 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7857 (tp30) REVERT: B 127 CYS cc_start: 0.7946 (m) cc_final: 0.7459 (m) REVERT: B 157 GLU cc_start: 0.8290 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 158 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: B 174 LYS cc_start: 0.8617 (mmpt) cc_final: 0.8314 (mmpt) REVERT: B 175 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8710 (m) REVERT: B 213 ARG cc_start: 0.8862 (ptp-110) cc_final: 0.8631 (ptm160) REVERT: B 216 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8771 (mmmm) REVERT: B 274 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8607 (p) REVERT: B 278 SER cc_start: 0.8509 (m) cc_final: 0.8205 (p) REVERT: B 291 GLN cc_start: 0.8313 (pp30) cc_final: 0.8091 (pp30) REVERT: B 325 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7376 (mm-30) REVERT: B 328 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7397 (OUTLIER) REVERT: B 407 GLU cc_start: 0.8071 (tt0) cc_final: 0.7762 (mt-10) REVERT: B 410 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7518 (mm-30) REVERT: B 412 GLU cc_start: 0.8233 (tp30) cc_final: 0.7620 (tp30) REVERT: B 414 ASN cc_start: 0.8449 (m110) cc_final: 0.8072 (m110) REVERT: B 421 GLU cc_start: 0.8256 (tt0) cc_final: 0.7890 (tm-30) REVERT: C 3 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7213 (pm20) REVERT: C 116 ASP cc_start: 0.7922 (p0) cc_final: 0.7706 (p0) REVERT: C 120 ASP cc_start: 0.7880 (m-30) cc_final: 0.7678 (m-30) REVERT: C 123 ARG cc_start: 0.8069 (tpp-160) cc_final: 0.7667 (tpp80) REVERT: C 154 MET cc_start: 0.9024 (mmm) cc_final: 0.8597 (mtm) REVERT: C 196 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: C 214 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8297 (ttp-110) REVERT: C 280 LYS cc_start: 0.9006 (mttp) cc_final: 0.8158 (mmtt) REVERT: C 308 ARG cc_start: 0.6698 (tpt170) cc_final: 0.6221 (tpt170) REVERT: C 322 ASP cc_start: 0.8222 (t70) cc_final: 0.7982 (t0) REVERT: C 386 GLU cc_start: 0.7719 (mp0) cc_final: 0.7399 (mp0) REVERT: C 417 GLU cc_start: 0.7716 (mp0) cc_final: 0.7473 (mp0) REVERT: C 420 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7599 (mm-30) REVERT: C 423 GLU cc_start: 0.8011 (tp30) cc_final: 0.7805 (mm-30) REVERT: C 424 ASP cc_start: 0.8087 (t70) cc_final: 0.7859 (t0) REVERT: C 433 GLU cc_start: 0.8380 (tt0) cc_final: 0.7741 (tm-30) REVERT: C 434 GLU cc_start: 0.8018 (pp20) cc_final: 0.7680 (pp20) REVERT: D 1 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8161 (ttp) REVERT: D 3 GLU cc_start: 0.8043 (mp0) cc_final: 0.7750 (mp0) REVERT: D 19 LYS cc_start: 0.9027 (tppp) cc_final: 0.8814 (tppp) REVERT: D 22 GLU cc_start: 0.8655 (tt0) cc_final: 0.8267 (tm-30) REVERT: D 26 ASP cc_start: 0.7637 (m-30) cc_final: 0.7362 (t0) REVERT: D 45 GLU cc_start: 0.8517 (tt0) cc_final: 0.8193 (tm-30) REVERT: D 57 ASN cc_start: 0.7373 (t0) cc_final: 0.6523 (t0) REVERT: D 64 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9028 (mt) REVERT: D 69 GLU cc_start: 0.7593 (pm20) cc_final: 0.7289 (pm20) REVERT: D 88 ASP cc_start: 0.8273 (t70) cc_final: 0.7780 (t0) REVERT: D 92 PHE cc_start: 0.8620 (p90) cc_final: 0.8357 (p90) REVERT: D 103 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8665 (mtpm) REVERT: D 161 ASP cc_start: 0.8657 (p0) cc_final: 0.8338 (p0) REVERT: D 174 LYS cc_start: 0.8711 (mptt) cc_final: 0.8413 (mptt) REVERT: D 181 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7869 (mt-10) REVERT: D 251 ARG cc_start: 0.8740 (tpp-160) cc_final: 0.8202 (ttm110) REVERT: D 257 MET cc_start: 0.8349 (mmm) cc_final: 0.8058 (mmm) REVERT: D 291 GLN cc_start: 0.8571 (pp30) cc_final: 0.8336 (pp30) REVERT: D 325 GLU cc_start: 0.8222 (tp30) cc_final: 0.7791 (tp30) REVERT: D 376 GLU cc_start: 0.7795 (mp0) cc_final: 0.7506 (mp0) REVERT: D 383 GLU cc_start: 0.8382 (tp30) cc_final: 0.8040 (tp30) REVERT: D 391 ARG cc_start: 0.8965 (mmm160) cc_final: 0.7363 (ptm160) REVERT: D 401 GLU cc_start: 0.7259 (mp0) cc_final: 0.6895 (mp0) REVERT: D 404 ASP cc_start: 0.8457 (m-30) cc_final: 0.7383 (m-30) REVERT: D 407 GLU cc_start: 0.8082 (mp0) cc_final: 0.7302 (mp0) REVERT: D 410 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7050 (pp20) REVERT: D 412 GLU cc_start: 0.7863 (tp30) cc_final: 0.7182 (tm-30) REVERT: D 416 ASN cc_start: 0.8326 (m-40) cc_final: 0.7359 (m-40) REVERT: D 424 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: E 59 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8223 (mtp180) REVERT: E 61 ASP cc_start: 0.7504 (m-30) cc_final: 0.7273 (m-30) REVERT: E 68 GLU cc_start: 0.8072 (tt0) cc_final: 0.7839 (tt0) REVERT: E 69 ASN cc_start: 0.8249 (t0) cc_final: 0.7855 (t0) REVERT: E 104 GLN cc_start: 0.7460 (mt0) cc_final: 0.7240 (mt0) REVERT: E 129 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7637 (tm-30) REVERT: E 152 PHE cc_start: 0.8503 (m-10) cc_final: 0.8242 (m-10) REVERT: E 181 THR cc_start: 0.6499 (OUTLIER) cc_final: 0.6281 (p) REVERT: E 187 ASP cc_start: 0.8281 (t0) cc_final: 0.7707 (t0) REVERT: E 340 SER cc_start: 0.8060 (t) cc_final: 0.7815 (t) REVERT: E 440 ARG cc_start: 0.8497 (mpt-90) cc_final: 0.8237 (mpp80) REVERT: E 457 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7866 (mm-30) REVERT: E 478 ASN cc_start: 0.8395 (t0) cc_final: 0.8028 (t0) REVERT: E 556 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7565 (mm-30) REVERT: E 569 MET cc_start: 0.7773 (mtp) cc_final: 0.7483 (mtm) REVERT: E 588 ASN cc_start: 0.8791 (m-40) cc_final: 0.8557 (m-40) outliers start: 49 outliers final: 13 residues processed: 458 average time/residue: 1.7444 time to fit residues: 876.5329 Evaluate side-chains 451 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 429 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 597 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 82 optimal weight: 0.0270 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 423 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS E 455 GLN ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088558 restraints weight = 28750.123| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.89 r_work: 0.3171 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17885 Z= 0.133 Angle : 0.570 8.679 24321 Z= 0.291 Chirality : 0.044 0.156 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.865 176.763 2519 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.71 % Allowed : 18.60 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2208 helix: 1.32 (0.17), residues: 921 sheet: 0.41 (0.28), residues: 354 loop : -0.65 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.008 0.001 HIS D 190 PHE 0.026 0.001 PHE E 75 TYR 0.018 0.001 TYR D 159 ARG 0.010 0.000 ARG C 221 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 784) hydrogen bonds : angle 4.46915 ( 2268) metal coordination : bond 0.00348 ( 2) covalent geometry : bond 0.00306 (17882) covalent geometry : angle 0.56976 (24321) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 426 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 83 TYR cc_start: 0.8875 (m-80) cc_final: 0.8485 (m-80) REVERT: A 116 ASP cc_start: 0.8147 (m-30) cc_final: 0.7673 (m-30) REVERT: A 117 LEU cc_start: 0.8359 (tp) cc_final: 0.7955 (tt) REVERT: A 120 ASP cc_start: 0.8001 (m-30) cc_final: 0.7763 (m-30) REVERT: A 254 GLU cc_start: 0.4664 (mm-30) cc_final: 0.3349 (mm-30) REVERT: A 290 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 338 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8469 (mtpp) REVERT: A 367 ASP cc_start: 0.8091 (p0) cc_final: 0.7719 (p0) REVERT: A 370 LYS cc_start: 0.8529 (tptt) cc_final: 0.8314 (tptt) REVERT: A 388 TRP cc_start: 0.8688 (m-10) cc_final: 0.8037 (m-10) REVERT: A 392 ASP cc_start: 0.8065 (m-30) cc_final: 0.7577 (m-30) REVERT: A 414 GLU cc_start: 0.8127 (mp0) cc_final: 0.7627 (mp0) REVERT: A 417 GLU cc_start: 0.7969 (tt0) cc_final: 0.7705 (mt-10) REVERT: A 420 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 423 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7933 (mm-30) REVERT: B 1 MET cc_start: 0.8540 (mtt) cc_final: 0.8329 (mtp) REVERT: B 36 TYR cc_start: 0.8734 (t80) cc_final: 0.8282 (t80) REVERT: B 53 GLU cc_start: 0.8167 (tt0) cc_final: 0.7669 (tm-30) REVERT: B 74 ASP cc_start: 0.8178 (t70) cc_final: 0.7927 (t0) REVERT: B 103 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8655 (mtpm) REVERT: B 114 ASP cc_start: 0.8183 (m-30) cc_final: 0.7943 (m-30) REVERT: B 118 ASP cc_start: 0.7939 (m-30) cc_final: 0.7631 (m-30) REVERT: B 123 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7867 (tp30) REVERT: B 127 CYS cc_start: 0.7931 (m) cc_final: 0.7469 (m) REVERT: B 157 GLU cc_start: 0.8348 (tt0) cc_final: 0.7922 (tm-30) REVERT: B 158 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: B 174 LYS cc_start: 0.8637 (mmpt) cc_final: 0.8277 (mmpt) REVERT: B 175 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8720 (m) REVERT: B 216 LYS cc_start: 0.9023 (mmtm) cc_final: 0.8757 (mmmm) REVERT: B 274 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8591 (p) REVERT: B 278 SER cc_start: 0.8556 (m) cc_final: 0.8244 (p) REVERT: B 291 GLN cc_start: 0.8303 (pp30) cc_final: 0.8076 (pp30) REVERT: B 325 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: B 328 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7422 (OUTLIER) REVERT: B 407 GLU cc_start: 0.8041 (tt0) cc_final: 0.7704 (mt-10) REVERT: B 410 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 412 GLU cc_start: 0.8212 (tp30) cc_final: 0.7622 (tp30) REVERT: B 414 ASN cc_start: 0.8420 (m110) cc_final: 0.8029 (m110) REVERT: B 417 ASP cc_start: 0.8310 (m-30) cc_final: 0.8064 (m-30) REVERT: B 421 GLU cc_start: 0.8257 (tt0) cc_final: 0.7990 (tm-30) REVERT: C 1 MET cc_start: 0.8426 (tpt) cc_final: 0.7951 (mmm) REVERT: C 3 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7048 (pm20) REVERT: C 116 ASP cc_start: 0.7978 (p0) cc_final: 0.7750 (p0) REVERT: C 120 ASP cc_start: 0.7906 (m-30) cc_final: 0.7682 (m-30) REVERT: C 123 ARG cc_start: 0.8090 (tpp-160) cc_final: 0.7672 (tpp80) REVERT: C 196 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: C 214 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8302 (ttp-110) REVERT: C 280 LYS cc_start: 0.8995 (mttp) cc_final: 0.8061 (mmmt) REVERT: C 284 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7516 (mp0) REVERT: C 308 ARG cc_start: 0.6696 (tpt170) cc_final: 0.5928 (tpt170) REVERT: C 322 ASP cc_start: 0.8197 (t70) cc_final: 0.7955 (t0) REVERT: C 417 GLU cc_start: 0.7782 (mp0) cc_final: 0.7435 (mp0) REVERT: C 420 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7565 (mm-30) REVERT: C 423 GLU cc_start: 0.8038 (tp30) cc_final: 0.7822 (mm-30) REVERT: C 424 ASP cc_start: 0.8107 (t70) cc_final: 0.7881 (t0) REVERT: C 433 GLU cc_start: 0.8414 (tt0) cc_final: 0.7715 (tm-30) REVERT: C 434 GLU cc_start: 0.8073 (pp20) cc_final: 0.7687 (pp20) REVERT: D 1 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8131 (ttp) REVERT: D 3 GLU cc_start: 0.8034 (mp0) cc_final: 0.7749 (mp0) REVERT: D 22 GLU cc_start: 0.8636 (tt0) cc_final: 0.8273 (tm-30) REVERT: D 26 ASP cc_start: 0.7581 (m-30) cc_final: 0.7339 (t0) REVERT: D 45 GLU cc_start: 0.8461 (tt0) cc_final: 0.8148 (tm-30) REVERT: D 57 ASN cc_start: 0.7431 (t0) cc_final: 0.6606 (t0) REVERT: D 64 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.9043 (mt) REVERT: D 69 GLU cc_start: 0.7600 (pm20) cc_final: 0.7226 (pm20) REVERT: D 88 ASP cc_start: 0.8281 (t70) cc_final: 0.7789 (t0) REVERT: D 92 PHE cc_start: 0.8611 (p90) cc_final: 0.8317 (p90) REVERT: D 103 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8636 (mtpm) REVERT: D 161 ASP cc_start: 0.8664 (p0) cc_final: 0.8331 (p0) REVERT: D 174 LYS cc_start: 0.8740 (mptt) cc_final: 0.8407 (mptt) REVERT: D 181 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7756 (mt-10) REVERT: D 190 HIS cc_start: 0.8063 (t-90) cc_final: 0.7630 (t70) REVERT: D 251 ARG cc_start: 0.8715 (tpp-160) cc_final: 0.8177 (ttm110) REVERT: D 257 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: D 291 GLN cc_start: 0.8541 (pp30) cc_final: 0.8277 (pp30) REVERT: D 309 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7952 (mtp85) REVERT: D 325 GLU cc_start: 0.8236 (tp30) cc_final: 0.7798 (tp30) REVERT: D 376 GLU cc_start: 0.7833 (mp0) cc_final: 0.7513 (mp0) REVERT: D 383 GLU cc_start: 0.8371 (tp30) cc_final: 0.8035 (tp30) REVERT: D 391 ARG cc_start: 0.8957 (mmm160) cc_final: 0.7251 (ptm-80) REVERT: D 404 ASP cc_start: 0.8473 (m-30) cc_final: 0.7537 (m-30) REVERT: D 407 GLU cc_start: 0.8118 (mp0) cc_final: 0.7338 (mp0) REVERT: D 412 GLU cc_start: 0.7925 (tp30) cc_final: 0.7524 (tm-30) REVERT: D 416 ASN cc_start: 0.8358 (m-40) cc_final: 0.7225 (m-40) REVERT: D 424 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8166 (pt0) REVERT: E 59 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8219 (mtp180) REVERT: E 68 GLU cc_start: 0.8102 (tt0) cc_final: 0.7844 (tt0) REVERT: E 69 ASN cc_start: 0.8284 (t0) cc_final: 0.7907 (t0) REVERT: E 104 GLN cc_start: 0.7476 (mt0) cc_final: 0.7150 (mt0) REVERT: E 129 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7654 (tm-30) REVERT: E 187 ASP cc_start: 0.8214 (t0) cc_final: 0.7658 (t0) REVERT: E 226 GLN cc_start: 0.8497 (mt0) cc_final: 0.8283 (mt0) REVERT: E 340 SER cc_start: 0.8053 (t) cc_final: 0.7813 (t) REVERT: E 440 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8190 (mpp80) REVERT: E 457 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7845 (mm-30) REVERT: E 478 ASN cc_start: 0.8407 (t0) cc_final: 0.7988 (t0) REVERT: E 556 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7600 (mm-30) REVERT: E 569 MET cc_start: 0.7734 (mtp) cc_final: 0.7461 (mtm) REVERT: E 588 ASN cc_start: 0.8843 (m-40) cc_final: 0.8616 (m-40) outliers start: 50 outliers final: 21 residues processed: 452 average time/residue: 2.0562 time to fit residues: 1021.5384 Evaluate side-chains 444 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 413 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 440 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 129 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN A 342 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN E 98 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.087104 restraints weight = 28746.348| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.88 r_work: 0.3144 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17885 Z= 0.187 Angle : 0.596 9.301 24321 Z= 0.304 Chirality : 0.045 0.155 2657 Planarity : 0.004 0.053 3175 Dihedral : 10.936 176.898 2519 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.87 % Allowed : 19.41 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2208 helix: 1.35 (0.17), residues: 917 sheet: 0.44 (0.29), residues: 344 loop : -0.60 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 21 HIS 0.009 0.001 HIS D 190 PHE 0.029 0.002 PHE E 75 TYR 0.018 0.001 TYR D 159 ARG 0.011 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 784) hydrogen bonds : angle 4.55240 ( 2268) metal coordination : bond 0.00608 ( 2) covalent geometry : bond 0.00433 (17882) covalent geometry : angle 0.59644 (24321) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 433 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 83 TYR cc_start: 0.8909 (m-80) cc_final: 0.8483 (m-80) REVERT: A 84 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7859 (ttm110) REVERT: A 116 ASP cc_start: 0.8144 (m-30) cc_final: 0.7694 (m-30) REVERT: A 117 LEU cc_start: 0.8428 (tp) cc_final: 0.7986 (tt) REVERT: A 120 ASP cc_start: 0.8006 (m-30) cc_final: 0.7769 (m-30) REVERT: A 154 MET cc_start: 0.8739 (mmp) cc_final: 0.8527 (mmm) REVERT: A 214 ARG cc_start: 0.8469 (ttp-110) cc_final: 0.8110 (ttp-110) REVERT: A 254 GLU cc_start: 0.5279 (mm-30) cc_final: 0.3783 (mm-30) REVERT: A 290 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8354 (mm-30) REVERT: A 338 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8495 (mtpp) REVERT: A 388 TRP cc_start: 0.8745 (m-10) cc_final: 0.8075 (m-10) REVERT: A 392 ASP cc_start: 0.8051 (m-30) cc_final: 0.7559 (m-30) REVERT: A 414 GLU cc_start: 0.8109 (mp0) cc_final: 0.7762 (mp0) REVERT: A 417 GLU cc_start: 0.7986 (tt0) cc_final: 0.7737 (mt-10) REVERT: A 420 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7720 (mm-30) REVERT: A 423 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7921 (mm-30) REVERT: B 19 LYS cc_start: 0.8923 (tptm) cc_final: 0.8514 (mmmt) REVERT: B 53 GLU cc_start: 0.8221 (tt0) cc_final: 0.7821 (tm-30) REVERT: B 74 ASP cc_start: 0.8288 (t70) cc_final: 0.8022 (OUTLIER) REVERT: B 103 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8662 (mtpm) REVERT: B 114 ASP cc_start: 0.8193 (m-30) cc_final: 0.7943 (m-30) REVERT: B 118 ASP cc_start: 0.7918 (m-30) cc_final: 0.7603 (m-30) REVERT: B 123 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7890 (tp30) REVERT: B 127 CYS cc_start: 0.7979 (m) cc_final: 0.7537 (m) REVERT: B 157 GLU cc_start: 0.8401 (tt0) cc_final: 0.7952 (tm-30) REVERT: B 158 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: B 174 LYS cc_start: 0.8629 (mmpt) cc_final: 0.8230 (mmpt) REVERT: B 175 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8725 (m) REVERT: B 213 ARG cc_start: 0.8881 (ptp-110) cc_final: 0.8618 (ptm160) REVERT: B 216 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8771 (mmmm) REVERT: B 274 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 278 SER cc_start: 0.8642 (m) cc_final: 0.8293 (p) REVERT: B 325 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: B 328 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7433 (OUTLIER) REVERT: B 407 GLU cc_start: 0.8078 (tt0) cc_final: 0.7725 (mt-10) REVERT: B 410 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 414 ASN cc_start: 0.8469 (m110) cc_final: 0.8112 (m110) REVERT: C 1 MET cc_start: 0.8432 (tpt) cc_final: 0.7623 (mmm) REVERT: C 3 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7077 (pm20) REVERT: C 112 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8035 (pmtt) REVERT: C 116 ASP cc_start: 0.7992 (p0) cc_final: 0.7751 (p0) REVERT: C 120 ASP cc_start: 0.7935 (m-30) cc_final: 0.7687 (m-30) REVERT: C 123 ARG cc_start: 0.8022 (tpp-160) cc_final: 0.7609 (tpp80) REVERT: C 164 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8836 (mmmm) REVERT: C 196 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: C 214 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8322 (ttp-110) REVERT: C 280 LYS cc_start: 0.9012 (mttp) cc_final: 0.8362 (mmtt) REVERT: C 290 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8313 (mm-30) REVERT: C 304 LYS cc_start: 0.8982 (mttm) cc_final: 0.8782 (mmtm) REVERT: C 308 ARG cc_start: 0.6737 (tpt170) cc_final: 0.6147 (tpt170) REVERT: C 322 ASP cc_start: 0.8196 (t70) cc_final: 0.7952 (t0) REVERT: C 377 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8373 (ttp) REVERT: C 386 GLU cc_start: 0.7895 (mp0) cc_final: 0.7535 (mp0) REVERT: C 417 GLU cc_start: 0.7888 (mp0) cc_final: 0.7507 (mp0) REVERT: C 420 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7581 (mm-30) REVERT: C 423 GLU cc_start: 0.8096 (tp30) cc_final: 0.7880 (mm-30) REVERT: C 424 ASP cc_start: 0.8148 (t70) cc_final: 0.7910 (t0) REVERT: C 433 GLU cc_start: 0.8451 (tt0) cc_final: 0.7844 (tm-30) REVERT: C 434 GLU cc_start: 0.8160 (pp20) cc_final: 0.7745 (pp20) REVERT: D 1 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8180 (ttp) REVERT: D 3 GLU cc_start: 0.8037 (mp0) cc_final: 0.7785 (mp0) REVERT: D 19 LYS cc_start: 0.8997 (tppp) cc_final: 0.8732 (tppp) REVERT: D 22 GLU cc_start: 0.8590 (tt0) cc_final: 0.8242 (tm-30) REVERT: D 45 GLU cc_start: 0.8478 (tt0) cc_final: 0.8042 (tm-30) REVERT: D 57 ASN cc_start: 0.7583 (t0) cc_final: 0.6767 (t0) REVERT: D 64 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9037 (mt) REVERT: D 69 GLU cc_start: 0.7546 (pm20) cc_final: 0.7169 (pm20) REVERT: D 88 ASP cc_start: 0.8296 (t70) cc_final: 0.7803 (t0) REVERT: D 92 PHE cc_start: 0.8668 (p90) cc_final: 0.8388 (p90) REVERT: D 103 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8615 (mtpm) REVERT: D 108 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7949 (mp0) REVERT: D 118 ASP cc_start: 0.8621 (t0) cc_final: 0.8417 (t0) REVERT: D 121 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8278 (mtm180) REVERT: D 157 GLU cc_start: 0.8210 (pp20) cc_final: 0.7918 (pp20) REVERT: D 161 ASP cc_start: 0.8646 (p0) cc_final: 0.8346 (p0) REVERT: D 174 LYS cc_start: 0.8758 (mptt) cc_final: 0.8415 (mptt) REVERT: D 181 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7903 (mt-10) REVERT: D 251 ARG cc_start: 0.8762 (tpp-160) cc_final: 0.8354 (ttm110) REVERT: D 257 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8117 (mmm) REVERT: D 291 GLN cc_start: 0.8548 (pp30) cc_final: 0.8292 (pp30) REVERT: D 318 ARG cc_start: 0.8942 (mtp180) cc_final: 0.8662 (mmm-85) REVERT: D 325 GLU cc_start: 0.8238 (tp30) cc_final: 0.7920 (tp30) REVERT: D 376 GLU cc_start: 0.7822 (mp0) cc_final: 0.7487 (mp0) REVERT: D 383 GLU cc_start: 0.8372 (tp30) cc_final: 0.8055 (tp30) REVERT: D 391 ARG cc_start: 0.9001 (mmm160) cc_final: 0.7349 (ptm160) REVERT: D 404 ASP cc_start: 0.8408 (m-30) cc_final: 0.7326 (m-30) REVERT: D 407 GLU cc_start: 0.8098 (mp0) cc_final: 0.7296 (mp0) REVERT: D 412 GLU cc_start: 0.7881 (tp30) cc_final: 0.7203 (tm-30) REVERT: D 416 ASN cc_start: 0.8353 (m-40) cc_final: 0.7202 (m-40) REVERT: E 21 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8060 (t70) REVERT: E 68 GLU cc_start: 0.8117 (tt0) cc_final: 0.7895 (tt0) REVERT: E 69 ASN cc_start: 0.8353 (t0) cc_final: 0.7993 (t0) REVERT: E 129 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7679 (tm-30) REVERT: E 187 ASP cc_start: 0.8289 (t0) cc_final: 0.7673 (t0) REVERT: E 226 GLN cc_start: 0.8648 (mt0) cc_final: 0.8408 (mt0) REVERT: E 340 SER cc_start: 0.8104 (t) cc_final: 0.7852 (t) REVERT: E 439 LYS cc_start: 0.8581 (ttmp) cc_final: 0.8209 (ttmm) REVERT: E 440 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8088 (mpp80) REVERT: E 478 ASN cc_start: 0.8414 (t0) cc_final: 0.7994 (t0) REVERT: E 556 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7655 (mm-30) REVERT: E 569 MET cc_start: 0.7723 (mtp) cc_final: 0.7513 (mtm) REVERT: E 588 ASN cc_start: 0.8870 (m-40) cc_final: 0.8669 (m-40) REVERT: E 593 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8063 (tpp) outliers start: 53 outliers final: 28 residues processed: 459 average time/residue: 1.8589 time to fit residues: 930.4728 Evaluate side-chains 462 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 422 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 440 ARG Chi-restraints excluded: chain E residue 593 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 214 optimal weight: 0.6980 chunk 197 optimal weight: 0.0770 chunk 136 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 177 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN A 256 GLN A 342 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088381 restraints weight = 28780.116| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.89 r_work: 0.3169 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17885 Z= 0.129 Angle : 0.581 9.132 24321 Z= 0.295 Chirality : 0.044 0.155 2657 Planarity : 0.004 0.054 3175 Dihedral : 10.772 174.728 2519 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.39 % Allowed : 20.07 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2208 helix: 1.40 (0.17), residues: 922 sheet: 0.41 (0.28), residues: 351 loop : -0.63 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 21 HIS 0.008 0.001 HIS D 190 PHE 0.028 0.001 PHE E 75 TYR 0.016 0.001 TYR D 159 ARG 0.012 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 784) hydrogen bonds : angle 4.44262 ( 2268) metal coordination : bond 0.00297 ( 2) covalent geometry : bond 0.00300 (17882) covalent geometry : angle 0.58091 (24321) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 430 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7715 (mt-10) REVERT: A 83 TYR cc_start: 0.8886 (m-80) cc_final: 0.8488 (m-80) REVERT: A 116 ASP cc_start: 0.8134 (m-30) cc_final: 0.7681 (m-30) REVERT: A 117 LEU cc_start: 0.8368 (tp) cc_final: 0.7955 (tt) REVERT: A 120 ASP cc_start: 0.8001 (m-30) cc_final: 0.7753 (m-30) REVERT: A 141 PHE cc_start: 0.8572 (m-80) cc_final: 0.8287 (m-80) REVERT: A 154 MET cc_start: 0.8714 (mmp) cc_final: 0.8497 (mmm) REVERT: A 214 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.8061 (ttp-110) REVERT: A 221 ARG cc_start: 0.8502 (ptp-110) cc_final: 0.8275 (ptp90) REVERT: A 254 GLU cc_start: 0.5177 (mm-30) cc_final: 0.3732 (mm-30) REVERT: A 290 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8349 (mm-30) REVERT: A 388 TRP cc_start: 0.8671 (m-10) cc_final: 0.8018 (m-10) REVERT: A 392 ASP cc_start: 0.8051 (m-30) cc_final: 0.7550 (m-30) REVERT: A 414 GLU cc_start: 0.8078 (mp0) cc_final: 0.7742 (mp0) REVERT: A 417 GLU cc_start: 0.7964 (tt0) cc_final: 0.7722 (mt-10) REVERT: A 420 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 423 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 19 LYS cc_start: 0.8882 (tptm) cc_final: 0.8501 (mmmt) REVERT: B 36 TYR cc_start: 0.8702 (t80) cc_final: 0.8224 (t80) REVERT: B 53 GLU cc_start: 0.8167 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 69 GLU cc_start: 0.8073 (pt0) cc_final: 0.7672 (pm20) REVERT: B 74 ASP cc_start: 0.8271 (t70) cc_final: 0.7997 (OUTLIER) REVERT: B 103 LYS cc_start: 0.8889 (mtpt) cc_final: 0.8662 (mtpm) REVERT: B 114 ASP cc_start: 0.8195 (m-30) cc_final: 0.7923 (m-30) REVERT: B 118 ASP cc_start: 0.7920 (m-30) cc_final: 0.7575 (m-30) REVERT: B 123 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7929 (tp30) REVERT: B 127 CYS cc_start: 0.7957 (m) cc_final: 0.7527 (m) REVERT: B 157 GLU cc_start: 0.8396 (tt0) cc_final: 0.7952 (tm-30) REVERT: B 158 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: B 174 LYS cc_start: 0.8650 (mmpt) cc_final: 0.8222 (mmpt) REVERT: B 175 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8725 (m) REVERT: B 274 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 278 SER cc_start: 0.8614 (m) cc_final: 0.8267 (p) REVERT: B 325 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: B 328 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7417 (OUTLIER) REVERT: B 343 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7483 (mp0) REVERT: B 407 GLU cc_start: 0.8026 (tt0) cc_final: 0.7679 (mt-10) REVERT: B 410 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 412 GLU cc_start: 0.8194 (tp30) cc_final: 0.7585 (tp30) REVERT: B 414 ASN cc_start: 0.8438 (m110) cc_final: 0.8079 (m110) REVERT: C 1 MET cc_start: 0.8431 (tpt) cc_final: 0.7940 (mmm) REVERT: C 3 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7000 (pm20) REVERT: C 116 ASP cc_start: 0.7985 (p0) cc_final: 0.7745 (p0) REVERT: C 120 ASP cc_start: 0.7905 (m-30) cc_final: 0.7673 (m-30) REVERT: C 123 ARG cc_start: 0.8075 (tpp-160) cc_final: 0.7641 (tpp80) REVERT: C 196 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: C 214 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.8208 (ttp-110) REVERT: C 280 LYS cc_start: 0.8987 (mttp) cc_final: 0.8358 (mmtt) REVERT: C 290 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8268 (mm-30) REVERT: C 308 ARG cc_start: 0.6722 (tpt170) cc_final: 0.5973 (tpt170) REVERT: C 322 ASP cc_start: 0.8166 (t70) cc_final: 0.7929 (t0) REVERT: C 377 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8377 (ttp) REVERT: C 417 GLU cc_start: 0.7888 (mp0) cc_final: 0.7510 (mp0) REVERT: C 420 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7576 (mm-30) REVERT: C 423 GLU cc_start: 0.8066 (tp30) cc_final: 0.7837 (mm-30) REVERT: C 424 ASP cc_start: 0.8110 (t70) cc_final: 0.7873 (t0) REVERT: C 433 GLU cc_start: 0.8459 (tt0) cc_final: 0.7877 (tm-30) REVERT: C 434 GLU cc_start: 0.8112 (pp20) cc_final: 0.7696 (pp20) REVERT: D 1 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: D 3 GLU cc_start: 0.8072 (mp0) cc_final: 0.7783 (mp0) REVERT: D 19 LYS cc_start: 0.8990 (tppp) cc_final: 0.8714 (tppp) REVERT: D 22 GLU cc_start: 0.8574 (tt0) cc_final: 0.8306 (tm-30) REVERT: D 45 GLU cc_start: 0.8476 (tt0) cc_final: 0.8026 (tm-30) REVERT: D 57 ASN cc_start: 0.7612 (t0) cc_final: 0.6791 (t0) REVERT: D 69 GLU cc_start: 0.7600 (pm20) cc_final: 0.7213 (pm20) REVERT: D 88 ASP cc_start: 0.8292 (t70) cc_final: 0.7806 (t0) REVERT: D 92 PHE cc_start: 0.8665 (p90) cc_final: 0.8345 (p90) REVERT: D 108 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7984 (mp0) REVERT: D 118 ASP cc_start: 0.8596 (t0) cc_final: 0.8392 (t0) REVERT: D 121 ARG cc_start: 0.8623 (ttm110) cc_final: 0.8258 (mtm180) REVERT: D 157 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7909 (pp20) REVERT: D 161 ASP cc_start: 0.8601 (p0) cc_final: 0.8312 (p0) REVERT: D 174 LYS cc_start: 0.8763 (mptt) cc_final: 0.8442 (mptt) REVERT: D 181 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7767 (mt-10) REVERT: D 251 ARG cc_start: 0.8736 (tpp-160) cc_final: 0.8318 (ttm110) REVERT: D 257 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: D 279 GLN cc_start: 0.8310 (pp30) cc_final: 0.7771 (tm130) REVERT: D 291 GLN cc_start: 0.8482 (pp30) cc_final: 0.8271 (pp30) REVERT: D 318 ARG cc_start: 0.8950 (mtp180) cc_final: 0.8680 (mmm-85) REVERT: D 325 GLU cc_start: 0.8233 (tp30) cc_final: 0.7892 (tp30) REVERT: D 376 GLU cc_start: 0.7817 (mp0) cc_final: 0.7459 (mp0) REVERT: D 383 GLU cc_start: 0.8380 (tp30) cc_final: 0.8060 (tp30) REVERT: D 391 ARG cc_start: 0.8980 (mmm160) cc_final: 0.7320 (ptm160) REVERT: D 404 ASP cc_start: 0.8403 (m-30) cc_final: 0.7346 (m-30) REVERT: D 407 GLU cc_start: 0.8063 (mp0) cc_final: 0.7315 (mp0) REVERT: D 412 GLU cc_start: 0.7840 (tp30) cc_final: 0.7160 (tm-30) REVERT: D 416 ASN cc_start: 0.8359 (m-40) cc_final: 0.7204 (m-40) REVERT: D 417 ASP cc_start: 0.8421 (m-30) cc_final: 0.8077 (m-30) REVERT: E 68 GLU cc_start: 0.8140 (tt0) cc_final: 0.7914 (tt0) REVERT: E 69 ASN cc_start: 0.8353 (t0) cc_final: 0.7987 (t0) REVERT: E 104 GLN cc_start: 0.7307 (mt0) cc_final: 0.7062 (mt0) REVERT: E 129 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7665 (tm-30) REVERT: E 187 ASP cc_start: 0.8233 (t0) cc_final: 0.7627 (t0) REVERT: E 226 GLN cc_start: 0.8592 (mt0) cc_final: 0.8353 (mt0) REVERT: E 340 SER cc_start: 0.8074 (t) cc_final: 0.7816 (t) REVERT: E 439 LYS cc_start: 0.8573 (ttmp) cc_final: 0.8202 (ttmm) REVERT: E 440 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8087 (mpp80) REVERT: E 457 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7836 (mm-30) REVERT: E 478 ASN cc_start: 0.8408 (t0) cc_final: 0.7974 (t0) REVERT: E 534 ASP cc_start: 0.7694 (p0) cc_final: 0.7426 (p0) REVERT: E 556 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7622 (mm-30) REVERT: E 569 MET cc_start: 0.7655 (mtp) cc_final: 0.7433 (mtm) outliers start: 44 outliers final: 23 residues processed: 452 average time/residue: 2.1840 time to fit residues: 1090.2248 Evaluate side-chains 457 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 426 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 440 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 342 GLN B 131 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087547 restraints weight = 28744.362| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.88 r_work: 0.3155 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17885 Z= 0.164 Angle : 0.599 9.416 24321 Z= 0.305 Chirality : 0.045 0.156 2657 Planarity : 0.004 0.052 3175 Dihedral : 10.775 175.826 2519 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.55 % Allowed : 20.12 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2208 helix: 1.36 (0.17), residues: 922 sheet: 0.37 (0.29), residues: 344 loop : -0.63 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 21 HIS 0.008 0.001 HIS D 190 PHE 0.032 0.002 PHE E 75 TYR 0.016 0.001 TYR D 159 ARG 0.013 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 784) hydrogen bonds : angle 4.48289 ( 2268) metal coordination : bond 0.00480 ( 2) covalent geometry : bond 0.00381 (17882) covalent geometry : angle 0.59863 (24321) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 430 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 83 TYR cc_start: 0.8910 (m-80) cc_final: 0.8481 (m-80) REVERT: A 116 ASP cc_start: 0.8170 (m-30) cc_final: 0.7699 (m-30) REVERT: A 117 LEU cc_start: 0.8399 (tp) cc_final: 0.7976 (tt) REVERT: A 120 ASP cc_start: 0.8027 (m-30) cc_final: 0.7767 (m-30) REVERT: A 214 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.8107 (ttp-110) REVERT: A 221 ARG cc_start: 0.8522 (ptp-110) cc_final: 0.8291 (ptp90) REVERT: A 254 GLU cc_start: 0.5419 (mm-30) cc_final: 0.3750 (mm-30) REVERT: A 290 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8357 (mm-30) REVERT: A 388 TRP cc_start: 0.8693 (m-10) cc_final: 0.8115 (m-10) REVERT: A 392 ASP cc_start: 0.8058 (m-30) cc_final: 0.7561 (m-30) REVERT: A 414 GLU cc_start: 0.8077 (mp0) cc_final: 0.7749 (mp0) REVERT: A 417 GLU cc_start: 0.7979 (tt0) cc_final: 0.7738 (mt-10) REVERT: A 420 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 423 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7935 (mm-30) REVERT: B 19 LYS cc_start: 0.8915 (tptm) cc_final: 0.8516 (mmmt) REVERT: B 53 GLU cc_start: 0.8191 (tt0) cc_final: 0.7758 (tm-30) REVERT: B 74 ASP cc_start: 0.8280 (t70) cc_final: 0.8011 (OUTLIER) REVERT: B 114 ASP cc_start: 0.8193 (m-30) cc_final: 0.7927 (m-30) REVERT: B 118 ASP cc_start: 0.7926 (m-30) cc_final: 0.7600 (m-30) REVERT: B 123 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7912 (tp30) REVERT: B 127 CYS cc_start: 0.7983 (m) cc_final: 0.7537 (m) REVERT: B 154 LYS cc_start: 0.8962 (mmtp) cc_final: 0.8628 (mttp) REVERT: B 157 GLU cc_start: 0.8410 (tt0) cc_final: 0.7973 (tm-30) REVERT: B 158 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: B 174 LYS cc_start: 0.8659 (mmpt) cc_final: 0.8242 (mmpt) REVERT: B 175 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8731 (m) REVERT: B 213 ARG cc_start: 0.8870 (ptp-110) cc_final: 0.8617 (ptm160) REVERT: B 274 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8666 (p) REVERT: B 278 SER cc_start: 0.8632 (m) cc_final: 0.8272 (p) REVERT: B 325 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: B 328 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7432 (OUTLIER) REVERT: B 343 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7464 (mp0) REVERT: B 407 GLU cc_start: 0.8055 (tt0) cc_final: 0.7686 (mt-10) REVERT: B 410 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 414 ASN cc_start: 0.8374 (m110) cc_final: 0.8000 (m110) REVERT: C 116 ASP cc_start: 0.8040 (p0) cc_final: 0.7771 (p0) REVERT: C 120 ASP cc_start: 0.7887 (m-30) cc_final: 0.7646 (m-30) REVERT: C 123 ARG cc_start: 0.7995 (tpp-160) cc_final: 0.7588 (tpp80) REVERT: C 164 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8826 (mmmm) REVERT: C 196 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: C 214 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8226 (ttp-110) REVERT: C 280 LYS cc_start: 0.8975 (mttp) cc_final: 0.7824 (mmtt) REVERT: C 284 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7279 (mp0) REVERT: C 308 ARG cc_start: 0.6754 (tpt170) cc_final: 0.5758 (tpt170) REVERT: C 322 ASP cc_start: 0.8148 (t70) cc_final: 0.7905 (t0) REVERT: C 377 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8378 (ttp) REVERT: C 417 GLU cc_start: 0.7958 (mp0) cc_final: 0.7524 (mp0) REVERT: C 420 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 424 ASP cc_start: 0.8142 (t70) cc_final: 0.7887 (t0) REVERT: C 431 ASP cc_start: 0.8291 (m-30) cc_final: 0.7740 (m-30) REVERT: C 433 GLU cc_start: 0.8439 (tt0) cc_final: 0.7889 (tm-30) REVERT: C 434 GLU cc_start: 0.8141 (pp20) cc_final: 0.7777 (pp20) REVERT: D 1 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8134 (ttp) REVERT: D 3 GLU cc_start: 0.8089 (mp0) cc_final: 0.7824 (mp0) REVERT: D 19 LYS cc_start: 0.9011 (tppp) cc_final: 0.8672 (tppp) REVERT: D 22 GLU cc_start: 0.8561 (tt0) cc_final: 0.8211 (tm-30) REVERT: D 45 GLU cc_start: 0.8515 (tt0) cc_final: 0.8026 (tm-30) REVERT: D 57 ASN cc_start: 0.7716 (t0) cc_final: 0.6926 (t0) REVERT: D 69 GLU cc_start: 0.7585 (pm20) cc_final: 0.7180 (pm20) REVERT: D 73 MET cc_start: 0.8768 (mpm) cc_final: 0.8446 (mpp) REVERT: D 88 ASP cc_start: 0.8235 (t70) cc_final: 0.7746 (t0) REVERT: D 92 PHE cc_start: 0.8674 (p90) cc_final: 0.8379 (p90) REVERT: D 121 ARG cc_start: 0.8594 (ttm110) cc_final: 0.8247 (mtm180) REVERT: D 157 GLU cc_start: 0.8251 (pp20) cc_final: 0.7944 (pp20) REVERT: D 161 ASP cc_start: 0.8568 (p0) cc_final: 0.8275 (p0) REVERT: D 174 LYS cc_start: 0.8765 (mptt) cc_final: 0.8429 (mptt) REVERT: D 181 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 251 ARG cc_start: 0.8765 (tpp-160) cc_final: 0.8367 (ttm110) REVERT: D 257 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: D 279 GLN cc_start: 0.8364 (pp30) cc_final: 0.7830 (tm130) REVERT: D 318 ARG cc_start: 0.8961 (mtp180) cc_final: 0.8681 (mmm-85) REVERT: D 325 GLU cc_start: 0.8245 (tp30) cc_final: 0.7916 (tp30) REVERT: D 376 GLU cc_start: 0.7842 (mp0) cc_final: 0.7467 (mp0) REVERT: D 383 GLU cc_start: 0.8351 (tp30) cc_final: 0.8052 (tp30) REVERT: D 391 ARG cc_start: 0.8985 (mmm160) cc_final: 0.7338 (ptm160) REVERT: D 404 ASP cc_start: 0.8388 (m-30) cc_final: 0.7315 (m-30) REVERT: D 407 GLU cc_start: 0.8055 (mp0) cc_final: 0.7291 (mp0) REVERT: D 417 ASP cc_start: 0.8436 (m-30) cc_final: 0.8053 (m-30) REVERT: E 21 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.8039 (t70) REVERT: E 68 GLU cc_start: 0.8147 (tt0) cc_final: 0.7892 (tt0) REVERT: E 69 ASN cc_start: 0.8369 (t0) cc_final: 0.8037 (t0) REVERT: E 104 GLN cc_start: 0.7329 (mt0) cc_final: 0.7080 (mt0) REVERT: E 129 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7686 (tm-30) REVERT: E 187 ASP cc_start: 0.8321 (t0) cc_final: 0.7774 (t0) REVERT: E 291 MET cc_start: 0.8791 (mtp) cc_final: 0.8524 (ttm) REVERT: E 340 SER cc_start: 0.8093 (t) cc_final: 0.7832 (t) REVERT: E 439 LYS cc_start: 0.8558 (ttmp) cc_final: 0.8194 (ttmm) REVERT: E 440 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8076 (mpp80) REVERT: E 457 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7857 (mm-30) REVERT: E 478 ASN cc_start: 0.8415 (t0) cc_final: 0.7969 (t0) REVERT: E 534 ASP cc_start: 0.7738 (p0) cc_final: 0.7449 (p0) REVERT: E 556 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7640 (mm-30) REVERT: E 569 MET cc_start: 0.7668 (mtp) cc_final: 0.7465 (mtm) outliers start: 47 outliers final: 28 residues processed: 456 average time/residue: 1.6885 time to fit residues: 841.8681 Evaluate side-chains 475 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 438 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 440 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 106 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 131 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.096726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088234 restraints weight = 28593.429| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.88 r_work: 0.3166 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17885 Z= 0.148 Angle : 0.609 9.393 24321 Z= 0.310 Chirality : 0.045 0.160 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.705 178.034 2519 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.17 % Allowed : 21.10 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2208 helix: 1.37 (0.17), residues: 923 sheet: 0.30 (0.28), residues: 344 loop : -0.62 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 21 HIS 0.007 0.001 HIS D 190 PHE 0.033 0.002 PHE E 75 TYR 0.016 0.001 TYR D 159 ARG 0.011 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 784) hydrogen bonds : angle 4.45227 ( 2268) metal coordination : bond 0.00421 ( 2) covalent geometry : bond 0.00345 (17882) covalent geometry : angle 0.60885 (24321) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 430 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 83 TYR cc_start: 0.8889 (m-80) cc_final: 0.8464 (m-80) REVERT: A 84 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7670 (mtm110) REVERT: A 116 ASP cc_start: 0.8157 (m-30) cc_final: 0.7712 (m-30) REVERT: A 117 LEU cc_start: 0.8385 (tp) cc_final: 0.7968 (tt) REVERT: A 120 ASP cc_start: 0.8035 (m-30) cc_final: 0.7792 (m-30) REVERT: A 141 PHE cc_start: 0.8497 (m-80) cc_final: 0.7987 (m-80) REVERT: A 154 MET cc_start: 0.8727 (mmp) cc_final: 0.8485 (mmm) REVERT: A 214 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8125 (ttp-110) REVERT: A 221 ARG cc_start: 0.8533 (ptp-110) cc_final: 0.8314 (ptp90) REVERT: A 254 GLU cc_start: 0.5375 (mm-30) cc_final: 0.3218 (tp30) REVERT: A 290 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 388 TRP cc_start: 0.8695 (m-10) cc_final: 0.8143 (m-10) REVERT: A 392 ASP cc_start: 0.8040 (m-30) cc_final: 0.7540 (m-30) REVERT: A 414 GLU cc_start: 0.8041 (mp0) cc_final: 0.7735 (mp0) REVERT: A 417 GLU cc_start: 0.7968 (tt0) cc_final: 0.7731 (mt-10) REVERT: A 420 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 423 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 19 LYS cc_start: 0.8886 (tptm) cc_final: 0.8507 (mmmt) REVERT: B 53 GLU cc_start: 0.8175 (tt0) cc_final: 0.7686 (tm-30) REVERT: B 69 GLU cc_start: 0.8036 (pt0) cc_final: 0.7659 (pm20) REVERT: B 74 ASP cc_start: 0.8252 (t70) cc_final: 0.7978 (OUTLIER) REVERT: B 84 ILE cc_start: 0.9012 (tt) cc_final: 0.8636 (pt) REVERT: B 114 ASP cc_start: 0.8208 (m-30) cc_final: 0.7954 (m-30) REVERT: B 118 ASP cc_start: 0.7911 (m-30) cc_final: 0.7583 (m-30) REVERT: B 123 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7934 (tp30) REVERT: B 127 CYS cc_start: 0.7986 (m) cc_final: 0.7543 (m) REVERT: B 154 LYS cc_start: 0.8963 (mmtp) cc_final: 0.8623 (mttp) REVERT: B 157 GLU cc_start: 0.8422 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 158 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: B 174 LYS cc_start: 0.8666 (mmpt) cc_final: 0.8246 (mmpt) REVERT: B 175 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8724 (m) REVERT: B 274 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8674 (p) REVERT: B 278 SER cc_start: 0.8632 (m) cc_final: 0.8277 (p) REVERT: B 325 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: B 328 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7442 (tp30) REVERT: B 343 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7466 (mp0) REVERT: B 407 GLU cc_start: 0.8011 (tt0) cc_final: 0.7636 (mt-10) REVERT: B 410 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 412 GLU cc_start: 0.8221 (tp30) cc_final: 0.7527 (tp30) REVERT: B 414 ASN cc_start: 0.8457 (m110) cc_final: 0.8210 (m110) REVERT: B 421 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8020 (tm-30) REVERT: C 116 ASP cc_start: 0.8023 (p0) cc_final: 0.7774 (p0) REVERT: C 120 ASP cc_start: 0.7909 (m-30) cc_final: 0.7671 (m-30) REVERT: C 123 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.7540 (tpp80) REVERT: C 164 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8819 (mmmm) REVERT: C 196 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: C 214 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8216 (ttp-110) REVERT: C 280 LYS cc_start: 0.8951 (mttp) cc_final: 0.8165 (mmpt) REVERT: C 284 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7340 (mp0) REVERT: C 308 ARG cc_start: 0.6744 (tpt170) cc_final: 0.5789 (tpt170) REVERT: C 322 ASP cc_start: 0.8062 (t70) cc_final: 0.7817 (t0) REVERT: C 377 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8392 (ttp) REVERT: C 417 GLU cc_start: 0.7967 (mp0) cc_final: 0.7521 (mp0) REVERT: C 420 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7643 (mm-30) REVERT: C 423 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7686 (mm-30) REVERT: C 424 ASP cc_start: 0.8080 (t70) cc_final: 0.7850 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8414 (tt0) cc_final: 0.7864 (tm-30) REVERT: C 434 GLU cc_start: 0.8072 (pp20) cc_final: 0.7655 (pp20) REVERT: D 1 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8122 (ttp) REVERT: D 3 GLU cc_start: 0.8141 (mp0) cc_final: 0.7867 (mp0) REVERT: D 19 LYS cc_start: 0.8998 (tppp) cc_final: 0.8644 (tppp) REVERT: D 22 GLU cc_start: 0.8551 (tt0) cc_final: 0.8248 (tm-30) REVERT: D 45 GLU cc_start: 0.8506 (tt0) cc_final: 0.8007 (tm-30) REVERT: D 57 ASN cc_start: 0.7758 (t0) cc_final: 0.6962 (t0) REVERT: D 69 GLU cc_start: 0.7619 (pm20) cc_final: 0.7238 (pm20) REVERT: D 88 ASP cc_start: 0.8228 (t70) cc_final: 0.7737 (t0) REVERT: D 92 PHE cc_start: 0.8673 (p90) cc_final: 0.8333 (p90) REVERT: D 121 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8293 (mtm180) REVERT: D 157 GLU cc_start: 0.8264 (pp20) cc_final: 0.7953 (pp20) REVERT: D 161 ASP cc_start: 0.8562 (p0) cc_final: 0.8280 (p0) REVERT: D 174 LYS cc_start: 0.8756 (mptt) cc_final: 0.8419 (mptt) REVERT: D 181 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 190 HIS cc_start: 0.7748 (t-90) cc_final: 0.7153 (t-90) REVERT: D 251 ARG cc_start: 0.8767 (tpp-160) cc_final: 0.8366 (ttm110) REVERT: D 257 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: D 279 GLN cc_start: 0.8366 (pp30) cc_final: 0.7894 (tm130) REVERT: D 318 ARG cc_start: 0.8955 (mtp180) cc_final: 0.8679 (mmm-85) REVERT: D 325 GLU cc_start: 0.8230 (tp30) cc_final: 0.7907 (tp30) REVERT: D 376 GLU cc_start: 0.7845 (mp0) cc_final: 0.7479 (mp0) REVERT: D 383 GLU cc_start: 0.8356 (tp30) cc_final: 0.8056 (tp30) REVERT: D 391 ARG cc_start: 0.8977 (mmm160) cc_final: 0.7353 (ptm160) REVERT: D 404 ASP cc_start: 0.8417 (m-30) cc_final: 0.7351 (m-30) REVERT: D 407 GLU cc_start: 0.8050 (mp0) cc_final: 0.7306 (mp0) REVERT: D 414 ASN cc_start: 0.8122 (p0) cc_final: 0.7308 (p0) REVERT: D 417 ASP cc_start: 0.8436 (m-30) cc_final: 0.8043 (m-30) REVERT: E 21 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.8073 (t70) REVERT: E 68 GLU cc_start: 0.8164 (tt0) cc_final: 0.7866 (tt0) REVERT: E 69 ASN cc_start: 0.8342 (t0) cc_final: 0.8003 (t0) REVERT: E 104 GLN cc_start: 0.7272 (mt0) cc_final: 0.7025 (mt0) REVERT: E 129 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7692 (tm-30) REVERT: E 187 ASP cc_start: 0.8235 (t0) cc_final: 0.7620 (t0) REVERT: E 314 GLN cc_start: 0.8201 (mp10) cc_final: 0.7942 (mm110) REVERT: E 340 SER cc_start: 0.8087 (t) cc_final: 0.7830 (t) REVERT: E 439 LYS cc_start: 0.8571 (ttmp) cc_final: 0.8209 (ttmm) REVERT: E 440 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8078 (mpp80) REVERT: E 457 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7829 (mm-30) REVERT: E 478 ASN cc_start: 0.8421 (t0) cc_final: 0.7968 (t0) REVERT: E 484 MET cc_start: 0.6867 (mtp) cc_final: 0.6569 (mtm) REVERT: E 534 ASP cc_start: 0.7744 (p0) cc_final: 0.7452 (p0) REVERT: E 556 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7612 (mm-30) outliers start: 40 outliers final: 27 residues processed: 449 average time/residue: 1.6648 time to fit residues: 817.4031 Evaluate side-chains 468 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 432 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 440 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 114 optimal weight: 0.1980 chunk 167 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 187 optimal weight: 0.0970 chunk 171 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 98 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088963 restraints weight = 28588.705| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.89 r_work: 0.3180 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17885 Z= 0.131 Angle : 0.601 9.518 24321 Z= 0.307 Chirality : 0.044 0.168 2657 Planarity : 0.004 0.048 3175 Dihedral : 10.546 177.506 2519 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.22 % Allowed : 21.53 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2208 helix: 1.44 (0.17), residues: 924 sheet: 0.38 (0.28), residues: 346 loop : -0.61 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 388 HIS 0.006 0.001 HIS D 190 PHE 0.033 0.001 PHE E 75 TYR 0.015 0.001 TYR D 159 ARG 0.011 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 784) hydrogen bonds : angle 4.40876 ( 2268) metal coordination : bond 0.00305 ( 2) covalent geometry : bond 0.00304 (17882) covalent geometry : angle 0.60139 (24321) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17257.09 seconds wall clock time: 305 minutes 14.20 seconds (18314.20 seconds total)