Starting phenix.real_space_refine on Wed Jan 22 00:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4l_42972/01_2025/8v4l_42972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4l_42972/01_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_42972/01_2025/8v4l_42972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4l_42972/01_2025/8v4l_42972.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4l_42972/01_2025/8v4l_42972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4l_42972/01_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-5571/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: 11.83, per 1000 atoms: 0.68 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: 4.54 Conformation dependent library (CDL) restraints added in 2.4 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: 2.11 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: 5.91 Time building geometry restraints manager: 5.21 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: 10.400 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 45.750 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.280 ------------------------------------------------------------------------------- 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 17882 Z= 0.425 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 *********************** 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 : 2.592 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: 1.5759 time to fit residues: 1029.9960 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 : 2.040 ------------------------------------------------------------------------------- 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 = 43)----------------| | 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: 0.3292 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 17882 Z= 0.183 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 *********************** 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 : 1.974 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: 0.7997 (t0) REVERT: A 83 TYR cc_start: 0.8599 (m-80) cc_final: 0.8347 (m-80) REVERT: A 116 ASP cc_start: 0.7675 (m-30) cc_final: 0.6953 (p0) REVERT: A 117 LEU cc_start: 0.7959 (tp) cc_final: 0.7656 (tt) REVERT: A 120 ASP cc_start: 0.7752 (m-30) cc_final: 0.7417 (m-30) REVERT: A 290 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 367 ASP cc_start: 0.7815 (p0) cc_final: 0.7537 (p0) REVERT: A 370 LYS cc_start: 0.8487 (tptt) cc_final: 0.8234 (tptt) REVERT: A 414 GLU cc_start: 0.7963 (mp0) cc_final: 0.7643 (pm20) REVERT: A 423 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7924 (mm-30) REVERT: B 19 LYS cc_start: 0.9036 (tptm) cc_final: 0.8598 (tppp) REVERT: B 81 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7429 (t80) REVERT: B 103 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8435 (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: 0.7617 (m) cc_final: 0.7076 (m) REVERT: B 158 GLU cc_start: 0.7857 (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: 0.9001 (mmtm) cc_final: 0.8710 (mmmm) REVERT: B 278 SER cc_start: 0.8607 (m) cc_final: 0.8197 (p) REVERT: B 291 GLN cc_start: 0.8300 (pp30) cc_final: 0.8012 (pp30) REVERT: B 324 LYS cc_start: 0.8493 (tptm) cc_final: 0.8083 (tppp) REVERT: B 328 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7352 (tp30) REVERT: B 391 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.7225 (mtp-110) REVERT: B 407 GLU cc_start: 0.7995 (tt0) cc_final: 0.7790 (mt-10) REVERT: B 412 GLU cc_start: 0.8226 (tp30) cc_final: 0.7814 (tp30) REVERT: B 414 ASN cc_start: 0.8055 (m110) cc_final: 0.7689 (m110) REVERT: B 417 ASP cc_start: 0.8162 (m-30) cc_final: 0.7628 (m-30) REVERT: B 421 GLU cc_start: 0.7891 (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: 0.8929 (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: 0.8657 (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: 0.8035 (t70) cc_final: 0.7817 (OUTLIER) REVERT: C 337 THR cc_start: 0.8854 (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: 0.7859 (m-30) cc_final: 0.7559 (m-30) REVERT: C 423 GLU cc_start: 0.8004 (tp30) cc_final: 0.7720 (mm-30) REVERT: D 3 GLU cc_start: 0.7800 (mp0) cc_final: 0.7179 (mp0) REVERT: D 19 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8673 (tppp) REVERT: D 22 GLU cc_start: 0.8580 (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: 0.8252 (t70) cc_final: 0.7827 (t0) REVERT: D 103 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8701 (mtpm) REVERT: D 123 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7979 (mm-30) REVERT: D 158 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7928 (mm-30) REVERT: D 159 TYR cc_start: 0.8334 (m-80) cc_final: 0.8077 (m-80) REVERT: D 174 LYS cc_start: 0.8387 (mptt) cc_final: 0.8161 (mptt) REVERT: D 181 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7677 (mt-10) REVERT: D 198 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8044 (mt-10) REVERT: D 203 ASP cc_start: 0.8144 (t0) cc_final: 0.7859 (t70) REVERT: D 257 MET cc_start: 0.8414 (mmm) cc_final: 0.8077 (mtp) REVERT: D 291 GLN cc_start: 0.8619 (pp30) cc_final: 0.8385 (pp30) REVERT: D 323 MET cc_start: 0.8375 (mmm) cc_final: 0.8095 (mmm) REVERT: D 325 GLU cc_start: 0.7956 (tp30) cc_final: 0.7702 (tp30) REVERT: D 383 GLU cc_start: 0.8163 (tp30) cc_final: 0.7744 (tp30) REVERT: D 391 ARG cc_start: 0.8344 (mmm160) cc_final: 0.6844 (ptm-80) REVERT: D 404 ASP cc_start: 0.8294 (m-30) cc_final: 0.7551 (m-30) REVERT: D 407 GLU cc_start: 0.8028 (mp0) cc_final: 0.7648 (mp0) REVERT: D 410 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7792 (tm-30) REVERT: D 412 GLU cc_start: 0.7909 (tp30) cc_final: 0.7695 (mm-30) REVERT: D 413 SER cc_start: 0.8557 (t) cc_final: 0.7858 (p) REVERT: D 417 ASP cc_start: 0.8199 (m-30) cc_final: 0.7987 (m-30) REVERT: E 59 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8238 (mtp180) REVERT: E 69 ASN cc_start: 0.8121 (t0) cc_final: 0.7744 (t0) REVERT: E 98 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7879 (mp10) REVERT: E 120 GLU cc_start: 0.7515 (mp0) cc_final: 0.7235 (mp0) REVERT: E 129 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7647 (tm-30) REVERT: E 187 ASP cc_start: 0.7964 (t0) cc_final: 0.7289 (t0) REVERT: E 278 GLN cc_start: 0.8498 (mt0) cc_final: 0.8294 (mt0) REVERT: E 291 MET cc_start: 0.8694 (mtm) cc_final: 0.8363 (mtm) REVERT: E 432 ASP cc_start: 0.7513 (m-30) cc_final: 0.7306 (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: 0.7854 (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: 1.6597 time to fit residues: 900.6279 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 : 1.894 ------------------------------------------------------------------------------- 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: 0.9990 chunk 213 optimal weight: 0.0030 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 153 optimal weight: 0.0060 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 190 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092475 restraints weight = 29433.899| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.93 r_work: 0.3255 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17882 Z= 0.183 Angle : 0.561 8.182 24321 Z= 0.286 Chirality : 0.043 0.165 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.379 156.999 2522 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.60 % Allowed : 16.21 % Favored : 81.18 % 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: 0.21 (0.18), residues: 2208 helix: 0.81 (0.17), residues: 920 sheet: 0.49 (0.28), residues: 362 loop : -0.62 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 21 HIS 0.011 0.001 HIS D 190 PHE 0.021 0.001 PHE E 75 TYR 0.016 0.001 TYR C 432 ARG 0.010 0.001 ARG B 306 *********************** 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: 48 poor density : 440 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8556 (p90) cc_final: 0.8204 (p90) REVERT: A 77 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7655 (mt-10) REVERT: A 83 TYR cc_start: 0.8663 (m-80) cc_final: 0.8372 (m-80) REVERT: A 116 ASP cc_start: 0.7875 (m-30) cc_final: 0.7253 (p0) REVERT: A 117 LEU cc_start: 0.8075 (tp) cc_final: 0.7659 (tt) REVERT: A 120 ASP cc_start: 0.7770 (m-30) cc_final: 0.7475 (m-30) REVERT: A 251 ASP cc_start: 0.7618 (m-30) cc_final: 0.7279 (p0) REVERT: A 254 GLU cc_start: 0.5853 (mm-30) cc_final: 0.4547 (tp30) REVERT: A 290 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 338 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8447 (ttpp) REVERT: A 367 ASP cc_start: 0.8098 (p0) cc_final: 0.7785 (p0) REVERT: A 370 LYS cc_start: 0.8476 (tptt) cc_final: 0.8221 (tptt) REVERT: A 414 GLU cc_start: 0.8017 (mp0) cc_final: 0.7579 (mp0) REVERT: A 417 GLU cc_start: 0.7949 (tt0) cc_final: 0.7731 (mt-10) REVERT: A 420 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 423 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7887 (mm-30) REVERT: B 1 MET cc_start: 0.8464 (mtt) cc_final: 0.8232 (mtt) REVERT: B 19 LYS cc_start: 0.8989 (tptm) cc_final: 0.8537 (tppp) REVERT: B 103 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8459 (mtpm) REVERT: B 118 ASP cc_start: 0.7898 (m-30) cc_final: 0.7597 (m-30) REVERT: B 123 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7751 (tp30) REVERT: B 127 CYS cc_start: 0.7888 (m) cc_final: 0.7315 (m) REVERT: B 154 LYS cc_start: 0.8877 (mmtp) cc_final: 0.8360 (mtpp) REVERT: B 158 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 174 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8183 (mmpt) REVERT: B 203 ASP cc_start: 0.7696 (t70) cc_final: 0.7460 (t0) REVERT: B 216 LYS cc_start: 0.9053 (mmtm) cc_final: 0.8731 (mmmm) REVERT: B 274 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8400 (p) REVERT: B 278 SER cc_start: 0.8558 (m) cc_final: 0.8212 (p) REVERT: B 291 GLN cc_start: 0.8316 (pp30) cc_final: 0.8032 (pp30) REVERT: B 328 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7338 (tp30) REVERT: B 407 GLU cc_start: 0.7984 (tt0) cc_final: 0.7721 (mt-10) REVERT: B 410 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7208 (mm-30) REVERT: B 412 GLU cc_start: 0.8198 (tp30) cc_final: 0.7717 (tp30) REVERT: B 414 ASN cc_start: 0.8291 (m110) cc_final: 0.7841 (m110) REVERT: B 417 ASP cc_start: 0.8193 (m-30) cc_final: 0.7812 (m-30) REVERT: C 50 ASN cc_start: 0.8747 (t0) cc_final: 0.8378 (t0) REVERT: C 123 ARG cc_start: 0.8017 (tpp-160) cc_final: 0.7590 (tpp80) REVERT: C 158 SER cc_start: 0.8964 (t) cc_final: 0.8752 (t) REVERT: C 196 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: C 207 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7099 (mt-10) REVERT: C 280 LYS cc_start: 0.8925 (mttp) cc_final: 0.7670 (mmtt) REVERT: C 284 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7364 (mp0) REVERT: C 308 ARG cc_start: 0.6697 (tpt170) cc_final: 0.5660 (tpt170) REVERT: C 322 ASP cc_start: 0.8029 (t70) cc_final: 0.7810 (t0) REVERT: C 386 GLU cc_start: 0.7714 (mp0) cc_final: 0.7428 (mp0) REVERT: C 420 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7506 (mm-30) REVERT: C 423 GLU cc_start: 0.7916 (tp30) cc_final: 0.7666 (mm-30) REVERT: C 431 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: C 434 GLU cc_start: 0.7845 (pp20) cc_final: 0.7626 (pp20) REVERT: D 3 GLU cc_start: 0.7908 (mp0) cc_final: 0.7282 (mp0) REVERT: D 22 GLU cc_start: 0.8637 (tt0) cc_final: 0.8034 (tp30) REVERT: D 45 GLU cc_start: 0.8321 (tt0) cc_final: 0.7990 (tm-30) REVERT: D 88 ASP cc_start: 0.8326 (t70) cc_final: 0.7847 (t0) REVERT: D 103 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8758 (mtpm) REVERT: D 123 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7928 (mm-30) REVERT: D 159 TYR cc_start: 0.8546 (m-80) cc_final: 0.8337 (m-80) REVERT: D 181 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7684 (mt-10) REVERT: D 190 HIS cc_start: 0.7673 (t-90) cc_final: 0.6406 (t-90) REVERT: D 198 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8045 (mt-10) REVERT: D 203 ASP cc_start: 0.8120 (t0) cc_final: 0.7826 (t70) REVERT: D 216 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8670 (mmmm) REVERT: D 251 ARG cc_start: 0.8742 (tpp-160) cc_final: 0.8386 (ttm110) REVERT: D 257 MET cc_start: 0.8433 (mmm) cc_final: 0.8210 (mtp) REVERT: D 291 GLN cc_start: 0.8587 (pp30) cc_final: 0.8276 (pp30) REVERT: D 376 GLU cc_start: 0.7727 (mp0) cc_final: 0.7181 (mp0) REVERT: D 383 GLU cc_start: 0.8183 (tp30) cc_final: 0.7735 (tp30) REVERT: D 391 ARG cc_start: 0.8512 (mmm160) cc_final: 0.7024 (ptm-80) REVERT: D 404 ASP cc_start: 0.8308 (m-30) cc_final: 0.7482 (m-30) REVERT: D 407 GLU cc_start: 0.8043 (mp0) cc_final: 0.7666 (mp0) REVERT: D 410 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7871 (tm-30) REVERT: D 412 GLU cc_start: 0.7965 (tp30) cc_final: 0.7692 (mm-30) REVERT: E 61 ASP cc_start: 0.7502 (m-30) cc_final: 0.7283 (m-30) REVERT: E 69 ASN cc_start: 0.8141 (t0) cc_final: 0.7785 (t0) REVERT: E 93 MET cc_start: 0.8021 (mmm) cc_final: 0.7805 (mmp) REVERT: E 120 GLU cc_start: 0.7382 (mp0) cc_final: 0.7133 (mp0) REVERT: E 129 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7577 (tm-30) REVERT: E 187 ASP cc_start: 0.8080 (t0) cc_final: 0.7432 (t0) REVERT: E 278 GLN cc_start: 0.8608 (mt0) cc_final: 0.8383 (mt0) REVERT: E 322 LEU cc_start: 0.8630 (mp) cc_final: 0.8413 (mm) REVERT: E 444 MET cc_start: 0.8537 (mtm) cc_final: 0.8210 (mtt) REVERT: E 478 ASN cc_start: 0.8342 (t0) cc_final: 0.7935 (t0) REVERT: E 519 TYR cc_start: 0.8658 (m-80) cc_final: 0.8448 (m-10) REVERT: E 534 ASP cc_start: 0.7671 (p0) cc_final: 0.7385 (p0) REVERT: E 556 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7611 (mm-30) REVERT: E 569 MET cc_start: 0.7786 (mtp) cc_final: 0.7485 (mtm) REVERT: E 588 ASN cc_start: 0.8712 (t0) cc_final: 0.8466 (m-40) outliers start: 48 outliers final: 12 residues processed: 465 average time/residue: 1.6200 time to fit residues: 826.0839 Evaluate side-chains 446 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 430 time to evaluate : 1.977 ------------------------------------------------------------------------------- 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 113 VAL 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 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 533 HIS 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: 0.8980 chunk 2 optimal weight: 0.7980 chunk 208 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 423 GLN C 101 ASN C 356 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 165 GLN E 170 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 573 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089270 restraints weight = 29095.376| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.89 r_work: 0.3191 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17882 Z= 0.238 Angle : 0.579 8.253 24321 Z= 0.297 Chirality : 0.045 0.160 2657 Planarity : 0.004 0.049 3175 Dihedral : 10.563 173.077 2519 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.98 % Allowed : 16.81 % Favored : 80.21 % 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: 0.47 (0.18), residues: 2208 helix: 1.16 (0.17), residues: 916 sheet: 0.45 (0.28), residues: 367 loop : -0.54 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 21 HIS 0.013 0.001 HIS E 323 PHE 0.023 0.002 PHE E 75 TYR 0.018 0.001 TYR E 430 ARG 0.017 0.001 ARG E 590 *********************** 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 499 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 444 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 83 TYR cc_start: 0.8756 (m-80) cc_final: 0.8435 (m-80) REVERT: A 116 ASP cc_start: 0.8051 (m-30) cc_final: 0.7537 (p0) REVERT: A 117 LEU cc_start: 0.8275 (tp) cc_final: 0.7820 (tt) REVERT: A 120 ASP cc_start: 0.7926 (m-30) cc_final: 0.7622 (m-30) REVERT: A 211 ASP cc_start: 0.8017 (m-30) cc_final: 0.7674 (m-30) REVERT: A 214 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.7813 (ttp-110) REVERT: A 254 GLU cc_start: 0.4299 (mm-30) cc_final: 0.3622 (mm-30) REVERT: A 277 SER cc_start: 0.8859 (t) cc_final: 0.8459 (p) REVERT: A 290 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8247 (mm-30) REVERT: A 338 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8498 (ttpp) REVERT: A 367 ASP cc_start: 0.8041 (p0) cc_final: 0.7736 (p0) REVERT: A 370 LYS cc_start: 0.8491 (tptt) cc_final: 0.8262 (tptt) REVERT: A 388 TRP cc_start: 0.8732 (m-10) cc_final: 0.8499 (m-10) REVERT: A 414 GLU cc_start: 0.8110 (mp0) cc_final: 0.7582 (mp0) REVERT: A 417 GLU cc_start: 0.8025 (tt0) cc_final: 0.7745 (mt-10) REVERT: A 423 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 1 MET cc_start: 0.8576 (mtt) cc_final: 0.8226 (mtm) REVERT: B 19 LYS cc_start: 0.8973 (tptm) cc_final: 0.8757 (tppt) REVERT: B 36 TYR cc_start: 0.8714 (t80) cc_final: 0.8462 (t80) REVERT: B 53 GLU cc_start: 0.8122 (tt0) cc_final: 0.7653 (mm-30) REVERT: B 74 ASP cc_start: 0.8064 (t0) cc_final: 0.7668 (t0) REVERT: B 103 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8523 (mtpm) REVERT: B 114 ASP cc_start: 0.8221 (m-30) cc_final: 0.7977 (m-30) REVERT: B 118 ASP cc_start: 0.7892 (m-30) cc_final: 0.7585 (m-30) REVERT: B 123 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7840 (tp30) REVERT: B 127 CYS cc_start: 0.7866 (m) cc_final: 0.7326 (m) REVERT: B 154 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8510 (mtpp) REVERT: B 158 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: B 174 LYS cc_start: 0.8553 (mmpt) cc_final: 0.8322 (mmpt) REVERT: B 175 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8636 (m) REVERT: B 216 LYS cc_start: 0.9082 (mmtm) cc_final: 0.8775 (mmmm) REVERT: B 274 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8453 (p) REVERT: B 278 SER cc_start: 0.8536 (m) cc_final: 0.8205 (p) REVERT: B 325 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7334 (tp30) REVERT: B 328 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7416 (tp30) REVERT: B 390 ARG cc_start: 0.8423 (mtm110) cc_final: 0.8208 (mtp-110) REVERT: B 407 GLU cc_start: 0.8188 (tt0) cc_final: 0.7871 (mt-10) REVERT: B 410 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7394 (mm-30) REVERT: B 414 ASN cc_start: 0.8378 (m110) cc_final: 0.7971 (m110) REVERT: B 417 ASP cc_start: 0.8249 (m-30) cc_final: 0.8017 (m-30) REVERT: C 50 ASN cc_start: 0.8764 (t0) cc_final: 0.8392 (t0) REVERT: C 116 ASP cc_start: 0.7836 (p0) cc_final: 0.7630 (p0) REVERT: C 120 ASP cc_start: 0.7921 (m-30) cc_final: 0.7696 (m-30) REVERT: C 123 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7537 (tpp80) REVERT: C 196 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: C 207 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7224 (mt-10) REVERT: C 280 LYS cc_start: 0.8909 (mttp) cc_final: 0.8351 (mtpt) REVERT: C 308 ARG cc_start: 0.6763 (tpt170) cc_final: 0.6259 (tpt170) REVERT: C 322 ASP cc_start: 0.8156 (t70) cc_final: 0.7901 (t0) REVERT: C 386 GLU cc_start: 0.7803 (mp0) cc_final: 0.7460 (mp0) REVERT: C 420 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7498 (mm-30) REVERT: C 423 GLU cc_start: 0.8012 (tp30) cc_final: 0.7726 (mm-30) REVERT: C 424 ASP cc_start: 0.8043 (t70) cc_final: 0.7824 (t0) REVERT: C 434 GLU cc_start: 0.7952 (pp20) cc_final: 0.7610 (pp20) REVERT: D 3 GLU cc_start: 0.7949 (mp0) cc_final: 0.7466 (mp0) REVERT: D 22 GLU cc_start: 0.8680 (tt0) cc_final: 0.8177 (tm-30) REVERT: D 45 GLU cc_start: 0.8385 (tt0) cc_final: 0.8022 (tm-30) REVERT: D 57 ASN cc_start: 0.7322 (t0) cc_final: 0.6445 (t0) REVERT: D 88 ASP cc_start: 0.8397 (t70) cc_final: 0.7909 (t0) REVERT: D 103 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8724 (mtpm) REVERT: D 123 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7909 (mm-30) REVERT: D 158 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8056 (mt-10) REVERT: D 181 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 198 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8143 (mt-10) REVERT: D 203 ASP cc_start: 0.8141 (t0) cc_final: 0.7840 (t70) REVERT: D 216 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8743 (mmmm) REVERT: D 251 ARG cc_start: 0.8766 (tpp-160) cc_final: 0.8210 (ttm110) REVERT: D 262 ARG cc_start: 0.8855 (mtm180) cc_final: 0.8602 (mtm180) REVERT: D 291 GLN cc_start: 0.8570 (pp30) cc_final: 0.8307 (pp30) REVERT: D 325 GLU cc_start: 0.8118 (tp30) cc_final: 0.7824 (tp30) REVERT: D 383 GLU cc_start: 0.8311 (tp30) cc_final: 0.7836 (tp30) REVERT: D 391 ARG cc_start: 0.8648 (mmm160) cc_final: 0.7189 (ptm160) REVERT: D 404 ASP cc_start: 0.8382 (m-30) cc_final: 0.7478 (m-30) REVERT: D 407 GLU cc_start: 0.8091 (mp0) cc_final: 0.7437 (mp0) REVERT: D 412 GLU cc_start: 0.7912 (tp30) cc_final: 0.7564 (tm-30) REVERT: D 416 ASN cc_start: 0.8295 (m-40) cc_final: 0.7327 (m110) REVERT: E 68 GLU cc_start: 0.8045 (tt0) cc_final: 0.7737 (tt0) REVERT: E 69 ASN cc_start: 0.8175 (t0) cc_final: 0.7785 (t0) REVERT: E 120 GLU cc_start: 0.7431 (mp0) cc_final: 0.7139 (mp0) REVERT: E 129 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7643 (tm-30) REVERT: E 181 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.6285 (p) REVERT: E 187 ASP cc_start: 0.8251 (t0) cc_final: 0.7562 (t0) REVERT: E 440 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8235 (mpp80) REVERT: E 444 MET cc_start: 0.8620 (mtm) cc_final: 0.8155 (mtt) REVERT: E 457 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7878 (mm-30) REVERT: E 478 ASN cc_start: 0.8388 (t0) cc_final: 0.8001 (t0) REVERT: E 519 TYR cc_start: 0.8635 (m-80) cc_final: 0.8362 (m-10) REVERT: E 534 ASP cc_start: 0.7684 (p0) cc_final: 0.7466 (p0) REVERT: E 556 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7530 (mm-30) REVERT: E 562 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8170 (ttp) REVERT: E 569 MET cc_start: 0.7727 (mtp) cc_final: 0.7372 (mtm) REVERT: E 573 ASN cc_start: 0.8065 (t0) cc_final: 0.7857 (t0) REVERT: E 588 ASN cc_start: 0.8730 (t0) cc_final: 0.8336 (m-40) outliers start: 55 outliers final: 20 residues processed: 474 average time/residue: 1.6740 time to fit residues: 870.0710 Evaluate side-chains 448 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 421 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 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 170 VAL Chi-restraints excluded: chain B residue 175 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 219 ILE Chi-restraints excluded: chain C residue 249 ASN 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 D residue 58 LYS 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 533 HIS Chi-restraints excluded: chain E residue 562 MET Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 256 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 423 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089202 restraints weight = 29033.063| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.88 r_work: 0.3176 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17882 Z= 0.251 Angle : 0.584 8.674 24321 Z= 0.296 Chirality : 0.045 0.158 2657 Planarity : 0.004 0.057 3175 Dihedral : 10.735 179.089 2519 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.93 % Allowed : 17.84 % Favored : 79.23 % 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: 0.54 (0.18), residues: 2208 helix: 1.29 (0.17), residues: 917 sheet: 0.46 (0.29), residues: 347 loop : -0.55 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 21 HIS 0.012 0.001 HIS D 190 PHE 0.027 0.002 PHE E 75 TYR 0.022 0.001 TYR D 159 ARG 0.016 0.001 ARG E 590 *********************** 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 480 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 426 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 83 TYR cc_start: 0.8827 (m-80) cc_final: 0.8472 (m-80) REVERT: A 116 ASP cc_start: 0.8089 (m-30) cc_final: 0.7435 (m-30) REVERT: A 117 LEU cc_start: 0.8297 (tp) cc_final: 0.7846 (tt) REVERT: A 120 ASP cc_start: 0.7968 (m-30) cc_final: 0.7680 (m-30) REVERT: A 211 ASP cc_start: 0.8026 (m-30) cc_final: 0.7666 (m-30) REVERT: A 214 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.8072 (ttp-110) REVERT: A 254 GLU cc_start: 0.4434 (mm-30) cc_final: 0.2987 (mm-30) REVERT: A 277 SER cc_start: 0.8878 (t) cc_final: 0.8499 (p) REVERT: A 290 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8245 (mm-30) REVERT: A 338 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8467 (ttpp) REVERT: A 367 ASP cc_start: 0.8099 (p0) cc_final: 0.7735 (p0) REVERT: A 370 LYS cc_start: 0.8543 (tptt) cc_final: 0.8323 (tptt) REVERT: A 377 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8397 (ttt) REVERT: A 388 TRP cc_start: 0.8681 (m-10) cc_final: 0.8427 (m-10) REVERT: A 414 GLU cc_start: 0.8091 (mp0) cc_final: 0.7740 (mp0) REVERT: A 417 GLU cc_start: 0.7987 (tt0) cc_final: 0.7717 (mt-10) REVERT: A 420 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 423 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7950 (mm-30) REVERT: B 1 MET cc_start: 0.8541 (mtt) cc_final: 0.8185 (mtm) REVERT: B 19 LYS cc_start: 0.8965 (tptm) cc_final: 0.8754 (tppt) REVERT: B 36 TYR cc_start: 0.8744 (t80) cc_final: 0.8434 (t80) REVERT: B 74 ASP cc_start: 0.8251 (t0) cc_final: 0.7911 (t0) REVERT: B 114 ASP cc_start: 0.8177 (m-30) cc_final: 0.7941 (m-30) REVERT: B 118 ASP cc_start: 0.7954 (m-30) cc_final: 0.7636 (m-30) REVERT: B 123 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7852 (tp30) REVERT: B 127 CYS cc_start: 0.7850 (m) cc_final: 0.7321 (m) REVERT: B 134 GLN cc_start: 0.8479 (mt0) cc_final: 0.8224 (pt0) REVERT: B 154 LYS cc_start: 0.8958 (mmtp) cc_final: 0.8586 (mtpp) REVERT: B 158 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: B 174 LYS cc_start: 0.8619 (mmpt) cc_final: 0.8323 (mmpt) REVERT: B 175 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8702 (m) REVERT: B 274 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 278 SER cc_start: 0.8538 (m) cc_final: 0.8235 (p) REVERT: B 325 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7362 (mm-30) REVERT: B 328 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7363 (tp30) REVERT: B 407 GLU cc_start: 0.8016 (tt0) cc_final: 0.7684 (mt-10) REVERT: B 410 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 412 GLU cc_start: 0.8220 (tp30) cc_final: 0.7630 (tp30) REVERT: B 414 ASN cc_start: 0.8409 (m110) cc_final: 0.7996 (m110) REVERT: B 417 ASP cc_start: 0.8296 (m-30) cc_final: 0.8043 (m-30) REVERT: B 421 GLU cc_start: 0.8269 (tt0) cc_final: 0.7947 (tm-30) REVERT: C 50 ASN cc_start: 0.8826 (t0) cc_final: 0.8452 (t0) REVERT: C 71 GLU cc_start: 0.7600 (pt0) cc_final: 0.7355 (pm20) REVERT: C 116 ASP cc_start: 0.7978 (p0) cc_final: 0.7755 (p0) REVERT: C 120 ASP cc_start: 0.7912 (m-30) cc_final: 0.7711 (m-30) REVERT: C 123 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7600 (tpp80) REVERT: C 196 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: C 207 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7378 (mt-10) REVERT: C 214 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8286 (ttp-110) REVERT: C 218 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8380 (t0) REVERT: C 277 SER cc_start: 0.8658 (t) cc_final: 0.8442 (p) REVERT: C 280 LYS cc_start: 0.8961 (mttp) cc_final: 0.8074 (mmtt) REVERT: C 308 ARG cc_start: 0.6658 (tpt170) cc_final: 0.6144 (tpt170) REVERT: C 322 ASP cc_start: 0.8139 (t70) cc_final: 0.7886 (t0) REVERT: C 386 GLU cc_start: 0.7797 (mp0) cc_final: 0.7465 (mp0) REVERT: C 417 GLU cc_start: 0.7657 (mp0) cc_final: 0.7413 (mp0) REVERT: C 420 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 423 GLU cc_start: 0.7988 (tp30) cc_final: 0.7752 (mm-30) REVERT: C 424 ASP cc_start: 0.8055 (t70) cc_final: 0.7826 (t0) REVERT: C 434 GLU cc_start: 0.8065 (pp20) cc_final: 0.7682 (pp20) REVERT: D 3 GLU cc_start: 0.8041 (mp0) cc_final: 0.7703 (mp0) REVERT: D 22 GLU cc_start: 0.8693 (tt0) cc_final: 0.8265 (tm-30) REVERT: D 26 ASP cc_start: 0.7582 (m-30) cc_final: 0.7305 (t0) REVERT: D 45 GLU cc_start: 0.8458 (tt0) cc_final: 0.8198 (tm-30) REVERT: D 57 ASN cc_start: 0.7504 (t0) cc_final: 0.6443 (t0) REVERT: D 69 GLU cc_start: 0.7760 (pm20) cc_final: 0.7275 (pm20) REVERT: D 88 ASP cc_start: 0.8342 (t70) cc_final: 0.7876 (t0) REVERT: D 103 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8775 (mtpm) REVERT: D 123 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7910 (mm-30) REVERT: D 158 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8303 (mt-10) REVERT: D 181 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7885 (mt-10) REVERT: D 190 HIS cc_start: 0.8008 (t-90) cc_final: 0.7348 (t70) REVERT: D 203 ASP cc_start: 0.8106 (t0) cc_final: 0.7822 (t70) REVERT: D 251 ARG cc_start: 0.8748 (tpp-160) cc_final: 0.8192 (ttm110) REVERT: D 262 ARG cc_start: 0.8883 (mtm180) cc_final: 0.8635 (mtm180) REVERT: D 291 GLN cc_start: 0.8587 (pp30) cc_final: 0.8322 (pp30) REVERT: D 325 GLU cc_start: 0.8194 (tp30) cc_final: 0.7782 (tp30) REVERT: D 376 GLU cc_start: 0.7807 (mp0) cc_final: 0.7527 (mp0) REVERT: D 383 GLU cc_start: 0.8377 (tp30) cc_final: 0.8056 (tp30) REVERT: D 391 ARG cc_start: 0.8850 (mmm160) cc_final: 0.7314 (ptm160) REVERT: D 404 ASP cc_start: 0.8447 (m-30) cc_final: 0.7391 (m-30) REVERT: D 407 GLU cc_start: 0.8116 (mp0) cc_final: 0.7386 (mp0) REVERT: D 412 GLU cc_start: 0.7815 (tp30) cc_final: 0.7442 (tm-30) REVERT: D 414 ASN cc_start: 0.8021 (p0) cc_final: 0.7769 (p0) REVERT: D 416 ASN cc_start: 0.8281 (m-40) cc_final: 0.7348 (m-40) REVERT: D 424 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8129 (pt0) REVERT: E 61 ASP cc_start: 0.7536 (m-30) cc_final: 0.7195 (m-30) REVERT: E 68 GLU cc_start: 0.8131 (tt0) cc_final: 0.7819 (tt0) REVERT: E 69 ASN cc_start: 0.8241 (t0) cc_final: 0.7838 (t0) REVERT: E 104 GLN cc_start: 0.7564 (mt0) cc_final: 0.7294 (mt0) REVERT: E 120 GLU cc_start: 0.7426 (mp0) cc_final: 0.7128 (mp0) REVERT: E 129 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7645 (tm-30) REVERT: E 187 ASP cc_start: 0.8292 (t0) cc_final: 0.7685 (t0) REVERT: E 313 ARG cc_start: 0.8697 (mmt90) cc_final: 0.8477 (mmm-85) REVERT: E 314 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8347 (mm-40) REVERT: E 457 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7854 (mm-30) REVERT: E 478 ASN cc_start: 0.8457 (t0) cc_final: 0.8075 (t0) REVERT: E 519 TYR cc_start: 0.8647 (m-80) cc_final: 0.8400 (m-10) REVERT: E 556 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7610 (mm-30) REVERT: E 569 MET cc_start: 0.7762 (mtp) cc_final: 0.7465 (mtm) REVERT: E 588 ASN cc_start: 0.8751 (t0) cc_final: 0.8432 (m-40) REVERT: E 593 MET cc_start: 0.8604 (tpp) cc_final: 0.8217 (tpp) outliers start: 54 outliers final: 18 residues processed: 454 average time/residue: 1.6278 time to fit residues: 808.8825 Evaluate side-chains 448 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 422 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 337 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 377 MET 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 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 244 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 35 GLN A 266 HIS B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 28 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN E 104 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086906 restraints weight = 28901.519| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.89 r_work: 0.3141 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 17882 Z= 0.304 Angle : 0.613 9.091 24321 Z= 0.314 Chirality : 0.046 0.158 2657 Planarity : 0.004 0.055 3175 Dihedral : 10.920 172.523 2519 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.98 % Allowed : 17.73 % Favored : 79.28 % 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: 0.48 (0.18), residues: 2208 helix: 1.26 (0.17), residues: 917 sheet: 0.35 (0.28), residues: 355 loop : -0.58 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 21 HIS 0.012 0.001 HIS D 190 PHE 0.029 0.002 PHE E 75 TYR 0.018 0.002 TYR A 432 ARG 0.017 0.001 ARG E 590 *********************** 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 488 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 433 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 83 TYR cc_start: 0.8893 (m-80) cc_final: 0.8485 (m-80) REVERT: A 116 ASP cc_start: 0.8173 (m-30) cc_final: 0.7557 (m-30) REVERT: A 117 LEU cc_start: 0.8425 (tp) cc_final: 0.7953 (tt) REVERT: A 120 ASP cc_start: 0.7945 (m-30) cc_final: 0.7705 (m-30) REVERT: A 149 PHE cc_start: 0.8750 (t80) cc_final: 0.8478 (t80) REVERT: A 154 MET cc_start: 0.8827 (mmp) cc_final: 0.8617 (mmm) REVERT: A 254 GLU cc_start: 0.6265 (mm-30) cc_final: 0.3860 (mm-30) REVERT: A 277 SER cc_start: 0.8924 (t) cc_final: 0.8675 (p) REVERT: A 290 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 313 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8580 (mtt) REVERT: A 338 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8479 (mtpp) REVERT: A 367 ASP cc_start: 0.8113 (p0) cc_final: 0.7758 (p0) REVERT: A 370 LYS cc_start: 0.8541 (tptt) cc_final: 0.8331 (tptt) REVERT: A 388 TRP cc_start: 0.8717 (m-10) cc_final: 0.8115 (m-10) REVERT: A 392 ASP cc_start: 0.8016 (m-30) cc_final: 0.7572 (m-30) REVERT: A 414 GLU cc_start: 0.8063 (mp0) cc_final: 0.7765 (mp0) REVERT: A 417 GLU cc_start: 0.8021 (tt0) cc_final: 0.7766 (mt-10) REVERT: A 420 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 423 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7944 (mm-30) REVERT: B 19 LYS cc_start: 0.8950 (tptm) cc_final: 0.8536 (mmmt) REVERT: B 53 GLU cc_start: 0.8253 (tt0) cc_final: 0.7889 (tp30) REVERT: B 74 ASP cc_start: 0.8287 (t0) cc_final: 0.8004 (t0) REVERT: B 103 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8665 (mtpm) REVERT: B 114 ASP cc_start: 0.8189 (m-30) cc_final: 0.7939 (m-30) REVERT: B 118 ASP cc_start: 0.7943 (m-30) cc_final: 0.7635 (m-30) REVERT: B 123 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7872 (tp30) REVERT: B 127 CYS cc_start: 0.7965 (m) cc_final: 0.7479 (m) REVERT: B 134 GLN cc_start: 0.8502 (mt0) cc_final: 0.8245 (pt0) REVERT: B 147 MET cc_start: 0.8652 (ttp) cc_final: 0.8446 (ttt) REVERT: B 154 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8755 (mtpp) REVERT: B 157 GLU cc_start: 0.8424 (tt0) cc_final: 0.8017 (tm-30) REVERT: B 174 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8248 (mmpt) REVERT: B 175 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8730 (m) REVERT: B 216 LYS cc_start: 0.9047 (mmtm) cc_final: 0.8768 (mmmm) REVERT: B 274 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 278 SER cc_start: 0.8595 (m) cc_final: 0.8270 (p) REVERT: B 325 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: B 328 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7439 (OUTLIER) REVERT: B 380 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.8020 (mtm180) REVERT: B 407 GLU cc_start: 0.8095 (tt0) cc_final: 0.7746 (mt-10) REVERT: B 410 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 414 ASN cc_start: 0.8458 (m110) cc_final: 0.8098 (m110) REVERT: B 421 GLU cc_start: 0.8323 (tt0) cc_final: 0.7965 (tm-30) REVERT: C 50 ASN cc_start: 0.8837 (t0) cc_final: 0.8502 (t0) REVERT: C 116 ASP cc_start: 0.8008 (p0) cc_final: 0.7759 (p0) REVERT: C 120 ASP cc_start: 0.7916 (m-30) cc_final: 0.7700 (m-30) REVERT: C 123 ARG cc_start: 0.8026 (tpp-160) cc_final: 0.7623 (tpp80) REVERT: C 196 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: C 207 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: C 214 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8271 (ttp-110) REVERT: C 280 LYS cc_start: 0.9025 (mttp) cc_final: 0.8531 (mtpt) REVERT: C 308 ARG cc_start: 0.6745 (tpt170) cc_final: 0.6139 (tpt170) REVERT: C 322 ASP cc_start: 0.8181 (t70) cc_final: 0.7919 (t0) REVERT: C 386 GLU cc_start: 0.8016 (mp0) cc_final: 0.7625 (mp0) REVERT: C 417 GLU cc_start: 0.7874 (mp0) cc_final: 0.7535 (mp0) REVERT: C 420 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7563 (mm-30) REVERT: C 423 GLU cc_start: 0.8090 (tp30) cc_final: 0.7861 (mm-30) REVERT: C 424 ASP cc_start: 0.8148 (t70) cc_final: 0.7932 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8466 (tt0) cc_final: 0.7793 (tm-30) REVERT: C 434 GLU cc_start: 0.8163 (pp20) cc_final: 0.7789 (pp20) REVERT: D 1 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8085 (ttp) REVERT: D 3 GLU cc_start: 0.8006 (mp0) cc_final: 0.7702 (mp0) REVERT: D 19 LYS cc_start: 0.8988 (tppp) cc_final: 0.8750 (tppp) REVERT: D 22 GLU cc_start: 0.8605 (tt0) cc_final: 0.8240 (tm-30) REVERT: D 26 ASP cc_start: 0.7706 (m-30) cc_final: 0.7416 (t0) REVERT: D 45 GLU cc_start: 0.8471 (tt0) cc_final: 0.8062 (tm-30) REVERT: D 57 ASN cc_start: 0.7753 (t0) cc_final: 0.6772 (t0) REVERT: D 69 GLU cc_start: 0.7717 (pm20) cc_final: 0.7120 (pm20) REVERT: D 88 ASP cc_start: 0.8269 (t70) cc_final: 0.7794 (t0) REVERT: D 92 PHE cc_start: 0.8627 (p90) cc_final: 0.8361 (p90) REVERT: D 103 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8662 (mtpm) REVERT: D 147 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8301 (ttp) REVERT: D 154 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.7854 (mptt) REVERT: D 157 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7773 (pp20) REVERT: D 181 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7872 (mt-10) REVERT: D 190 HIS cc_start: 0.8096 (t-90) cc_final: 0.7288 (t70) REVERT: D 203 ASP cc_start: 0.8112 (t0) cc_final: 0.7822 (t70) REVERT: D 251 ARG cc_start: 0.8778 (tpp-160) cc_final: 0.8266 (ttm110) REVERT: D 291 GLN cc_start: 0.8566 (pp30) cc_final: 0.8331 (pp30) REVERT: D 325 GLU cc_start: 0.8331 (tp30) cc_final: 0.7888 (tp30) REVERT: D 376 GLU cc_start: 0.7843 (mp0) cc_final: 0.7543 (mp0) REVERT: D 383 GLU cc_start: 0.8418 (tp30) cc_final: 0.8094 (tp30) REVERT: D 391 ARG cc_start: 0.8989 (mmm160) cc_final: 0.7382 (ptm160) REVERT: D 404 ASP cc_start: 0.8405 (m-30) cc_final: 0.7284 (m-30) REVERT: D 407 GLU cc_start: 0.8144 (mp0) cc_final: 0.7366 (mp0) REVERT: D 410 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7909 (tm-30) REVERT: D 417 ASP cc_start: 0.8437 (m-30) cc_final: 0.8225 (m-30) REVERT: E 61 ASP cc_start: 0.7544 (m-30) cc_final: 0.7316 (m-30) REVERT: E 69 ASN cc_start: 0.8314 (t0) cc_final: 0.7928 (t0) REVERT: E 104 GLN cc_start: 0.7684 (mt0) cc_final: 0.7280 (mt0) REVERT: E 120 GLU cc_start: 0.7484 (mp0) cc_final: 0.7150 (mp0) REVERT: E 129 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7665 (tm-30) REVERT: E 152 PHE cc_start: 0.8498 (m-10) cc_final: 0.8295 (m-10) REVERT: E 187 ASP cc_start: 0.8331 (t0) cc_final: 0.7735 (t0) REVERT: E 226 GLN cc_start: 0.8522 (mt0) cc_final: 0.8296 (mt0) REVERT: E 439 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8238 (ttmm) REVERT: E 444 MET cc_start: 0.8684 (mtm) cc_final: 0.8446 (mtt) REVERT: E 457 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7857 (mm-30) REVERT: E 478 ASN cc_start: 0.8427 (t0) cc_final: 0.7994 (t0) REVERT: E 519 TYR cc_start: 0.8621 (m-80) cc_final: 0.8396 (m-10) REVERT: E 556 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7629 (mm-30) REVERT: E 569 MET cc_start: 0.7755 (mtp) cc_final: 0.7522 (mtm) REVERT: E 588 ASN cc_start: 0.8826 (t0) cc_final: 0.8571 (m-40) outliers start: 55 outliers final: 26 residues processed: 460 average time/residue: 1.6759 time to fit residues: 846.7014 Evaluate side-chains 455 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 421 time to evaluate : 2.300 ------------------------------------------------------------------------------- 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 275 VAL Chi-restraints excluded: chain A residue 313 MET 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 65 LEU Chi-restraints excluded: chain B residue 113 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 C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 GLU 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 D residue 1 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 170 VAL 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 184 SER Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 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** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087954 restraints weight = 28677.648| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.89 r_work: 0.3161 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17882 Z= 0.228 Angle : 0.591 8.932 24321 Z= 0.300 Chirality : 0.045 0.162 2657 Planarity : 0.004 0.055 3175 Dihedral : 10.885 177.414 2519 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.82 % Allowed : 19.20 % Favored : 77.98 % 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: 0.50 (0.18), residues: 2208 helix: 1.35 (0.17), residues: 919 sheet: 0.28 (0.28), residues: 354 loop : -0.62 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 21 HIS 0.011 0.001 HIS D 190 PHE 0.029 0.002 PHE E 75 TYR 0.015 0.001 TYR D 159 ARG 0.012 0.001 ARG E 590 *********************** 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 488 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 436 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7670 (ptp90) REVERT: A 3 GLU cc_start: 0.7664 (mp0) cc_final: 0.7351 (mp0) REVERT: A 77 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 83 TYR cc_start: 0.8894 (m-80) cc_final: 0.8482 (m-80) REVERT: A 116 ASP cc_start: 0.8156 (m-30) cc_final: 0.7520 (m-30) REVERT: A 117 LEU cc_start: 0.8374 (tp) cc_final: 0.7934 (tt) REVERT: A 120 ASP cc_start: 0.7983 (m-30) cc_final: 0.7602 (m-30) REVERT: A 149 PHE cc_start: 0.8704 (t80) cc_final: 0.8452 (t80) REVERT: A 154 MET cc_start: 0.8791 (mmp) cc_final: 0.8575 (mmm) REVERT: A 254 GLU cc_start: 0.5814 (mm-30) cc_final: 0.3504 (mm-30) REVERT: A 290 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8335 (mm-30) REVERT: A 338 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8473 (mtpp) REVERT: A 370 LYS cc_start: 0.8508 (tptt) cc_final: 0.8300 (tptt) REVERT: A 388 TRP cc_start: 0.8675 (m-10) cc_final: 0.8034 (m-10) REVERT: A 392 ASP cc_start: 0.8005 (m-30) cc_final: 0.7533 (m-30) REVERT: A 414 GLU cc_start: 0.8075 (mp0) cc_final: 0.7775 (mp0) REVERT: A 417 GLU cc_start: 0.7978 (tt0) cc_final: 0.7735 (mt-10) REVERT: A 420 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 423 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7931 (mm-30) REVERT: B 36 TYR cc_start: 0.8739 (t80) cc_final: 0.8314 (t80) REVERT: B 53 GLU cc_start: 0.8231 (tt0) cc_final: 0.7888 (tp30) REVERT: B 69 GLU cc_start: 0.8114 (pt0) cc_final: 0.7722 (pm20) REVERT: B 74 ASP cc_start: 0.8345 (t0) cc_final: 0.8029 (t0) REVERT: B 103 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8641 (mtpm) REVERT: B 114 ASP cc_start: 0.8205 (m-30) cc_final: 0.7951 (m-30) REVERT: B 118 ASP cc_start: 0.7935 (m-30) cc_final: 0.7619 (m-30) REVERT: B 123 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7902 (tp30) REVERT: B 127 CYS cc_start: 0.7931 (m) cc_final: 0.7499 (m) REVERT: B 134 GLN cc_start: 0.8492 (mt0) cc_final: 0.8245 (pt0) REVERT: B 154 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8582 (mtpp) REVERT: B 157 GLU cc_start: 0.8409 (tt0) cc_final: 0.7964 (tm-30) REVERT: B 158 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: B 174 LYS cc_start: 0.8654 (mmpt) cc_final: 0.8193 (mmpt) REVERT: B 175 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8727 (m) REVERT: B 213 ARG cc_start: 0.8876 (ptp-110) cc_final: 0.8623 (ptm160) REVERT: B 216 LYS cc_start: 0.9027 (mmtm) cc_final: 0.8762 (mmmm) REVERT: B 274 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8603 (p) REVERT: B 278 SER cc_start: 0.8629 (m) cc_final: 0.8294 (p) REVERT: B 325 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: B 328 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7411 (OUTLIER) REVERT: B 407 GLU cc_start: 0.8056 (tt0) cc_final: 0.7710 (mt-10) REVERT: B 410 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7563 (mm-30) REVERT: B 412 GLU cc_start: 0.8196 (tp30) cc_final: 0.7653 (tp30) REVERT: B 414 ASN cc_start: 0.8433 (m110) cc_final: 0.8065 (m110) REVERT: B 421 GLU cc_start: 0.8321 (tt0) cc_final: 0.8057 (tm-30) REVERT: C 50 ASN cc_start: 0.8793 (t0) cc_final: 0.8435 (t0) REVERT: C 116 ASP cc_start: 0.7992 (p0) cc_final: 0.7733 (p0) REVERT: C 120 ASP cc_start: 0.7927 (m-30) cc_final: 0.7712 (m-30) REVERT: C 123 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7622 (tpp80) REVERT: C 196 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: C 207 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: C 214 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8214 (ttp-110) REVERT: C 280 LYS cc_start: 0.8975 (mttp) cc_final: 0.8462 (mmpt) REVERT: C 308 ARG cc_start: 0.6730 (tpt170) cc_final: 0.6137 (tpt170) REVERT: C 322 ASP cc_start: 0.8158 (t70) cc_final: 0.7913 (t0) REVERT: C 386 GLU cc_start: 0.7661 (mp0) cc_final: 0.7354 (mp0) REVERT: C 417 GLU cc_start: 0.7887 (mp0) cc_final: 0.7511 (mp0) REVERT: C 420 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 423 GLU cc_start: 0.8056 (tp30) cc_final: 0.7841 (mm-30) REVERT: C 424 ASP cc_start: 0.8122 (t70) cc_final: 0.7893 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8506 (tt0) cc_final: 0.7863 (tm-30) REVERT: C 434 GLU cc_start: 0.8120 (pp20) cc_final: 0.7774 (pp20) REVERT: D 1 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8124 (ttp) REVERT: D 3 GLU cc_start: 0.8051 (mp0) cc_final: 0.7772 (mp0) REVERT: D 22 GLU cc_start: 0.8580 (tt0) cc_final: 0.8225 (tm-30) REVERT: D 26 ASP cc_start: 0.7630 (m-30) cc_final: 0.7428 (t0) REVERT: D 45 GLU cc_start: 0.8439 (tt0) cc_final: 0.8042 (tm-30) REVERT: D 57 ASN cc_start: 0.7787 (t0) cc_final: 0.6796 (t0) REVERT: D 69 GLU cc_start: 0.7730 (pm20) cc_final: 0.7350 (pm20) REVERT: D 88 ASP cc_start: 0.8279 (t70) cc_final: 0.7820 (t0) REVERT: D 92 PHE cc_start: 0.8643 (p90) cc_final: 0.8381 (p90) REVERT: D 103 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8638 (mtpm) REVERT: D 121 ARG cc_start: 0.8641 (ttm110) cc_final: 0.8342 (mtm180) REVERT: D 123 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7902 (mm-30) REVERT: D 147 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8304 (ttp) REVERT: D 154 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8000 (mptt) REVERT: D 181 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7774 (mt-10) REVERT: D 190 HIS cc_start: 0.8023 (t-90) cc_final: 0.6974 (t70) REVERT: D 203 ASP cc_start: 0.8102 (t0) cc_final: 0.7810 (t70) REVERT: D 279 GLN cc_start: 0.8229 (pp30) cc_final: 0.7984 (pp30) REVERT: D 291 GLN cc_start: 0.8529 (pp30) cc_final: 0.8249 (pp30) REVERT: D 325 GLU cc_start: 0.8219 (tp30) cc_final: 0.7927 (tp30) REVERT: D 376 GLU cc_start: 0.7845 (mp0) cc_final: 0.7531 (mp0) REVERT: D 383 GLU cc_start: 0.8398 (tp30) cc_final: 0.8078 (tp30) REVERT: D 391 ARG cc_start: 0.8982 (mmm160) cc_final: 0.7328 (ptm160) REVERT: D 401 GLU cc_start: 0.7272 (mp0) cc_final: 0.7060 (mp0) REVERT: D 404 ASP cc_start: 0.8441 (m-30) cc_final: 0.7296 (m-30) REVERT: D 407 GLU cc_start: 0.8130 (mp0) cc_final: 0.7362 (mp0) REVERT: D 410 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7859 (tm-30) REVERT: D 424 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: E 68 GLU cc_start: 0.8086 (tt0) cc_final: 0.7839 (tt0) REVERT: E 69 ASN cc_start: 0.8299 (t0) cc_final: 0.7918 (t0) REVERT: E 104 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: E 120 GLU cc_start: 0.7463 (mp0) cc_final: 0.7152 (mp0) REVERT: E 129 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7675 (tm-30) REVERT: E 187 ASP cc_start: 0.8329 (t0) cc_final: 0.7656 (t0) REVERT: E 226 GLN cc_start: 0.8579 (mt0) cc_final: 0.8361 (mt0) REVERT: E 439 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8288 (ttmm) REVERT: E 444 MET cc_start: 0.8690 (mtm) cc_final: 0.8412 (mtt) REVERT: E 457 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7854 (mm-30) REVERT: E 478 ASN cc_start: 0.8416 (t0) cc_final: 0.7981 (t0) REVERT: E 556 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7633 (mm-30) REVERT: E 569 MET cc_start: 0.7711 (mtp) cc_final: 0.7483 (mtm) REVERT: E 588 ASN cc_start: 0.8844 (t0) cc_final: 0.8601 (m-40) outliers start: 52 outliers final: 28 residues processed: 464 average time/residue: 1.6822 time to fit residues: 852.2698 Evaluate side-chains 471 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 434 time to evaluate : 1.944 ------------------------------------------------------------------------------- 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 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 THR 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 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 255 PHE 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 122 LYS Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 GLU 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 65 THR Chi-restraints excluded: chain E residue 104 GLN 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 524 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 214 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 423 GLN ** C 133 GLN ** 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 375 GLN D 384 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087951 restraints weight = 28716.464| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.88 r_work: 0.3161 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17882 Z= 0.231 Angle : 0.592 9.110 24321 Z= 0.301 Chirality : 0.044 0.155 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.821 174.293 2519 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.87 % Allowed : 19.90 % Favored : 77.22 % 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: 0.54 (0.18), residues: 2208 helix: 1.38 (0.17), residues: 921 sheet: 0.28 (0.28), residues: 351 loop : -0.60 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 21 HIS 0.011 0.001 HIS D 190 PHE 0.030 0.002 PHE E 75 TYR 0.023 0.001 TYR D 36 ARG 0.011 0.001 ARG E 590 *********************** 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 501 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 448 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7655 (mp0) cc_final: 0.7334 (mp0) REVERT: A 77 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 83 TYR cc_start: 0.8888 (m-80) cc_final: 0.8472 (m-80) REVERT: A 84 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7692 (mtm110) REVERT: A 116 ASP cc_start: 0.8147 (m-30) cc_final: 0.7557 (m-30) REVERT: A 117 LEU cc_start: 0.8388 (tp) cc_final: 0.7934 (tt) REVERT: A 120 ASP cc_start: 0.7979 (m-30) cc_final: 0.7625 (m-30) REVERT: A 121 ARG cc_start: 0.8005 (tpp-160) cc_final: 0.7569 (mmm-85) REVERT: A 149 PHE cc_start: 0.8596 (t80) cc_final: 0.8318 (t80) REVERT: A 211 ASP cc_start: 0.8063 (m-30) cc_final: 0.7752 (m-30) REVERT: A 254 GLU cc_start: 0.5865 (mm-30) cc_final: 0.3660 (mm-30) REVERT: A 290 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8314 (mm-30) REVERT: A 338 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8483 (mtpp) REVERT: A 388 TRP cc_start: 0.8663 (m-10) cc_final: 0.8070 (m-10) REVERT: A 392 ASP cc_start: 0.8008 (m-30) cc_final: 0.7533 (m-30) REVERT: A 414 GLU cc_start: 0.8074 (mp0) cc_final: 0.7757 (mp0) REVERT: A 417 GLU cc_start: 0.7956 (tt0) cc_final: 0.7719 (mt-10) REVERT: A 420 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 423 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 19 LYS cc_start: 0.8900 (tptm) cc_final: 0.8517 (mmmt) REVERT: B 36 TYR cc_start: 0.8735 (t80) cc_final: 0.8299 (t80) REVERT: B 53 GLU cc_start: 0.8224 (tt0) cc_final: 0.8012 (tp30) REVERT: B 69 GLU cc_start: 0.8071 (pt0) cc_final: 0.7684 (pm20) REVERT: B 103 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8640 (mtpm) REVERT: B 114 ASP cc_start: 0.8224 (m-30) cc_final: 0.7969 (m-30) REVERT: B 118 ASP cc_start: 0.7940 (m-30) cc_final: 0.7627 (m-30) REVERT: B 123 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7922 (tp30) REVERT: B 127 CYS cc_start: 0.7973 (m) cc_final: 0.7525 (m) REVERT: B 134 GLN cc_start: 0.8474 (mt0) cc_final: 0.8245 (pt0) REVERT: B 154 LYS cc_start: 0.8945 (mmtp) cc_final: 0.8717 (mtpp) REVERT: B 157 GLU cc_start: 0.8399 (tt0) cc_final: 0.7936 (tm-30) REVERT: B 158 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: B 174 LYS cc_start: 0.8663 (mmpt) cc_final: 0.8201 (mmpt) REVERT: B 175 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8736 (m) REVERT: B 216 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8770 (mmmm) REVERT: B 274 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8623 (p) REVERT: B 278 SER cc_start: 0.8659 (m) cc_final: 0.8317 (p) REVERT: B 325 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: B 328 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7388 (OUTLIER) REVERT: B 407 GLU cc_start: 0.8048 (tt0) cc_final: 0.7688 (mt-10) REVERT: B 410 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 412 GLU cc_start: 0.8171 (tp30) cc_final: 0.7585 (tp30) REVERT: B 414 ASN cc_start: 0.8464 (m110) cc_final: 0.8186 (m110) REVERT: B 417 ASP cc_start: 0.8260 (m-30) cc_final: 0.8010 (m-30) REVERT: B 421 GLU cc_start: 0.8320 (tt0) cc_final: 0.8057 (tm-30) REVERT: C 116 ASP cc_start: 0.7985 (p0) cc_final: 0.7747 (p0) REVERT: C 120 ASP cc_start: 0.7904 (m-30) cc_final: 0.7696 (m-30) REVERT: C 123 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7581 (tpp80) REVERT: C 164 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8880 (mmmm) REVERT: C 196 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: C 207 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: C 214 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8203 (ttp-110) REVERT: C 280 LYS cc_start: 0.8983 (mttp) cc_final: 0.7982 (mmmt) REVERT: C 284 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7521 (mp0) REVERT: C 308 ARG cc_start: 0.6755 (tpt170) cc_final: 0.6184 (tpt170) REVERT: C 322 ASP cc_start: 0.8153 (t70) cc_final: 0.7909 (t0) REVERT: C 377 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8348 (ttp) REVERT: C 386 GLU cc_start: 0.7639 (mp0) cc_final: 0.7354 (mp0) REVERT: C 417 GLU cc_start: 0.7891 (mp0) cc_final: 0.7517 (mp0) REVERT: C 420 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7584 (mm-30) REVERT: C 423 GLU cc_start: 0.8110 (tp30) cc_final: 0.7879 (mm-30) REVERT: C 424 ASP cc_start: 0.8122 (t70) cc_final: 0.7890 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8518 (tt0) cc_final: 0.7870 (tm-30) REVERT: C 434 GLU cc_start: 0.8128 (pp20) cc_final: 0.7794 (pp20) REVERT: D 1 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8099 (ttp) REVERT: D 3 GLU cc_start: 0.8046 (mp0) cc_final: 0.7768 (mp0) REVERT: D 19 LYS cc_start: 0.8978 (tppp) cc_final: 0.8723 (tppp) REVERT: D 22 GLU cc_start: 0.8580 (tt0) cc_final: 0.8262 (tm-30) REVERT: D 45 GLU cc_start: 0.8440 (tt0) cc_final: 0.8038 (tm-30) REVERT: D 57 ASN cc_start: 0.7869 (t0) cc_final: 0.6871 (t0) REVERT: D 69 GLU cc_start: 0.7729 (pm20) cc_final: 0.7347 (pm20) REVERT: D 88 ASP cc_start: 0.8295 (t70) cc_final: 0.7823 (t0) REVERT: D 92 PHE cc_start: 0.8668 (p90) cc_final: 0.8390 (p90) REVERT: D 103 LYS cc_start: 0.8996 (mtpt) cc_final: 0.8627 (mtpm) REVERT: D 121 ARG cc_start: 0.8631 (ttm110) cc_final: 0.8343 (mtm180) REVERT: D 147 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8287 (ttp) REVERT: D 154 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.7975 (mptt) REVERT: D 181 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7765 (mt-10) REVERT: D 190 HIS cc_start: 0.8060 (t-90) cc_final: 0.7052 (t70) REVERT: D 203 ASP cc_start: 0.8097 (t0) cc_final: 0.7833 (t70) REVERT: D 291 GLN cc_start: 0.8497 (pp30) cc_final: 0.8217 (pp30) REVERT: D 325 GLU cc_start: 0.8227 (tp30) cc_final: 0.7922 (tp30) REVERT: D 376 GLU cc_start: 0.7840 (mp0) cc_final: 0.7489 (mp0) REVERT: D 383 GLU cc_start: 0.8368 (tp30) cc_final: 0.8060 (tp30) REVERT: D 391 ARG cc_start: 0.8975 (mmm160) cc_final: 0.7330 (ptm160) REVERT: D 401 GLU cc_start: 0.7310 (mp0) cc_final: 0.7068 (mp0) REVERT: D 404 ASP cc_start: 0.8412 (m-30) cc_final: 0.7666 (m-30) REVERT: D 407 GLU cc_start: 0.8135 (mp0) cc_final: 0.7490 (mp0) REVERT: D 410 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7841 (tm-30) REVERT: D 417 ASP cc_start: 0.8380 (m-30) cc_final: 0.8042 (m-30) REVERT: E 21 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.8028 (t70) REVERT: E 68 GLU cc_start: 0.8091 (tt0) cc_final: 0.7821 (tt0) REVERT: E 69 ASN cc_start: 0.8320 (t0) cc_final: 0.7969 (t0) REVERT: E 120 GLU cc_start: 0.7448 (mp0) cc_final: 0.7125 (mp0) REVERT: E 129 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7706 (tm-30) REVERT: E 187 ASP cc_start: 0.8318 (t0) cc_final: 0.7663 (t0) REVERT: E 439 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8229 (ttmm) REVERT: E 444 MET cc_start: 0.8694 (mtm) cc_final: 0.8424 (mtt) REVERT: E 457 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7832 (mm-30) REVERT: E 478 ASN cc_start: 0.8419 (t0) cc_final: 0.7970 (t0) REVERT: E 534 ASP cc_start: 0.7672 (p0) cc_final: 0.7393 (p0) REVERT: E 535 ASN cc_start: 0.7809 (p0) cc_final: 0.7546 (p0) REVERT: E 556 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7643 (mm-30) REVERT: E 588 ASN cc_start: 0.8837 (t0) cc_final: 0.8594 (m-40) outliers start: 53 outliers final: 28 residues processed: 474 average time/residue: 1.6700 time to fit residues: 864.6689 Evaluate side-chains 466 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 428 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 LYS 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 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 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 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 64 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 170 VAL 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 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 13 optimal weight: 0.4980 chunk 101 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 256 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** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 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 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 = 0.3422 r_free = 0.3422 target = 0.096649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088247 restraints weight = 28812.275| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.89 r_work: 0.3167 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17882 Z= 0.211 Angle : 0.602 9.185 24321 Z= 0.304 Chirality : 0.044 0.154 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.714 177.625 2519 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.77 % Allowed : 20.66 % Favored : 76.57 % 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: 0.62 (0.18), residues: 2208 helix: 1.45 (0.17), residues: 922 sheet: 0.36 (0.29), residues: 346 loop : -0.57 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 21 HIS 0.010 0.001 HIS D 190 PHE 0.031 0.001 PHE E 75 TYR 0.017 0.001 TYR D 159 ARG 0.012 0.001 ARG D 359 *********************** 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 491 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 440 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7554 (mp0) cc_final: 0.7257 (mp0) REVERT: A 77 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 83 TYR cc_start: 0.8891 (m-80) cc_final: 0.8497 (m-80) REVERT: A 84 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7745 (mtm110) REVERT: A 116 ASP cc_start: 0.8133 (m-30) cc_final: 0.7668 (m-30) REVERT: A 117 LEU cc_start: 0.8348 (tp) cc_final: 0.7948 (tt) REVERT: A 120 ASP cc_start: 0.7996 (m-30) cc_final: 0.7758 (m-30) REVERT: A 121 ARG cc_start: 0.7995 (tpp-160) cc_final: 0.7562 (mmm-85) REVERT: A 149 PHE cc_start: 0.8587 (t80) cc_final: 0.8291 (t80) REVERT: A 254 GLU cc_start: 0.5886 (mm-30) cc_final: 0.3638 (mm-30) REVERT: A 290 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 388 TRP cc_start: 0.8647 (m-10) cc_final: 0.8043 (m-10) REVERT: A 392 ASP cc_start: 0.8001 (m-30) cc_final: 0.7518 (m-30) REVERT: A 414 GLU cc_start: 0.8080 (mp0) cc_final: 0.7778 (mp0) REVERT: A 417 GLU cc_start: 0.7959 (tt0) cc_final: 0.7723 (mt-10) REVERT: A 420 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 423 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 19 LYS cc_start: 0.8887 (tptm) cc_final: 0.8505 (mmmt) REVERT: B 36 TYR cc_start: 0.8733 (t80) cc_final: 0.8310 (t80) REVERT: B 53 GLU cc_start: 0.8221 (tt0) cc_final: 0.7982 (tp30) REVERT: B 69 GLU cc_start: 0.8032 (pt0) cc_final: 0.7648 (pm20) REVERT: B 74 ASP cc_start: 0.8291 (t70) cc_final: 0.8021 (OUTLIER) REVERT: B 114 ASP cc_start: 0.8210 (m-30) cc_final: 0.7931 (m-30) REVERT: B 118 ASP cc_start: 0.7931 (m-30) cc_final: 0.7574 (m-30) REVERT: B 123 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7909 (tp30) REVERT: B 127 CYS cc_start: 0.7978 (m) cc_final: 0.7533 (m) REVERT: B 134 GLN cc_start: 0.8451 (mt0) cc_final: 0.8220 (pt0) REVERT: B 154 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8708 (mtpp) REVERT: B 157 GLU cc_start: 0.8430 (tt0) cc_final: 0.7964 (tm-30) REVERT: B 158 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: B 174 LYS cc_start: 0.8680 (mmpt) cc_final: 0.8217 (mmpt) REVERT: B 175 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8708 (m) REVERT: B 213 ARG cc_start: 0.8872 (ptp-110) cc_final: 0.8529 (ptm160) REVERT: B 216 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8766 (mmmm) REVERT: B 274 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 278 SER cc_start: 0.8658 (m) cc_final: 0.8325 (p) REVERT: B 325 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: B 328 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7408 (OUTLIER) REVERT: B 343 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7551 (mp0) REVERT: B 407 GLU cc_start: 0.8012 (tt0) cc_final: 0.7658 (mt-10) REVERT: B 410 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 414 ASN cc_start: 0.8434 (m110) cc_final: 0.8099 (m110) REVERT: B 417 ASP cc_start: 0.8259 (m-30) cc_final: 0.7888 (m-30) REVERT: C 112 LYS cc_start: 0.8181 (pmtt) cc_final: 0.7951 (pmtt) REVERT: C 116 ASP cc_start: 0.8017 (p0) cc_final: 0.7772 (p0) REVERT: C 120 ASP cc_start: 0.7925 (m-30) cc_final: 0.7708 (m-30) REVERT: C 123 ARG cc_start: 0.7964 (tpp-160) cc_final: 0.7580 (tpp80) REVERT: C 164 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8874 (mmmm) REVERT: C 196 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: C 207 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: C 214 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8204 (ttp-110) REVERT: C 280 LYS cc_start: 0.8958 (mttp) cc_final: 0.7966 (mmmt) REVERT: C 308 ARG cc_start: 0.6782 (tpt170) cc_final: 0.6468 (tpt170) REVERT: C 322 ASP cc_start: 0.8153 (t70) cc_final: 0.7907 (t0) REVERT: C 411 GLU cc_start: 0.8220 (mm-30) cc_final: 0.8017 (mm-30) REVERT: C 417 GLU cc_start: 0.7884 (mp0) cc_final: 0.7458 (mp0) REVERT: C 420 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 424 ASP cc_start: 0.8101 (t70) cc_final: 0.7860 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8546 (tt0) cc_final: 0.7906 (tm-30) REVERT: C 434 GLU cc_start: 0.8084 (pp20) cc_final: 0.7719 (pp20) REVERT: D 3 GLU cc_start: 0.8072 (mp0) cc_final: 0.7792 (mp0) REVERT: D 19 LYS cc_start: 0.8989 (tppp) cc_final: 0.8728 (tppp) REVERT: D 22 GLU cc_start: 0.8548 (tt0) cc_final: 0.8222 (tm-30) REVERT: D 45 GLU cc_start: 0.8457 (tt0) cc_final: 0.8037 (tm-30) REVERT: D 57 ASN cc_start: 0.7881 (t0) cc_final: 0.6901 (t0) REVERT: D 69 GLU cc_start: 0.7739 (pm20) cc_final: 0.7384 (pm20) REVERT: D 73 MET cc_start: 0.8795 (mpm) cc_final: 0.8583 (mmp) REVERT: D 88 ASP cc_start: 0.8314 (t70) cc_final: 0.7837 (t0) REVERT: D 92 PHE cc_start: 0.8671 (p90) cc_final: 0.8380 (p90) REVERT: D 103 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8563 (mtpm) REVERT: D 108 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8180 (mp0) REVERT: D 121 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8338 (mtm180) REVERT: D 147 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8275 (ttp) REVERT: D 154 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7960 (mptt) REVERT: D 181 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7807 (mt-10) REVERT: D 190 HIS cc_start: 0.8036 (t-90) cc_final: 0.6908 (t70) REVERT: D 203 ASP cc_start: 0.8104 (t0) cc_final: 0.7879 (t70) REVERT: D 251 ARG cc_start: 0.8695 (ttp-170) cc_final: 0.8426 (ttm110) REVERT: D 279 GLN cc_start: 0.8318 (pp30) cc_final: 0.7882 (tm130) REVERT: D 291 GLN cc_start: 0.8496 (pp30) cc_final: 0.8275 (pp30) REVERT: D 325 GLU cc_start: 0.8232 (tp30) cc_final: 0.7919 (tp30) REVERT: D 376 GLU cc_start: 0.7846 (mp0) cc_final: 0.7472 (mp0) REVERT: D 383 GLU cc_start: 0.8370 (tp30) cc_final: 0.8062 (tp30) REVERT: D 391 ARG cc_start: 0.8963 (mmm160) cc_final: 0.7339 (ptm160) REVERT: D 401 GLU cc_start: 0.7329 (mp0) cc_final: 0.7081 (mp0) REVERT: D 404 ASP cc_start: 0.8406 (m-30) cc_final: 0.7699 (m-30) REVERT: D 407 GLU cc_start: 0.8147 (mp0) cc_final: 0.7551 (mp0) REVERT: D 410 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7854 (tm-30) REVERT: E 21 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8024 (t70) REVERT: E 68 GLU cc_start: 0.8105 (tt0) cc_final: 0.7838 (tt0) REVERT: E 69 ASN cc_start: 0.8320 (t0) cc_final: 0.7963 (t0) REVERT: E 120 GLU cc_start: 0.7427 (mp0) cc_final: 0.7100 (mp0) REVERT: E 129 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7716 (tm-30) REVERT: E 187 ASP cc_start: 0.8303 (t0) cc_final: 0.7637 (t0) REVERT: E 226 GLN cc_start: 0.8512 (mt0) cc_final: 0.8302 (mt0) REVERT: E 291 MET cc_start: 0.8731 (mtp) cc_final: 0.8466 (ttm) REVERT: E 439 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8245 (ttmm) REVERT: E 457 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7857 (mm-30) REVERT: E 478 ASN cc_start: 0.8426 (t0) cc_final: 0.7976 (t0) REVERT: E 534 ASP cc_start: 0.7690 (p0) cc_final: 0.7388 (p0) REVERT: E 535 ASN cc_start: 0.7824 (p0) cc_final: 0.7556 (p0) REVERT: E 556 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7614 (mm-30) REVERT: E 588 ASN cc_start: 0.8846 (t0) cc_final: 0.8618 (m-40) outliers start: 51 outliers final: 29 residues processed: 465 average time/residue: 1.6763 time to fit residues: 852.4485 Evaluate side-chains 471 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 435 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 LYS 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 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 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 170 VAL 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 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 106 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 77 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 220 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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** ** E 104 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088178 restraints weight = 28830.381| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.88 r_work: 0.3163 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17882 Z= 0.230 Angle : 0.611 9.506 24321 Z= 0.311 Chirality : 0.044 0.154 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.683 178.095 2519 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.28 % Allowed : 21.31 % Favored : 76.41 % 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 (0.18), residues: 922 sheet: 0.28 (0.29), residues: 351 loop : -0.58 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.010 0.001 HIS D 190 PHE 0.031 0.002 PHE E 75 TYR 0.016 0.001 TYR D 159 ARG 0.010 0.001 ARG E 590 ********************** 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 482 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 440 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7522 (mp0) cc_final: 0.7119 (mp0) REVERT: A 77 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 83 TYR cc_start: 0.8888 (m-80) cc_final: 0.8490 (m-80) REVERT: A 84 ARG cc_start: 0.8047 (ttm110) cc_final: 0.7805 (mtm110) REVERT: A 116 ASP cc_start: 0.8139 (m-30) cc_final: 0.7679 (m-30) REVERT: A 117 LEU cc_start: 0.8334 (tp) cc_final: 0.7933 (tt) REVERT: A 120 ASP cc_start: 0.8069 (m-30) cc_final: 0.7777 (m-30) REVERT: A 121 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7639 (mmm-85) REVERT: A 149 PHE cc_start: 0.8661 (t80) cc_final: 0.8334 (t80) REVERT: A 211 ASP cc_start: 0.8063 (m-30) cc_final: 0.7745 (m-30) REVERT: A 221 ARG cc_start: 0.8434 (ptp-110) cc_final: 0.8211 (ptp90) REVERT: A 254 GLU cc_start: 0.5714 (mm-30) cc_final: 0.3367 (mm-30) REVERT: A 290 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8327 (mm-30) REVERT: A 326 LYS cc_start: 0.8521 (pttp) cc_final: 0.8114 (ptpt) REVERT: A 388 TRP cc_start: 0.8643 (m-10) cc_final: 0.8044 (m-10) REVERT: A 392 ASP cc_start: 0.8000 (m-30) cc_final: 0.7518 (m-30) REVERT: A 414 GLU cc_start: 0.8077 (mp0) cc_final: 0.7763 (mp0) REVERT: A 417 GLU cc_start: 0.7938 (tt0) cc_final: 0.7728 (mt-10) REVERT: A 420 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7622 (mm-30) REVERT: A 423 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7931 (mm-30) REVERT: B 19 LYS cc_start: 0.8902 (tptm) cc_final: 0.8505 (mmmt) REVERT: B 53 GLU cc_start: 0.8227 (tt0) cc_final: 0.8009 (tp30) REVERT: B 69 GLU cc_start: 0.8018 (pt0) cc_final: 0.7632 (pm20) REVERT: B 74 ASP cc_start: 0.8282 (t70) cc_final: 0.8011 (OUTLIER) REVERT: B 114 ASP cc_start: 0.8215 (m-30) cc_final: 0.7957 (m-30) REVERT: B 118 ASP cc_start: 0.7925 (m-30) cc_final: 0.7598 (m-30) REVERT: B 123 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7905 (tp30) REVERT: B 127 CYS cc_start: 0.7976 (m) cc_final: 0.7534 (m) REVERT: B 134 GLN cc_start: 0.8447 (mt0) cc_final: 0.8220 (pt0) REVERT: B 154 LYS cc_start: 0.8937 (mmtp) cc_final: 0.8702 (mtpp) REVERT: B 157 GLU cc_start: 0.8453 (tt0) cc_final: 0.7969 (tm-30) REVERT: B 158 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: B 174 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8237 (mmpt) REVERT: B 175 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8726 (m) REVERT: B 274 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 278 SER cc_start: 0.8672 (m) cc_final: 0.8333 (p) REVERT: B 325 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: B 328 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7402 (OUTLIER) REVERT: B 343 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7545 (mp0) REVERT: B 407 GLU cc_start: 0.8009 (tt0) cc_final: 0.7643 (mt-10) REVERT: B 410 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 414 ASN cc_start: 0.8436 (m110) cc_final: 0.8093 (m110) REVERT: B 416 ASN cc_start: 0.8357 (m-40) cc_final: 0.7782 (m-40) REVERT: B 417 ASP cc_start: 0.8120 (m-30) cc_final: 0.7900 (m-30) REVERT: C 112 LYS cc_start: 0.8171 (pmtt) cc_final: 0.7962 (pmtt) REVERT: C 116 ASP cc_start: 0.8038 (p0) cc_final: 0.7755 (p0) REVERT: C 120 ASP cc_start: 0.7902 (m-30) cc_final: 0.7668 (m-30) REVERT: C 123 ARG cc_start: 0.7969 (tpp-160) cc_final: 0.7582 (tpp80) REVERT: C 164 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8831 (mmmm) REVERT: C 196 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: C 207 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: C 214 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8209 (ttp-110) REVERT: C 280 LYS cc_start: 0.8770 (mttp) cc_final: 0.8565 (mmtt) REVERT: C 308 ARG cc_start: 0.6780 (tpt170) cc_final: 0.6474 (tpt170) REVERT: C 322 ASP cc_start: 0.8134 (t70) cc_final: 0.7897 (t0) REVERT: C 377 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8364 (ttp) REVERT: C 411 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7992 (mm-30) REVERT: C 417 GLU cc_start: 0.7941 (mp0) cc_final: 0.7450 (mp0) REVERT: C 420 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7720 (mm-30) REVERT: C 423 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 424 ASP cc_start: 0.8069 (t70) cc_final: 0.7823 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8526 (tt0) cc_final: 0.7897 (tm-30) REVERT: C 434 GLU cc_start: 0.8084 (pp20) cc_final: 0.7714 (pp20) REVERT: D 3 GLU cc_start: 0.8065 (mp0) cc_final: 0.7835 (mp0) REVERT: D 22 GLU cc_start: 0.8554 (tt0) cc_final: 0.8295 (tm-30) REVERT: D 45 GLU cc_start: 0.8445 (tt0) cc_final: 0.8018 (tm-30) REVERT: D 57 ASN cc_start: 0.7893 (t0) cc_final: 0.6916 (t0) REVERT: D 69 GLU cc_start: 0.7727 (pm20) cc_final: 0.7374 (pm20) REVERT: D 73 MET cc_start: 0.8810 (mpm) cc_final: 0.8576 (mmp) REVERT: D 88 ASP cc_start: 0.8234 (t70) cc_final: 0.7749 (t0) REVERT: D 92 PHE cc_start: 0.8670 (p90) cc_final: 0.8376 (p90) REVERT: D 103 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8564 (mtpm) REVERT: D 108 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8174 (mp0) REVERT: D 121 ARG cc_start: 0.8644 (ttm110) cc_final: 0.8337 (mtm180) REVERT: D 147 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8296 (ttp) REVERT: D 154 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.7950 (mptt) REVERT: D 181 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7816 (mt-10) REVERT: D 190 HIS cc_start: 0.8014 (t-90) cc_final: 0.7020 (t70) REVERT: D 203 ASP cc_start: 0.8089 (t0) cc_final: 0.7874 (t70) REVERT: D 251 ARG cc_start: 0.8727 (ttp-170) cc_final: 0.8415 (ttm110) REVERT: D 279 GLN cc_start: 0.8292 (pp30) cc_final: 0.7805 (tm130) REVERT: D 291 GLN cc_start: 0.8473 (pp30) cc_final: 0.8270 (pp30) REVERT: D 325 GLU cc_start: 0.8229 (tp30) cc_final: 0.7913 (tp30) REVERT: D 376 GLU cc_start: 0.7863 (mp0) cc_final: 0.7482 (mp0) REVERT: D 383 GLU cc_start: 0.8344 (tp30) cc_final: 0.8046 (tp30) REVERT: D 391 ARG cc_start: 0.8949 (mmm160) cc_final: 0.7344 (ptm160) REVERT: D 401 GLU cc_start: 0.7337 (mp0) cc_final: 0.7095 (mp0) REVERT: D 404 ASP cc_start: 0.8387 (m-30) cc_final: 0.7684 (m-30) REVERT: D 407 GLU cc_start: 0.8140 (mp0) cc_final: 0.7548 (mp0) REVERT: D 410 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7831 (tm-30) REVERT: D 417 ASP cc_start: 0.8374 (m-30) cc_final: 0.8031 (m-30) REVERT: E 21 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8018 (t70) REVERT: E 68 GLU cc_start: 0.8112 (tt0) cc_final: 0.7846 (tt0) REVERT: E 69 ASN cc_start: 0.8317 (t0) cc_final: 0.7959 (t0) REVERT: E 104 GLN cc_start: 0.7389 (mt0) cc_final: 0.7141 (mt0) REVERT: E 120 GLU cc_start: 0.7430 (mp0) cc_final: 0.7100 (mp0) REVERT: E 129 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7703 (tm-30) REVERT: E 187 ASP cc_start: 0.8298 (t0) cc_final: 0.7636 (t0) REVERT: E 226 GLN cc_start: 0.8587 (mt0) cc_final: 0.8313 (mt0) REVERT: E 291 MET cc_start: 0.8717 (mtp) cc_final: 0.8440 (ttm) REVERT: E 439 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8227 (ttmm) REVERT: E 457 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7863 (mm-30) REVERT: E 478 ASN cc_start: 0.8398 (t0) cc_final: 0.7940 (t0) REVERT: E 534 ASP cc_start: 0.7692 (p0) cc_final: 0.7384 (p0) REVERT: E 535 ASN cc_start: 0.7827 (p0) cc_final: 0.7560 (p0) REVERT: E 556 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7608 (mm-30) REVERT: E 588 ASN cc_start: 0.8835 (t0) cc_final: 0.8611 (m-40) outliers start: 42 outliers final: 29 residues processed: 461 average time/residue: 1.6479 time to fit residues: 830.4976 Evaluate side-chains 466 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 429 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 LYS 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 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 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 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 64 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 170 VAL 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 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 459 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 114 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 187 optimal weight: 0.3980 chunk 171 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** E 104 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087974 restraints weight = 28707.089| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.87 r_work: 0.3161 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17882 Z= 0.245 Angle : 0.615 9.686 24321 Z= 0.311 Chirality : 0.045 0.159 2657 Planarity : 0.004 0.052 3175 Dihedral : 10.688 178.852 2519 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.49 % Allowed : 21.20 % Favored : 76.30 % 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: 1.41 (0.17), residues: 922 sheet: 0.28 (0.29), residues: 346 loop : -0.57 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.010 0.001 HIS D 190 PHE 0.032 0.002 PHE E 75 TYR 0.017 0.001 TYR D 159 ARG 0.012 0.001 ARG D 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16132.89 seconds wall clock time: 284 minutes 40.61 seconds (17080.61 seconds total)