Starting phenix.real_space_refine on Sun Aug 24 06:21:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4l_42972/08_2025/8v4l_42972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4l_42972/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v4l_42972/08_2025/8v4l_42972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4l_42972/08_2025/8v4l_42972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v4l_42972/08_2025/8v4l_42972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4l_42972/08_2025/8v4l_42972.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG: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: {'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} 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: {'UNK:plan-1': 4, 'GLU:plan': 1} 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: {'GLU:plan': 14, 'ARG:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 1} 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: 4.72, per 1000 atoms: 0.27 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: 1.46 Conformation dependent library (CDL) restraints added in 667.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.66 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: 2.94 Time building geometry restraints manager: 1.91 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 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 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: 8.990 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.580 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 17885 Z= 0.315 Angle : 1.052 13.274 24321 Z= 0.568 Chirality : 0.061 0.463 2657 Planarity : 0.009 0.102 3175 Dihedral : 14.216 140.105 6475 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG D 359 TYR 0.044 0.003 TYR A 432 PHE 0.031 0.003 PHE C 255 TRP 0.020 0.003 TRP D 344 HIS 0.009 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00641 (17882) covalent geometry : angle 1.05202 (24321) hydrogen bonds : bond 0.16943 ( 784) hydrogen bonds : angle 7.31356 ( 2268) metal coordination : bond 0.00568 ( 2) Misc. bond : bond 0.04547 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 595 time to evaluate : 0.622 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: 0.7522 (p90) REVERT: A 55 GLU cc_start: 0.7832 (tt0) cc_final: 0.7225 (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: 0.6876 (m-30) REVERT: A 124 LYS cc_start: 0.7498 (mttt) cc_final: 0.7252 (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: 0.7157 (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: 0.7011 (pm20) REVERT: A 420 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 423 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7423 (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: 0.7005 (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: 0.7503 (mt-10) REVERT: B 410 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7086 (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: 0.7198 (p0) REVERT: C 117 LEU cc_start: 0.7839 (tp) cc_final: 0.7604 (tt) REVERT: C 120 ASP cc_start: 0.7648 (m-30) cc_final: 0.7420 (m-30) REVERT: C 123 ARG cc_start: 0.7347 (tpp-160) cc_final: 0.7015 (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: 0.8073 (mptt) REVERT: D 175 VAL cc_start: 0.8429 (m) cc_final: 0.7625 (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: 0.7102 (t70) REVERT: D 205 GLU cc_start: 0.7943 (tt0) cc_final: 0.7393 (mp0) REVERT: D 209 ASP cc_start: 0.7469 (t0) cc_final: 0.7121 (t0) REVERT: D 213 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7703 (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: 0.8096 (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: 0.6400 time to fit residues: 418.1949 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 : 0.673 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 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 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 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 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 = 0.3506 r_free = 0.3506 target = 0.101536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093175 restraints weight = 29566.579| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.93 r_work: 0.3268 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17885 Z= 0.142 Angle : 0.588 9.262 24321 Z= 0.304 Chirality : 0.044 0.174 2657 Planarity : 0.005 0.061 3175 Dihedral : 10.706 145.081 2522 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.49 % Allowed : 12.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.17), residues: 2208 helix: 0.06 (0.16), residues: 922 sheet: 0.38 (0.27), residues: 366 loop : -0.78 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 221 TYR 0.011 0.001 TYR A 172 PHE 0.026 0.002 PHE A 255 TRP 0.020 0.002 TRP E 592 HIS 0.007 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00320 (17882) covalent geometry : angle 0.58786 (24321) hydrogen bonds : bond 0.04552 ( 784) hydrogen bonds : angle 4.91754 ( 2268) metal coordination : bond 0.00420 ( 2) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 468 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8508 (p90) cc_final: 0.8166 (p90) REVERT: A 50 ASN cc_start: 0.8502 (t0) cc_final: 0.8040 (t0) REVERT: A 55 GLU cc_start: 0.7688 (tt0) cc_final: 0.7435 (tm-30) REVERT: A 83 TYR cc_start: 0.8636 (m-80) cc_final: 0.8368 (m-80) REVERT: A 116 ASP cc_start: 0.7720 (m-30) cc_final: 0.6976 (p0) REVERT: A 117 LEU cc_start: 0.8042 (tp) cc_final: 0.7674 (tt) REVERT: A 120 ASP cc_start: 0.7782 (m-30) cc_final: 0.7436 (m-30) REVERT: A 154 MET cc_start: 0.8869 (mmm) cc_final: 0.8650 (mmp) REVERT: A 290 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 309 HIS cc_start: 0.8306 (m170) cc_final: 0.8101 (m170) REVERT: A 367 ASP cc_start: 0.7845 (p0) cc_final: 0.7563 (p0) REVERT: A 370 LYS cc_start: 0.8487 (tptt) cc_final: 0.8238 (tptt) REVERT: A 414 GLU cc_start: 0.7978 (mp0) cc_final: 0.7662 (pm20) REVERT: A 423 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 19 LYS cc_start: 0.9034 (tptm) cc_final: 0.8606 (tppp) REVERT: B 81 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7638 (t80) REVERT: B 118 ASP cc_start: 0.7989 (m-30) cc_final: 0.7690 (m-30) REVERT: B 123 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7655 (tp30) REVERT: B 127 CYS cc_start: 0.7658 (m) cc_final: 0.7110 (m) REVERT: B 158 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: B 181 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7444 (tm-30) REVERT: B 203 ASP cc_start: 0.7895 (t70) cc_final: 0.7685 (t0) REVERT: B 216 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8729 (mmmm) REVERT: B 278 SER cc_start: 0.8624 (m) cc_final: 0.8204 (p) REVERT: B 291 GLN cc_start: 0.8296 (pp30) cc_final: 0.8034 (pp30) REVERT: B 328 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7371 (tp30) REVERT: B 391 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.7206 (mtp-110) REVERT: B 407 GLU cc_start: 0.8043 (tt0) cc_final: 0.7831 (mt-10) REVERT: B 412 GLU cc_start: 0.8220 (tp30) cc_final: 0.7803 (tp30) REVERT: B 414 ASN cc_start: 0.8124 (m110) cc_final: 0.7762 (m110) REVERT: B 417 ASP cc_start: 0.8164 (m-30) cc_final: 0.7685 (m-30) REVERT: B 421 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 50 ASN cc_start: 0.8639 (t0) cc_final: 0.8262 (t0) REVERT: C 116 ASP cc_start: 0.7668 (p0) cc_final: 0.7451 (p0) REVERT: C 123 ARG cc_start: 0.8037 (tpp-160) cc_final: 0.7644 (tpp80) REVERT: C 158 SER cc_start: 0.8944 (t) cc_final: 0.8723 (t) REVERT: C 211 ASP cc_start: 0.8127 (m-30) cc_final: 0.7895 (p0) REVERT: C 280 LYS cc_start: 0.8891 (mttp) cc_final: 0.7891 (mtpt) REVERT: C 284 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7152 (mp0) REVERT: C 322 ASP cc_start: 0.8074 (t70) cc_final: 0.7829 (t0) REVERT: C 337 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 377 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7910 (tmm) REVERT: C 386 GLU cc_start: 0.7753 (mp0) cc_final: 0.7493 (mp0) REVERT: C 423 GLU cc_start: 0.8015 (tp30) cc_final: 0.7740 (mm-30) REVERT: C 429 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7905 (mt-10) REVERT: D 3 GLU cc_start: 0.7862 (mp0) cc_final: 0.7245 (mp0) REVERT: D 19 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8656 (tppp) REVERT: D 22 GLU cc_start: 0.8602 (tt0) cc_final: 0.8008 (tp30) REVERT: D 45 GLU cc_start: 0.8325 (tt0) cc_final: 0.8004 (tm-30) REVERT: D 88 ASP cc_start: 0.8260 (t70) cc_final: 0.7833 (t0) REVERT: D 103 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8704 (mtpm) REVERT: D 123 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8012 (mm-30) REVERT: D 158 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7959 (mm-30) REVERT: D 159 TYR cc_start: 0.8394 (m-80) cc_final: 0.8137 (m-80) REVERT: D 174 LYS cc_start: 0.8429 (mptt) cc_final: 0.8206 (mptt) REVERT: D 181 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7663 (mt-10) REVERT: D 198 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8071 (mt-10) REVERT: D 203 ASP cc_start: 0.8169 (t0) cc_final: 0.7899 (t70) REVERT: D 257 MET cc_start: 0.8418 (mmm) cc_final: 0.8114 (mtp) REVERT: D 291 GLN cc_start: 0.8620 (pp30) cc_final: 0.8392 (pp30) REVERT: D 323 MET cc_start: 0.8373 (mmm) cc_final: 0.8165 (mmm) REVERT: D 325 GLU cc_start: 0.7977 (tp30) cc_final: 0.7739 (tp30) REVERT: D 376 GLU cc_start: 0.7793 (mp0) cc_final: 0.7244 (mp0) REVERT: D 383 GLU cc_start: 0.8165 (tp30) cc_final: 0.7751 (tp30) REVERT: D 391 ARG cc_start: 0.8411 (mmm160) cc_final: 0.6977 (ptm160) REVERT: D 404 ASP cc_start: 0.8282 (m-30) cc_final: 0.7517 (m-30) REVERT: D 407 GLU cc_start: 0.8042 (mp0) cc_final: 0.7653 (mp0) REVERT: D 410 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7797 (tm-30) REVERT: D 413 SER cc_start: 0.8501 (t) cc_final: 0.7796 (p) REVERT: D 417 ASP cc_start: 0.8214 (m-30) cc_final: 0.7998 (m-30) REVERT: E 59 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8242 (mtp180) REVERT: E 69 ASN cc_start: 0.8127 (t0) cc_final: 0.7748 (t0) REVERT: E 98 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7885 (mp10) REVERT: E 120 GLU cc_start: 0.7493 (mp0) cc_final: 0.7211 (mp0) REVERT: E 129 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7655 (tm-30) REVERT: E 187 ASP cc_start: 0.8025 (t0) cc_final: 0.7349 (t0) REVERT: E 291 MET cc_start: 0.8704 (mtm) cc_final: 0.8370 (mtm) REVERT: E 340 SER cc_start: 0.7686 (t) cc_final: 0.7398 (t) REVERT: E 439 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8253 (ttpp) REVERT: E 457 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7883 (mm-30) REVERT: E 478 ASN cc_start: 0.8314 (t0) cc_final: 0.7976 (t0) REVERT: E 519 TYR cc_start: 0.8674 (m-80) cc_final: 0.8469 (m-10) REVERT: E 556 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7547 (mm-30) REVERT: E 578 ILE cc_start: 0.8520 (tp) cc_final: 0.8283 (tt) outliers start: 46 outliers final: 13 residues processed: 489 average time/residue: 0.7003 time to fit residues: 374.0901 Evaluate side-chains 453 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 435 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 C residue 377 MET 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 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 32 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 91 optimal weight: 0.0670 chunk 72 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 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 D 348 ASN E 278 GLN ** E 301 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 = 0.3481 r_free = 0.3481 target = 0.100067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091649 restraints weight = 29550.926| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.93 r_work: 0.3241 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17885 Z= 0.128 Angle : 0.564 7.788 24321 Z= 0.288 Chirality : 0.044 0.167 2657 Planarity : 0.004 0.052 3175 Dihedral : 10.501 162.138 2522 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.93 % Allowed : 15.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2208 helix: 0.79 (0.17), residues: 919 sheet: 0.43 (0.28), residues: 353 loop : -0.63 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 306 TYR 0.018 0.001 TYR B 340 PHE 0.020 0.001 PHE E 75 TRP 0.012 0.001 TRP A 21 HIS 0.010 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00292 (17882) covalent geometry : angle 0.56449 (24321) hydrogen bonds : bond 0.03942 ( 784) hydrogen bonds : angle 4.53826 ( 2268) metal coordination : bond 0.00299 ( 2) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 444 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.8565 (p90) cc_final: 0.8225 (p90) REVERT: A 77 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 83 TYR cc_start: 0.8689 (m-80) cc_final: 0.8391 (m-80) REVERT: A 116 ASP cc_start: 0.7921 (m-30) cc_final: 0.7276 (p0) REVERT: A 117 LEU cc_start: 0.8103 (tp) cc_final: 0.7706 (tt) REVERT: A 120 ASP cc_start: 0.7892 (m-30) cc_final: 0.7548 (m-30) REVERT: A 214 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8225 (ttp-110) REVERT: A 290 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 338 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8468 (ttpp) REVERT: A 367 ASP cc_start: 0.8067 (p0) cc_final: 0.7766 (p0) REVERT: A 370 LYS cc_start: 0.8484 (tptt) cc_final: 0.8241 (tptt) REVERT: A 414 GLU cc_start: 0.8058 (mp0) cc_final: 0.7549 (mp0) REVERT: A 417 GLU cc_start: 0.7926 (tt0) cc_final: 0.7695 (mt-10) REVERT: A 420 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 423 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 438 ASP cc_start: 0.8030 (m-30) cc_final: 0.7712 (m-30) REVERT: B 1 MET cc_start: 0.8486 (mtt) cc_final: 0.8252 (mtt) REVERT: B 19 LYS cc_start: 0.8991 (tptm) cc_final: 0.8671 (tppp) REVERT: B 114 ASP cc_start: 0.8168 (m-30) cc_final: 0.7931 (m-30) REVERT: B 118 ASP cc_start: 0.7918 (m-30) cc_final: 0.7606 (m-30) REVERT: B 123 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7767 (tp30) REVERT: B 127 CYS cc_start: 0.7896 (m) cc_final: 0.7389 (m) REVERT: B 154 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8345 (mtpp) REVERT: B 158 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 174 LYS cc_start: 0.8495 (mmpt) cc_final: 0.8227 (mmpt) REVERT: B 203 ASP cc_start: 0.7855 (t70) cc_final: 0.7607 (t0) REVERT: B 216 LYS cc_start: 0.9059 (mmtm) cc_final: 0.8743 (mmmm) REVERT: B 274 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8444 (p) REVERT: B 278 SER cc_start: 0.8566 (m) cc_final: 0.8238 (p) REVERT: B 291 GLN cc_start: 0.8312 (pp30) cc_final: 0.8030 (pp30) REVERT: B 324 LYS cc_start: 0.8609 (tptp) cc_final: 0.8230 (tppp) REVERT: B 328 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7362 (tp30) REVERT: B 407 GLU cc_start: 0.7994 (tt0) cc_final: 0.7742 (mt-10) REVERT: B 410 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 412 GLU cc_start: 0.8189 (tp30) cc_final: 0.7853 (tp30) REVERT: B 414 ASN cc_start: 0.8331 (m110) cc_final: 0.7890 (m110) REVERT: B 417 ASP cc_start: 0.8209 (m-30) cc_final: 0.7832 (m-30) REVERT: C 3 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: C 50 ASN cc_start: 0.8753 (t0) cc_final: 0.8308 (t0) REVERT: C 123 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7598 (tpp80) REVERT: C 158 SER cc_start: 0.8983 (t) cc_final: 0.8773 (t) REVERT: C 196 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: C 280 LYS cc_start: 0.8924 (mttp) cc_final: 0.7639 (mmtt) REVERT: C 284 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7314 (mp0) REVERT: C 308 ARG cc_start: 0.6723 (tpt170) cc_final: 0.5942 (tpt170) REVERT: C 322 ASP cc_start: 0.8086 (t70) cc_final: 0.7856 (t0) REVERT: C 386 GLU cc_start: 0.7730 (mp0) cc_final: 0.7444 (mp0) REVERT: C 392 ASP cc_start: 0.7993 (m-30) cc_final: 0.7597 (m-30) REVERT: C 420 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7506 (mm-30) REVERT: C 423 GLU cc_start: 0.7988 (tp30) cc_final: 0.7721 (mm-30) REVERT: C 424 ASP cc_start: 0.8101 (t70) cc_final: 0.7843 (t0) REVERT: C 429 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7996 (mt-10) REVERT: C 431 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: C 434 GLU cc_start: 0.7851 (pp20) cc_final: 0.7602 (pp20) REVERT: D 3 GLU cc_start: 0.7921 (mp0) cc_final: 0.7285 (mp0) REVERT: D 22 GLU cc_start: 0.8677 (tt0) cc_final: 0.8067 (tp30) REVERT: D 45 GLU cc_start: 0.8347 (tt0) cc_final: 0.8009 (tm-30) REVERT: D 69 GLU cc_start: 0.7544 (pm20) cc_final: 0.7314 (pm20) REVERT: D 88 ASP cc_start: 0.8336 (t70) cc_final: 0.7874 (t0) REVERT: D 103 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8760 (mtpm) REVERT: D 122 LYS cc_start: 0.8739 (tppt) cc_final: 0.8537 (tppt) REVERT: D 123 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7972 (mm-30) REVERT: D 154 LYS cc_start: 0.9011 (mptp) cc_final: 0.8800 (mptt) REVERT: D 159 TYR cc_start: 0.8576 (m-80) cc_final: 0.8369 (m-80) REVERT: D 181 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7686 (mt-10) REVERT: D 198 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8072 (mt-10) REVERT: D 203 ASP cc_start: 0.8169 (t0) cc_final: 0.7863 (t70) REVERT: D 216 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8707 (mmmm) REVERT: D 251 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8421 (ttm110) REVERT: D 257 MET cc_start: 0.8437 (mmm) cc_final: 0.8222 (mtp) REVERT: D 291 GLN cc_start: 0.8583 (pp30) cc_final: 0.8278 (pp30) REVERT: D 325 GLU cc_start: 0.7967 (tp30) cc_final: 0.7756 (tp30) REVERT: D 383 GLU cc_start: 0.8190 (tp30) cc_final: 0.7751 (tp30) REVERT: D 391 ARG cc_start: 0.8547 (mmm160) cc_final: 0.7036 (ptm-80) REVERT: D 404 ASP cc_start: 0.8296 (m-30) cc_final: 0.7465 (m-30) REVERT: D 407 GLU cc_start: 0.8017 (mp0) cc_final: 0.7641 (mp0) REVERT: D 410 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7763 (tm-30) REVERT: D 413 SER cc_start: 0.8433 (t) cc_final: 0.8036 (p) REVERT: E 61 ASP cc_start: 0.7544 (m-30) cc_final: 0.7335 (m-30) REVERT: E 69 ASN cc_start: 0.8169 (t0) cc_final: 0.7811 (t0) REVERT: E 120 GLU cc_start: 0.7383 (mp0) cc_final: 0.7114 (mp0) REVERT: E 129 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7611 (tm-30) REVERT: E 187 ASP cc_start: 0.8097 (t0) cc_final: 0.7506 (t0) REVERT: E 291 MET cc_start: 0.8671 (mtm) cc_final: 0.8284 (mtm) REVERT: E 340 SER cc_start: 0.7756 (t) cc_final: 0.7439 (t) REVERT: E 478 ASN cc_start: 0.8369 (t0) cc_final: 0.7965 (t0) REVERT: E 519 TYR cc_start: 0.8661 (m-80) cc_final: 0.8447 (m-10) REVERT: E 556 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7527 (mm-30) REVERT: E 569 MET cc_start: 0.7772 (mtp) cc_final: 0.7459 (mtm) outliers start: 54 outliers final: 12 residues processed: 469 average time/residue: 0.7561 time to fit residues: 388.9890 Evaluate side-chains 446 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 428 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 337 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 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 D residue 251 ARG Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 65 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 80 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** B 384 GLN B 423 GLN C 28 HIS C 128 GLN C 356 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 165 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087480 restraints weight = 29333.968| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.89 r_work: 0.3160 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: 0.8262 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17885 Z= 0.196 Angle : 0.606 8.494 24321 Z= 0.311 Chirality : 0.046 0.157 2657 Planarity : 0.005 0.052 3175 Dihedral : 10.907 179.790 2519 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.31 % Allowed : 16.59 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.18), residues: 2208 helix: 1.11 (0.17), residues: 917 sheet: 0.47 (0.29), residues: 355 loop : -0.61 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 590 TYR 0.017 0.002 TYR B 340 PHE 0.024 0.002 PHE E 75 TRP 0.014 0.002 TRP C 21 HIS 0.012 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00450 (17882) covalent geometry : angle 0.60588 (24321) hydrogen bonds : bond 0.04465 ( 784) hydrogen bonds : angle 4.57593 ( 2268) metal coordination : bond 0.00709 ( 2) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 446 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 83 TYR cc_start: 0.8801 (m-80) cc_final: 0.8412 (m-80) REVERT: A 116 ASP cc_start: 0.8080 (m-30) cc_final: 0.7541 (m-30) REVERT: A 117 LEU cc_start: 0.8358 (tp) cc_final: 0.7954 (tt) REVERT: A 120 ASP cc_start: 0.8014 (m-30) cc_final: 0.7766 (m-30) REVERT: A 154 MET cc_start: 0.8961 (mmm) cc_final: 0.8674 (mmp) REVERT: A 214 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8106 (ttp-110) REVERT: A 251 ASP cc_start: 0.7736 (m-30) cc_final: 0.7455 (p0) REVERT: A 254 GLU cc_start: 0.5005 (mm-30) cc_final: 0.3347 (tp30) REVERT: A 277 SER cc_start: 0.8919 (t) cc_final: 0.8531 (p) REVERT: A 290 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8237 (mm-30) REVERT: A 309 HIS cc_start: 0.8552 (m170) cc_final: 0.8277 (m170) REVERT: A 338 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8485 (ttpp) REVERT: A 367 ASP cc_start: 0.8008 (p0) cc_final: 0.7653 (p0) REVERT: A 370 LYS cc_start: 0.8506 (tptt) cc_final: 0.8292 (tptt) REVERT: A 388 TRP cc_start: 0.8769 (m-10) cc_final: 0.8156 (m-10) REVERT: A 392 ASP cc_start: 0.8111 (m-30) cc_final: 0.7636 (m-30) REVERT: A 414 GLU cc_start: 0.8049 (mp0) cc_final: 0.7658 (mp0) REVERT: A 417 GLU cc_start: 0.8034 (tt0) cc_final: 0.7804 (mt-10) REVERT: A 423 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 1 MET cc_start: 0.8566 (mtt) cc_final: 0.8182 (mtm) REVERT: B 19 LYS cc_start: 0.8963 (tptm) cc_final: 0.8755 (tppt) REVERT: B 36 TYR cc_start: 0.8746 (t80) cc_final: 0.8498 (t80) REVERT: B 53 GLU cc_start: 0.8115 (tt0) cc_final: 0.7658 (mm-30) REVERT: B 74 ASP cc_start: 0.8223 (t0) cc_final: 0.7880 (t0) REVERT: B 114 ASP cc_start: 0.8231 (m-30) cc_final: 0.7978 (m-30) REVERT: B 118 ASP cc_start: 0.7898 (m-30) cc_final: 0.7554 (m-30) REVERT: B 123 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7884 (tp30) REVERT: B 127 CYS cc_start: 0.7900 (m) cc_final: 0.7357 (m) REVERT: B 154 LYS cc_start: 0.8950 (mmtp) cc_final: 0.8477 (mtpp) REVERT: B 158 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: B 174 LYS cc_start: 0.8588 (mmpt) cc_final: 0.8346 (mmpt) REVERT: B 175 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8710 (m) REVERT: B 216 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8791 (mmmm) REVERT: B 274 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 278 SER cc_start: 0.8550 (m) cc_final: 0.8239 (p) REVERT: B 291 GLN cc_start: 0.8292 (pp30) cc_final: 0.8060 (pp30) REVERT: B 325 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: B 328 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7436 (OUTLIER) REVERT: B 407 GLU cc_start: 0.8122 (tt0) cc_final: 0.7765 (mt-10) REVERT: B 410 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 412 GLU cc_start: 0.8266 (tp30) cc_final: 0.7743 (tp30) REVERT: B 414 ASN cc_start: 0.8454 (m110) cc_final: 0.8050 (m110) REVERT: C 3 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7120 (pm20) REVERT: C 123 ARG cc_start: 0.8009 (tpp-160) cc_final: 0.7609 (tpp80) REVERT: C 154 MET cc_start: 0.9026 (mmm) cc_final: 0.8661 (mtm) REVERT: C 196 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: C 207 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7319 (mt-10) REVERT: C 214 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8273 (ttp-110) REVERT: C 280 LYS cc_start: 0.8913 (mttp) cc_final: 0.8429 (mtpt) REVERT: C 308 ARG cc_start: 0.6677 (tpt170) cc_final: 0.6159 (tpt170) REVERT: C 322 ASP cc_start: 0.8194 (t70) cc_final: 0.7949 (t0) REVERT: C 386 GLU cc_start: 0.7985 (mp0) cc_final: 0.7604 (mp0) REVERT: C 392 ASP cc_start: 0.8178 (m-30) cc_final: 0.7795 (m-30) REVERT: C 420 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7604 (mm-30) REVERT: C 423 GLU cc_start: 0.8130 (tp30) cc_final: 0.7874 (mm-30) REVERT: C 424 ASP cc_start: 0.8034 (t70) cc_final: 0.7807 (t0) REVERT: C 429 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8031 (mt-10) REVERT: C 434 GLU cc_start: 0.8021 (pp20) cc_final: 0.7672 (pp20) REVERT: D 3 GLU cc_start: 0.7978 (mp0) cc_final: 0.7642 (mp0) REVERT: D 22 GLU cc_start: 0.8710 (tt0) cc_final: 0.8301 (tm-30) REVERT: D 26 ASP cc_start: 0.7688 (m-30) cc_final: 0.7372 (t0) REVERT: D 45 GLU cc_start: 0.8435 (tt0) cc_final: 0.8184 (tm-30) REVERT: D 57 ASN cc_start: 0.7410 (t0) cc_final: 0.6390 (t0) REVERT: D 64 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8972 (mt) REVERT: D 69 GLU cc_start: 0.7534 (pm20) cc_final: 0.7234 (pm20) REVERT: D 88 ASP cc_start: 0.8447 (t70) cc_final: 0.7960 (t0) REVERT: D 103 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8733 (mtpm) REVERT: D 123 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7894 (mm-30) REVERT: D 154 LYS cc_start: 0.9115 (mptp) cc_final: 0.8675 (mptt) REVERT: D 158 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8163 (mt-10) REVERT: D 161 ASP cc_start: 0.8661 (p0) cc_final: 0.8379 (p0) REVERT: D 181 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7834 (mt-10) REVERT: D 198 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8171 (mt-10) REVERT: D 203 ASP cc_start: 0.8155 (t0) cc_final: 0.7879 (t70) REVERT: D 251 ARG cc_start: 0.8777 (tpp-160) cc_final: 0.8244 (ttm110) REVERT: D 262 ARG cc_start: 0.8872 (mtm180) cc_final: 0.8658 (mtm180) REVERT: D 291 GLN cc_start: 0.8597 (pp30) cc_final: 0.8350 (pp30) REVERT: D 325 GLU cc_start: 0.8136 (tp30) cc_final: 0.7773 (tp30) REVERT: D 376 GLU cc_start: 0.7780 (mp0) cc_final: 0.7525 (mp0) REVERT: D 383 GLU cc_start: 0.8328 (tp30) cc_final: 0.7852 (tp30) REVERT: D 391 ARG cc_start: 0.8769 (mmm160) cc_final: 0.7290 (ptm160) REVERT: D 404 ASP cc_start: 0.8343 (m-30) cc_final: 0.7277 (m-30) REVERT: D 407 GLU cc_start: 0.8076 (mp0) cc_final: 0.7353 (mp0) REVERT: D 413 SER cc_start: 0.8521 (t) cc_final: 0.8131 (p) REVERT: D 414 ASN cc_start: 0.7978 (p0) cc_final: 0.7609 (p0) REVERT: E 61 ASP cc_start: 0.7582 (m-30) cc_final: 0.7279 (m-30) REVERT: E 68 GLU cc_start: 0.8090 (tt0) cc_final: 0.7837 (tt0) REVERT: E 69 ASN cc_start: 0.8194 (t0) cc_final: 0.7827 (t0) REVERT: E 120 GLU cc_start: 0.7463 (mp0) cc_final: 0.7183 (mp0) REVERT: E 129 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7688 (tm-30) REVERT: E 181 THR cc_start: 0.6546 (OUTLIER) cc_final: 0.6336 (p) REVERT: E 187 ASP cc_start: 0.8266 (t0) cc_final: 0.7655 (t0) REVERT: E 340 SER cc_start: 0.8082 (t) cc_final: 0.7732 (t) REVERT: E 440 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8096 (mpp80) REVERT: E 444 MET cc_start: 0.8676 (mtm) cc_final: 0.8338 (ttm) REVERT: E 457 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7988 (mm-30) REVERT: E 478 ASN cc_start: 0.8424 (t0) cc_final: 0.8059 (t0) REVERT: E 519 TYR cc_start: 0.8646 (m-80) cc_final: 0.8378 (m-10) REVERT: E 556 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 562 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8125 (ttp) REVERT: E 569 MET cc_start: 0.7762 (mtp) cc_final: 0.7397 (mtm) outliers start: 61 outliers final: 20 residues processed: 480 average time/residue: 0.6812 time to fit residues: 358.0188 Evaluate side-chains 463 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 435 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 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 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 219 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 64 ILE 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 323 HIS Chi-restraints excluded: chain E residue 440 ARG 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 80 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 342 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** D 416 ASN E 98 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088084 restraints weight = 28590.596| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.89 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: 0.8252 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17885 Z= 0.160 Angle : 0.582 8.757 24321 Z= 0.295 Chirality : 0.045 0.159 2657 Planarity : 0.004 0.055 3175 Dihedral : 10.873 176.140 2519 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.93 % Allowed : 17.52 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.18), residues: 2208 helix: 1.26 (0.17), residues: 918 sheet: 0.43 (0.28), residues: 352 loop : -0.62 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 590 TYR 0.029 0.001 TYR B 340 PHE 0.026 0.002 PHE E 75 TRP 0.013 0.002 TRP C 21 HIS 0.013 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00372 (17882) covalent geometry : angle 0.58167 (24321) hydrogen bonds : bond 0.04055 ( 784) hydrogen bonds : angle 4.51842 ( 2268) metal coordination : bond 0.00528 ( 2) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 428 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 83 TYR cc_start: 0.8868 (m-80) cc_final: 0.8502 (m-80) REVERT: A 116 ASP cc_start: 0.8100 (m-30) cc_final: 0.7580 (m-30) REVERT: A 117 LEU cc_start: 0.8303 (tp) cc_final: 0.7892 (tt) REVERT: A 120 ASP cc_start: 0.7999 (m-30) cc_final: 0.7793 (m-30) REVERT: A 154 MET cc_start: 0.8863 (mmm) cc_final: 0.8613 (mmp) REVERT: A 214 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8151 (ttp-110) REVERT: A 251 ASP cc_start: 0.7826 (m-30) cc_final: 0.7606 (t0) REVERT: A 254 GLU cc_start: 0.5062 (mm-30) cc_final: 0.4092 (mm-30) REVERT: A 277 SER cc_start: 0.8902 (t) cc_final: 0.8539 (p) REVERT: A 290 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8249 (mm-30) REVERT: A 309 HIS cc_start: 0.8571 (m170) cc_final: 0.8310 (m170) REVERT: A 338 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8447 (ttpp) REVERT: A 367 ASP cc_start: 0.8110 (p0) cc_final: 0.7742 (p0) REVERT: A 370 LYS cc_start: 0.8543 (tptt) cc_final: 0.8315 (tptt) REVERT: A 388 TRP cc_start: 0.8726 (m-10) cc_final: 0.8047 (m-10) REVERT: A 392 ASP cc_start: 0.8076 (m-30) cc_final: 0.7589 (m-30) REVERT: A 414 GLU cc_start: 0.8085 (mp0) cc_final: 0.7763 (mp0) REVERT: A 417 GLU cc_start: 0.7957 (tt0) cc_final: 0.7703 (mt-10) REVERT: A 420 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 423 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 1 MET cc_start: 0.8538 (mtt) cc_final: 0.8176 (mtm) REVERT: B 36 TYR cc_start: 0.8766 (t80) cc_final: 0.8275 (t80) REVERT: B 53 GLU cc_start: 0.8186 (tt0) cc_final: 0.7808 (tp30) REVERT: B 103 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8505 (mtpm) REVERT: B 114 ASP cc_start: 0.8187 (m-30) cc_final: 0.7940 (m-30) REVERT: B 118 ASP cc_start: 0.7942 (m-30) cc_final: 0.7629 (m-30) REVERT: B 123 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7873 (tp30) REVERT: B 127 CYS cc_start: 0.7885 (m) cc_final: 0.7402 (m) REVERT: B 154 LYS cc_start: 0.8956 (mmtp) cc_final: 0.8491 (mtpp) REVERT: B 158 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: B 174 LYS cc_start: 0.8616 (mmpt) cc_final: 0.8330 (mmpt) REVERT: B 175 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8711 (m) REVERT: B 274 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8597 (p) REVERT: B 278 SER cc_start: 0.8531 (m) cc_final: 0.8226 (p) REVERT: B 291 GLN cc_start: 0.8322 (pp30) cc_final: 0.8103 (pp30) REVERT: B 325 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: B 328 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7384 (OUTLIER) REVERT: B 407 GLU cc_start: 0.8101 (tt0) cc_final: 0.7736 (mt-10) REVERT: B 410 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 412 GLU cc_start: 0.8238 (tp30) cc_final: 0.7547 (tp30) REVERT: B 414 ASN cc_start: 0.8418 (m110) cc_final: 0.8032 (m110) REVERT: B 421 GLU cc_start: 0.8323 (tt0) cc_final: 0.7984 (tm-30) REVERT: C 3 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7233 (pm20) REVERT: C 123 ARG cc_start: 0.8026 (tpp-160) cc_final: 0.7603 (tpp80) REVERT: C 154 MET cc_start: 0.9006 (mmm) cc_final: 0.8799 (mmm) REVERT: C 196 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: C 207 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 214 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8275 (ttp-110) REVERT: C 218 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8397 (t0) REVERT: C 277 SER cc_start: 0.8722 (t) cc_final: 0.8511 (p) REVERT: C 280 LYS cc_start: 0.9026 (mttp) cc_final: 0.8343 (mtpt) REVERT: C 284 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7590 (mp0) REVERT: C 308 ARG cc_start: 0.6687 (tpt170) cc_final: 0.6170 (tpt170) REVERT: C 322 ASP cc_start: 0.8172 (t70) cc_final: 0.7920 (t0) REVERT: C 377 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8354 (ttp) REVERT: C 386 GLU cc_start: 0.7833 (mp0) cc_final: 0.7489 (mp0) REVERT: C 392 ASP cc_start: 0.8091 (m-30) cc_final: 0.7756 (m-30) REVERT: C 417 GLU cc_start: 0.7655 (mp0) cc_final: 0.7410 (mp0) REVERT: C 420 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7607 (mm-30) REVERT: C 423 GLU cc_start: 0.8017 (tp30) cc_final: 0.7800 (mm-30) REVERT: C 424 ASP cc_start: 0.8077 (t70) cc_final: 0.7843 (t0) REVERT: C 433 GLU cc_start: 0.8349 (tt0) cc_final: 0.7718 (tm-30) REVERT: C 434 GLU cc_start: 0.8069 (pp20) cc_final: 0.7735 (pp20) REVERT: D 3 GLU cc_start: 0.8001 (mp0) cc_final: 0.7671 (mp0) REVERT: D 19 LYS cc_start: 0.8984 (tppp) cc_final: 0.8772 (tppp) REVERT: D 22 GLU cc_start: 0.8640 (tt0) cc_final: 0.8219 (tm-30) REVERT: D 26 ASP cc_start: 0.7622 (m-30) cc_final: 0.7354 (t0) REVERT: D 45 GLU cc_start: 0.8456 (tt0) cc_final: 0.8165 (tm-30) REVERT: D 57 ASN cc_start: 0.7570 (t0) cc_final: 0.6502 (t0) REVERT: D 64 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9009 (mt) REVERT: D 69 GLU cc_start: 0.7589 (pm20) cc_final: 0.7273 (pm20) REVERT: D 88 ASP cc_start: 0.8311 (t70) cc_final: 0.7830 (t0) REVERT: D 103 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8750 (mtpm) REVERT: D 123 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7895 (mm-30) REVERT: D 158 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8302 (mt-10) REVERT: D 161 ASP cc_start: 0.8681 (p0) cc_final: 0.8352 (p0) REVERT: D 181 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7878 (mt-10) REVERT: D 190 HIS cc_start: 0.8006 (t-90) cc_final: 0.7035 (t70) REVERT: D 198 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8181 (mt-10) REVERT: D 203 ASP cc_start: 0.8111 (t0) cc_final: 0.7840 (t70) REVERT: D 251 ARG cc_start: 0.8750 (tpp-160) cc_final: 0.8221 (ttm110) REVERT: D 262 ARG cc_start: 0.8902 (mtm180) cc_final: 0.8668 (mtm180) REVERT: D 291 GLN cc_start: 0.8552 (pp30) cc_final: 0.8317 (pp30) REVERT: D 325 GLU cc_start: 0.8225 (tp30) cc_final: 0.7792 (tp30) REVERT: D 376 GLU cc_start: 0.7794 (mp0) cc_final: 0.7520 (mp0) REVERT: D 383 GLU cc_start: 0.8373 (tp30) cc_final: 0.8037 (tp30) REVERT: D 391 ARG cc_start: 0.8891 (mmm160) cc_final: 0.7322 (ptm160) REVERT: D 404 ASP cc_start: 0.8451 (m-30) cc_final: 0.7365 (m-30) REVERT: D 407 GLU cc_start: 0.8121 (mp0) cc_final: 0.7383 (mp0) REVERT: D 414 ASN cc_start: 0.7898 (p0) cc_final: 0.7635 (p0) REVERT: D 424 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8134 (pt0) REVERT: E 69 ASN cc_start: 0.8267 (t0) cc_final: 0.7873 (t0) REVERT: E 129 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7700 (tm-30) REVERT: E 181 THR cc_start: 0.6470 (OUTLIER) cc_final: 0.6263 (p) REVERT: E 187 ASP cc_start: 0.8328 (t0) cc_final: 0.7721 (t0) REVERT: E 291 MET cc_start: 0.8743 (mtp) cc_final: 0.8246 (mtm) REVERT: E 340 SER cc_start: 0.8062 (t) cc_final: 0.7697 (t) REVERT: E 444 MET cc_start: 0.8584 (mtm) cc_final: 0.8262 (ttm) REVERT: E 457 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7889 (mm-30) REVERT: E 478 ASN cc_start: 0.8433 (t0) cc_final: 0.8041 (t0) REVERT: E 519 TYR cc_start: 0.8631 (m-80) cc_final: 0.8411 (m-10) REVERT: E 556 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7620 (mm-30) REVERT: E 569 MET cc_start: 0.7791 (mtp) cc_final: 0.7522 (mtm) outliers start: 54 outliers final: 22 residues processed: 454 average time/residue: 0.6692 time to fit residues: 333.0106 Evaluate side-chains 462 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 431 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 372 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 LEU 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 44 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 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 524 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 43 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 180 optimal weight: 0.2980 chunk 163 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 342 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 384 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** 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 = 0.3419 r_free = 0.3419 target = 0.096439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087979 restraints weight = 28455.277| |-----------------------------------------------------------------------------| 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: 0.3018 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17885 Z= 0.154 Angle : 0.573 8.926 24321 Z= 0.291 Chirality : 0.044 0.161 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.848 175.496 2519 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.25 % Allowed : 17.79 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2208 helix: 1.35 (0.17), residues: 919 sheet: 0.44 (0.29), residues: 344 loop : -0.59 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 590 TYR 0.024 0.001 TYR B 340 PHE 0.028 0.002 PHE E 75 TRP 0.013 0.002 TRP C 21 HIS 0.009 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00357 (17882) covalent geometry : angle 0.57306 (24321) hydrogen bonds : bond 0.03959 ( 784) hydrogen bonds : angle 4.47682 ( 2268) metal coordination : bond 0.00478 ( 2) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 423 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 83 TYR cc_start: 0.8874 (m-80) cc_final: 0.8500 (m-80) REVERT: A 116 ASP cc_start: 0.8137 (m-30) cc_final: 0.7637 (m-30) REVERT: A 117 LEU cc_start: 0.8360 (tp) cc_final: 0.7943 (tt) REVERT: A 120 ASP cc_start: 0.7910 (m-30) cc_final: 0.7690 (m-30) REVERT: A 154 MET cc_start: 0.8857 (mmm) cc_final: 0.8582 (mmp) REVERT: A 211 ASP cc_start: 0.8051 (m-30) cc_final: 0.7822 (m-30) REVERT: A 251 ASP cc_start: 0.7812 (m-30) cc_final: 0.7601 (t0) REVERT: A 254 GLU cc_start: 0.4182 (mm-30) cc_final: 0.2862 (mm-30) REVERT: A 277 SER cc_start: 0.8924 (t) cc_final: 0.8686 (p) REVERT: A 290 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8232 (mm-30) REVERT: A 309 HIS cc_start: 0.8585 (m170) cc_final: 0.8332 (m170) REVERT: A 338 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8454 (mtpp) REVERT: A 367 ASP cc_start: 0.8099 (p0) cc_final: 0.7731 (p0) REVERT: A 370 LYS cc_start: 0.8531 (tptt) cc_final: 0.8315 (tptt) REVERT: A 388 TRP cc_start: 0.8716 (m-10) cc_final: 0.8043 (m-10) REVERT: A 392 ASP cc_start: 0.8052 (m-30) cc_final: 0.7569 (m-30) REVERT: A 414 GLU cc_start: 0.8086 (mp0) cc_final: 0.7768 (mp0) REVERT: A 417 GLU cc_start: 0.7944 (tt0) cc_final: 0.7726 (mt-10) REVERT: A 420 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 423 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7944 (mm-30) REVERT: B 1 MET cc_start: 0.8574 (mtt) cc_final: 0.8241 (mtp) REVERT: B 36 TYR cc_start: 0.8770 (t80) cc_final: 0.8300 (t80) REVERT: B 53 GLU cc_start: 0.8187 (tt0) cc_final: 0.7795 (tm-30) REVERT: B 74 ASP cc_start: 0.8187 (t70) cc_final: 0.7928 (t0) REVERT: B 114 ASP cc_start: 0.8214 (m-30) cc_final: 0.7934 (m-30) REVERT: B 118 ASP cc_start: 0.7941 (m-30) cc_final: 0.7607 (m-30) REVERT: B 123 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7881 (tp30) REVERT: B 127 CYS cc_start: 0.7916 (m) cc_final: 0.7444 (m) REVERT: B 134 GLN cc_start: 0.8483 (mt0) cc_final: 0.8258 (pt0) REVERT: B 154 LYS cc_start: 0.8926 (mmtp) cc_final: 0.8483 (mtpp) REVERT: B 158 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: B 174 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8277 (mmpt) REVERT: B 175 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8732 (m) REVERT: B 216 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8768 (mmmm) REVERT: B 274 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8601 (p) REVERT: B 278 SER cc_start: 0.8579 (m) cc_final: 0.8253 (p) REVERT: B 291 GLN cc_start: 0.8312 (pp30) cc_final: 0.8078 (pp30) REVERT: B 325 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: B 328 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7397 (OUTLIER) REVERT: B 380 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7569 (mtm180) REVERT: B 383 GLU cc_start: 0.7957 (pp20) cc_final: 0.7544 (pp20) REVERT: B 407 GLU cc_start: 0.8081 (tt0) cc_final: 0.7770 (mt-10) REVERT: B 410 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 414 ASN cc_start: 0.8412 (m110) cc_final: 0.8068 (m110) REVERT: B 421 GLU cc_start: 0.8292 (tt0) cc_final: 0.7936 (tm-30) REVERT: C 123 ARG cc_start: 0.8041 (tpp-160) cc_final: 0.7617 (tpp80) REVERT: C 196 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: C 207 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7472 (mt-10) REVERT: C 214 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.8188 (ttp-110) REVERT: C 280 LYS cc_start: 0.9014 (mttp) cc_final: 0.8365 (mmpt) REVERT: C 308 ARG cc_start: 0.6712 (tpt170) cc_final: 0.6125 (tpt170) REVERT: C 322 ASP cc_start: 0.8157 (t70) cc_final: 0.7908 (t0) REVERT: C 386 GLU cc_start: 0.7687 (mp0) cc_final: 0.7354 (mp0) REVERT: C 417 GLU cc_start: 0.7774 (mp0) cc_final: 0.7499 (mp0) REVERT: C 420 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7608 (mm-30) REVERT: C 423 GLU cc_start: 0.8021 (tp30) cc_final: 0.7806 (mm-30) REVERT: C 424 ASP cc_start: 0.8086 (t70) cc_final: 0.7854 (t0) REVERT: C 433 GLU cc_start: 0.8464 (tt0) cc_final: 0.7784 (tm-30) REVERT: C 434 GLU cc_start: 0.8112 (pp20) cc_final: 0.7771 (pp20) REVERT: D 3 GLU cc_start: 0.8028 (mp0) cc_final: 0.7727 (mp0) REVERT: D 22 GLU cc_start: 0.8606 (tt0) cc_final: 0.8231 (tm-30) REVERT: D 26 ASP cc_start: 0.7619 (m-30) cc_final: 0.7400 (t0) REVERT: D 45 GLU cc_start: 0.8444 (tt0) cc_final: 0.8044 (tm-30) REVERT: D 57 ASN cc_start: 0.7726 (t0) cc_final: 0.6725 (t0) REVERT: D 64 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9003 (mt) REVERT: D 69 GLU cc_start: 0.7364 (pm20) cc_final: 0.7022 (pm20) REVERT: D 88 ASP cc_start: 0.8287 (t70) cc_final: 0.7812 (t0) REVERT: D 92 PHE cc_start: 0.8623 (p90) cc_final: 0.8354 (p90) REVERT: D 103 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8735 (mtpm) REVERT: D 161 ASP cc_start: 0.8646 (p0) cc_final: 0.8272 (p0) REVERT: D 181 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 190 HIS cc_start: 0.8040 (t-90) cc_final: 0.6018 (t70) REVERT: D 198 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8166 (mt-10) REVERT: D 203 ASP cc_start: 0.8148 (t0) cc_final: 0.7877 (t70) REVERT: D 251 ARG cc_start: 0.8749 (tpp-160) cc_final: 0.8352 (ttm110) REVERT: D 291 GLN cc_start: 0.8536 (pp30) cc_final: 0.8273 (pp30) REVERT: D 309 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7958 (mtp85) REVERT: D 325 GLU cc_start: 0.8211 (tp30) cc_final: 0.7788 (tp30) REVERT: D 376 GLU cc_start: 0.7847 (mp0) cc_final: 0.7529 (mp0) REVERT: D 383 GLU cc_start: 0.8366 (tp30) cc_final: 0.8048 (tp30) REVERT: D 391 ARG cc_start: 0.8963 (mmm160) cc_final: 0.7289 (ptm-80) REVERT: D 404 ASP cc_start: 0.8442 (m-30) cc_final: 0.7686 (m-30) REVERT: D 407 GLU cc_start: 0.8132 (mp0) cc_final: 0.7466 (mp0) REVERT: D 410 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7766 (tm-30) REVERT: D 414 ASN cc_start: 0.7906 (p0) cc_final: 0.7671 (p0) REVERT: D 424 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: E 21 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8024 (t70) REVERT: E 68 GLU cc_start: 0.8097 (tt0) cc_final: 0.7833 (tt0) REVERT: E 69 ASN cc_start: 0.8325 (t0) cc_final: 0.7942 (t0) REVERT: E 129 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7668 (tm-30) REVERT: E 187 ASP cc_start: 0.8311 (t0) cc_final: 0.7708 (t0) REVERT: E 226 GLN cc_start: 0.8535 (mt0) cc_final: 0.8265 (mt0) REVERT: E 340 SER cc_start: 0.8081 (t) cc_final: 0.7716 (t) REVERT: E 440 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8110 (mpp80) REVERT: E 444 MET cc_start: 0.8517 (mtm) cc_final: 0.8205 (ttm) REVERT: E 457 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7902 (mm-30) REVERT: E 478 ASN cc_start: 0.8427 (t0) cc_final: 0.7989 (t0) REVERT: E 556 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7604 (mm-30) REVERT: E 569 MET cc_start: 0.7750 (mtp) cc_final: 0.7492 (mtm) outliers start: 60 outliers final: 27 residues processed: 456 average time/residue: 0.6781 time to fit residues: 339.7464 Evaluate side-chains 457 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 422 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 193 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 128 ASP 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 21 HIS Chi-restraints excluded: chain E residue 53 GLU 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 309 VAL Chi-restraints excluded: chain E residue 440 ARG Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 170 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 chunk 103 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 163 optimal weight: 0.0170 chunk 199 optimal weight: 0.9980 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088400 restraints weight = 28822.817| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.90 r_work: 0.3168 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17885 Z= 0.131 Angle : 0.570 9.161 24321 Z= 0.287 Chirality : 0.044 0.155 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.767 174.916 2519 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.09 % Allowed : 19.09 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2208 helix: 1.45 (0.17), residues: 921 sheet: 0.40 (0.29), residues: 344 loop : -0.56 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 221 TYR 0.023 0.001 TYR B 340 PHE 0.028 0.001 PHE E 75 TRP 0.013 0.001 TRP C 21 HIS 0.007 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00304 (17882) covalent geometry : angle 0.57022 (24321) hydrogen bonds : bond 0.03734 ( 784) hydrogen bonds : angle 4.41266 ( 2268) metal coordination : bond 0.00345 ( 2) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 439 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7662 (mp0) cc_final: 0.7345 (mp0) REVERT: A 49 PHE cc_start: 0.8325 (p90) cc_final: 0.8093 (p90) REVERT: A 77 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7670 (mt-10) REVERT: A 83 TYR cc_start: 0.8875 (m-80) cc_final: 0.8500 (m-80) REVERT: A 116 ASP cc_start: 0.8104 (m-30) cc_final: 0.7616 (m-30) REVERT: A 117 LEU cc_start: 0.8298 (tp) cc_final: 0.7901 (tt) REVERT: A 120 ASP cc_start: 0.7976 (m-30) cc_final: 0.7714 (m-30) REVERT: A 154 MET cc_start: 0.8845 (mmm) cc_final: 0.8568 (mmp) REVERT: A 214 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8353 (ttp80) REVERT: A 221 ARG cc_start: 0.8499 (ptp-110) cc_final: 0.8275 (ptp90) REVERT: A 254 GLU cc_start: 0.5293 (mm-30) cc_final: 0.3920 (mm-30) REVERT: A 290 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8214 (mm-30) REVERT: A 309 HIS cc_start: 0.8575 (m170) cc_final: 0.8331 (m170) REVERT: A 370 LYS cc_start: 0.8512 (tptt) cc_final: 0.8303 (tptt) REVERT: A 388 TRP cc_start: 0.8666 (m-10) cc_final: 0.8028 (m-10) REVERT: A 392 ASP cc_start: 0.8061 (m-30) cc_final: 0.7562 (m-30) REVERT: A 414 GLU cc_start: 0.8084 (mp0) cc_final: 0.7768 (mp0) REVERT: A 417 GLU cc_start: 0.7915 (tt0) cc_final: 0.7696 (mt-10) REVERT: A 420 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 423 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7925 (mm-30) REVERT: B 1 MET cc_start: 0.8581 (mtt) cc_final: 0.8271 (mtp) REVERT: B 36 TYR cc_start: 0.8763 (t80) cc_final: 0.8296 (t80) REVERT: B 53 GLU cc_start: 0.8156 (tt0) cc_final: 0.7689 (tm-30) REVERT: B 69 GLU cc_start: 0.8045 (pt0) cc_final: 0.7625 (pm20) REVERT: B 74 ASP cc_start: 0.8193 (t70) cc_final: 0.7927 (OUTLIER) REVERT: B 114 ASP cc_start: 0.8212 (m-30) cc_final: 0.7955 (m-30) REVERT: B 118 ASP cc_start: 0.7934 (m-30) cc_final: 0.7622 (m-30) REVERT: B 123 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7885 (tp30) REVERT: B 127 CYS cc_start: 0.7948 (m) cc_final: 0.7469 (m) REVERT: B 134 GLN cc_start: 0.8478 (mt0) cc_final: 0.8264 (pt0) REVERT: B 154 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8444 (mtpp) REVERT: B 157 GLU cc_start: 0.8401 (tt0) cc_final: 0.7941 (tm-30) REVERT: B 158 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: B 174 LYS cc_start: 0.8664 (mmpt) cc_final: 0.8226 (mmpt) REVERT: B 175 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8724 (m) REVERT: B 213 ARG cc_start: 0.8858 (ptp-110) cc_final: 0.8606 (ptm160) REVERT: B 216 LYS cc_start: 0.9046 (mmtm) cc_final: 0.8774 (mmmm) REVERT: B 274 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 278 SER cc_start: 0.8621 (m) cc_final: 0.8283 (p) REVERT: B 325 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: B 328 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7372 (OUTLIER) REVERT: B 380 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7960 (mtm180) REVERT: B 407 GLU cc_start: 0.8092 (tt0) cc_final: 0.7718 (mt-10) REVERT: B 410 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 414 ASN cc_start: 0.8406 (m110) cc_final: 0.8061 (m110) REVERT: B 421 GLU cc_start: 0.8305 (tt0) cc_final: 0.8057 (tm-30) REVERT: C 3 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7205 (pm20) REVERT: C 123 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7602 (tpp80) REVERT: C 196 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: C 207 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 214 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.8205 (ttp-110) REVERT: C 280 LYS cc_start: 0.8928 (mttp) cc_final: 0.8382 (mmpt) REVERT: C 308 ARG cc_start: 0.6689 (tpt170) cc_final: 0.5693 (tpt170) REVERT: C 322 ASP cc_start: 0.8150 (t70) cc_final: 0.7907 (t0) REVERT: C 377 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8376 (ttp) REVERT: C 417 GLU cc_start: 0.7834 (mp0) cc_final: 0.7494 (mp0) REVERT: C 420 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7578 (mm-30) REVERT: C 423 GLU cc_start: 0.8050 (tp30) cc_final: 0.7837 (mm-30) REVERT: C 424 ASP cc_start: 0.8115 (t70) cc_final: 0.7883 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8479 (tt0) cc_final: 0.7810 (tm-30) REVERT: C 434 GLU cc_start: 0.8118 (pp20) cc_final: 0.7786 (pp20) REVERT: D 1 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8130 (ttp) REVERT: D 3 GLU cc_start: 0.8057 (mp0) cc_final: 0.7813 (mp0) REVERT: D 19 LYS cc_start: 0.8986 (tppp) cc_final: 0.8730 (tppp) REVERT: D 22 GLU cc_start: 0.8571 (tt0) cc_final: 0.8236 (tm-30) REVERT: D 45 GLU cc_start: 0.8427 (tt0) cc_final: 0.8036 (tm-30) REVERT: D 57 ASN cc_start: 0.7794 (t0) cc_final: 0.6781 (t0) REVERT: D 64 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9017 (mt) REVERT: D 69 GLU cc_start: 0.7370 (pm20) cc_final: 0.7048 (pm20) REVERT: D 88 ASP cc_start: 0.8273 (t70) cc_final: 0.7788 (t0) REVERT: D 92 PHE cc_start: 0.8639 (p90) cc_final: 0.8347 (p90) REVERT: D 103 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8717 (mtpm) REVERT: D 121 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8342 (mtm180) REVERT: D 123 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7930 (mm-30) REVERT: D 157 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7833 (pp20) REVERT: D 161 ASP cc_start: 0.8639 (p0) cc_final: 0.8281 (p0) REVERT: D 181 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7733 (mt-10) REVERT: D 190 HIS cc_start: 0.8053 (t-90) cc_final: 0.7657 (t70) REVERT: D 198 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8215 (mt-10) REVERT: D 203 ASP cc_start: 0.8131 (t0) cc_final: 0.7858 (t70) REVERT: D 251 ARG cc_start: 0.8742 (tpp-160) cc_final: 0.8344 (ttm110) REVERT: D 279 GLN cc_start: 0.8212 (pp30) cc_final: 0.7760 (tm130) REVERT: D 289 LEU cc_start: 0.8466 (mp) cc_final: 0.8256 (mp) REVERT: D 291 GLN cc_start: 0.8508 (pp30) cc_final: 0.8287 (pp30) REVERT: D 325 GLU cc_start: 0.8201 (tp30) cc_final: 0.7776 (tp30) REVERT: D 376 GLU cc_start: 0.7795 (mp0) cc_final: 0.7483 (mp0) REVERT: D 383 GLU cc_start: 0.8356 (tp30) cc_final: 0.8040 (tp30) REVERT: D 391 ARG cc_start: 0.8953 (mmm160) cc_final: 0.7314 (ptm160) REVERT: D 404 ASP cc_start: 0.8424 (m-30) cc_final: 0.7649 (m-30) REVERT: D 407 GLU cc_start: 0.8153 (mp0) cc_final: 0.7507 (mp0) REVERT: D 414 ASN cc_start: 0.7918 (p0) cc_final: 0.7714 (p0) REVERT: D 424 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: E 21 HIS cc_start: 0.8515 (OUTLIER) cc_final: 0.8056 (t70) REVERT: E 68 GLU cc_start: 0.8097 (tt0) cc_final: 0.7830 (tt0) REVERT: E 69 ASN cc_start: 0.8349 (t0) cc_final: 0.8016 (t0) REVERT: E 129 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 187 ASP cc_start: 0.8297 (t0) cc_final: 0.7660 (t0) REVERT: E 340 SER cc_start: 0.8078 (t) cc_final: 0.7720 (t) REVERT: E 444 MET cc_start: 0.8490 (mtm) cc_final: 0.8184 (ttm) REVERT: E 457 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7881 (mm-30) REVERT: E 478 ASN cc_start: 0.8422 (t0) cc_final: 0.7995 (t0) REVERT: E 556 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7620 (mm-30) REVERT: E 569 MET cc_start: 0.7709 (mtp) cc_final: 0.7451 (mtm) outliers start: 57 outliers final: 27 residues processed: 467 average time/residue: 0.6660 time to fit residues: 339.5598 Evaluate side-chains 456 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 421 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 349 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 375 VAL 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 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 21 HIS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 256 GLN A 342 GLN B 131 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN D 375 GLN ** D 414 ASN ** 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087516 restraints weight = 28692.153| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.89 r_work: 0.3153 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17885 Z= 0.164 Angle : 0.591 9.543 24321 Z= 0.301 Chirality : 0.045 0.157 2657 Planarity : 0.004 0.052 3175 Dihedral : 10.767 174.343 2519 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.09 % Allowed : 19.79 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 2208 helix: 1.44 (0.17), residues: 923 sheet: 0.34 (0.29), residues: 346 loop : -0.55 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 221 TYR 0.027 0.001 TYR B 340 PHE 0.029 0.002 PHE E 75 TRP 0.013 0.002 TRP C 21 HIS 0.008 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00382 (17882) covalent geometry : angle 0.59134 (24321) hydrogen bonds : bond 0.04003 ( 784) hydrogen bonds : angle 4.46587 ( 2268) metal coordination : bond 0.00500 ( 2) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 424 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 83 TYR cc_start: 0.8885 (m-80) cc_final: 0.8493 (m-80) REVERT: A 84 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7693 (mtm110) REVERT: A 116 ASP cc_start: 0.8132 (m-30) cc_final: 0.7622 (m-30) REVERT: A 117 LEU cc_start: 0.8337 (tp) cc_final: 0.7911 (tt) REVERT: A 120 ASP cc_start: 0.7992 (m-30) cc_final: 0.7691 (m-30) REVERT: A 154 MET cc_start: 0.8850 (mmm) cc_final: 0.8566 (mmp) REVERT: A 214 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8387 (ttp-110) REVERT: A 254 GLU cc_start: 0.5786 (mm-30) cc_final: 0.4133 (mm-30) REVERT: A 290 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 309 HIS cc_start: 0.8591 (m170) cc_final: 0.8331 (m170) REVERT: A 388 TRP cc_start: 0.8713 (m-10) cc_final: 0.8039 (m-10) REVERT: A 392 ASP cc_start: 0.8049 (m-30) cc_final: 0.7555 (m-30) REVERT: A 414 GLU cc_start: 0.8072 (mp0) cc_final: 0.7759 (mp0) REVERT: A 417 GLU cc_start: 0.7951 (tt0) cc_final: 0.7725 (mt-10) REVERT: A 420 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 423 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 53 GLU cc_start: 0.8217 (tt0) cc_final: 0.7718 (tm-30) REVERT: B 69 GLU cc_start: 0.8021 (pt0) cc_final: 0.7637 (pm20) REVERT: B 74 ASP cc_start: 0.8266 (t70) cc_final: 0.7980 (OUTLIER) REVERT: B 114 ASP cc_start: 0.8212 (m-30) cc_final: 0.7950 (m-30) REVERT: B 118 ASP cc_start: 0.7926 (m-30) cc_final: 0.7609 (m-30) REVERT: B 123 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7912 (tp30) REVERT: B 127 CYS cc_start: 0.7936 (m) cc_final: 0.7498 (m) REVERT: B 134 GLN cc_start: 0.8487 (mt0) cc_final: 0.8283 (pt0) REVERT: B 154 LYS cc_start: 0.8935 (mmtp) cc_final: 0.8457 (mtpp) REVERT: B 157 GLU cc_start: 0.8396 (tt0) cc_final: 0.7952 (tm-30) REVERT: B 158 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: B 174 LYS cc_start: 0.8668 (mmpt) cc_final: 0.8201 (mmpt) REVERT: B 175 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8736 (m) REVERT: B 216 LYS cc_start: 0.9044 (mmtm) cc_final: 0.8776 (mmmm) REVERT: B 274 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8638 (p) REVERT: B 278 SER cc_start: 0.8647 (m) cc_final: 0.8297 (p) REVERT: B 325 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: B 328 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7366 (OUTLIER) REVERT: B 380 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7950 (mtm180) REVERT: B 407 GLU cc_start: 0.8078 (tt0) cc_final: 0.7701 (mt-10) REVERT: B 410 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 414 ASN cc_start: 0.8434 (m110) cc_final: 0.8088 (m110) REVERT: C 3 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7162 (pm20) REVERT: C 123 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7595 (tpp80) REVERT: C 196 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: C 207 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7459 (mt-10) REVERT: C 214 ARG cc_start: 0.8557 (ttp-110) cc_final: 0.8261 (ttp-110) REVERT: C 280 LYS cc_start: 0.9018 (mttp) cc_final: 0.8490 (mmmt) REVERT: C 284 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8120 (mt-10) REVERT: C 290 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8369 (mm-30) REVERT: C 308 ARG cc_start: 0.6753 (tpt170) cc_final: 0.5745 (tpt170) REVERT: C 322 ASP cc_start: 0.8150 (t70) cc_final: 0.7911 (t0) REVERT: C 377 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8355 (ttp) REVERT: C 386 GLU cc_start: 0.7648 (mp0) cc_final: 0.7337 (mp0) REVERT: C 417 GLU cc_start: 0.7924 (mp0) cc_final: 0.7498 (mp0) REVERT: C 420 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7588 (mm-30) REVERT: C 423 GLU cc_start: 0.8063 (tp30) cc_final: 0.7848 (mm-30) REVERT: C 424 ASP cc_start: 0.8124 (t70) cc_final: 0.7876 (t0) REVERT: C 433 GLU cc_start: 0.8511 (tt0) cc_final: 0.7864 (tm-30) REVERT: C 434 GLU cc_start: 0.8101 (pp20) cc_final: 0.7754 (pp20) REVERT: D 1 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8170 (ttp) REVERT: D 3 GLU cc_start: 0.8013 (mp0) cc_final: 0.7731 (mp0) REVERT: D 22 GLU cc_start: 0.8564 (tt0) cc_final: 0.8239 (tm-30) REVERT: D 45 GLU cc_start: 0.8451 (tt0) cc_final: 0.8053 (tm-30) REVERT: D 57 ASN cc_start: 0.7840 (t0) cc_final: 0.6842 (t0) REVERT: D 64 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9027 (mt) REVERT: D 69 GLU cc_start: 0.7371 (pm20) cc_final: 0.7053 (pm20) REVERT: D 88 ASP cc_start: 0.8281 (t70) cc_final: 0.7796 (t0) REVERT: D 92 PHE cc_start: 0.8653 (p90) cc_final: 0.8374 (p90) REVERT: D 103 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8633 (mtpm) REVERT: D 108 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7870 (mp0) REVERT: D 121 ARG cc_start: 0.8619 (ttm110) cc_final: 0.8334 (mtm180) REVERT: D 157 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: D 161 ASP cc_start: 0.8605 (p0) cc_final: 0.8338 (p0) REVERT: D 181 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7760 (mt-10) REVERT: D 190 HIS cc_start: 0.8117 (t-90) cc_final: 0.7200 (t70) REVERT: D 203 ASP cc_start: 0.8109 (t0) cc_final: 0.7858 (t70) REVERT: D 251 ARG cc_start: 0.8754 (tpp-160) cc_final: 0.8377 (ttm110) REVERT: D 279 GLN cc_start: 0.8203 (pp30) cc_final: 0.7882 (tm130) REVERT: D 291 GLN cc_start: 0.8519 (pp30) cc_final: 0.8308 (pp30) REVERT: D 325 GLU cc_start: 0.8196 (tp30) cc_final: 0.7761 (tp30) REVERT: D 376 GLU cc_start: 0.7879 (mp0) cc_final: 0.7532 (mp0) REVERT: D 383 GLU cc_start: 0.8375 (tp30) cc_final: 0.8048 (tp30) REVERT: D 391 ARG cc_start: 0.8961 (mmm160) cc_final: 0.7336 (ptm160) REVERT: D 404 ASP cc_start: 0.8414 (m-30) cc_final: 0.7619 (m-30) REVERT: D 407 GLU cc_start: 0.8154 (mp0) cc_final: 0.7489 (mp0) REVERT: D 410 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7858 (tm-30) REVERT: D 417 ASP cc_start: 0.8451 (m-30) cc_final: 0.8248 (m-30) REVERT: D 424 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: E 21 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.8043 (t70) REVERT: E 68 GLU cc_start: 0.8111 (tt0) cc_final: 0.7858 (tt0) REVERT: E 69 ASN cc_start: 0.8337 (t0) cc_final: 0.7993 (t0) REVERT: E 104 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: E 129 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7656 (tm-30) REVERT: E 187 ASP cc_start: 0.8308 (t0) cc_final: 0.7654 (t0) REVERT: E 226 GLN cc_start: 0.8641 (mt0) cc_final: 0.8424 (mt0) REVERT: E 314 GLN cc_start: 0.8358 (mp10) cc_final: 0.8020 (mp10) REVERT: E 340 SER cc_start: 0.8108 (t) cc_final: 0.7756 (t) REVERT: E 440 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8137 (mpt-90) REVERT: E 444 MET cc_start: 0.8493 (mtm) cc_final: 0.8221 (mtm) REVERT: E 457 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7907 (mm-30) REVERT: E 478 ASN cc_start: 0.8412 (t0) cc_final: 0.7971 (t0) REVERT: E 556 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7621 (mm-30) REVERT: E 569 MET cc_start: 0.7714 (mtp) cc_final: 0.7489 (mtm) outliers start: 57 outliers final: 29 residues processed: 456 average time/residue: 0.6276 time to fit residues: 313.8083 Evaluate side-chains 455 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 415 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 221 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 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 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 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 21 HIS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 92 ILE 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 440 ARG Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 213 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 189 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 128 GLN B 131 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088008 restraints weight = 28722.860| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.90 r_work: 0.3158 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17885 Z= 0.147 Angle : 0.586 9.420 24321 Z= 0.298 Chirality : 0.044 0.169 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.684 175.595 2519 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.82 % Allowed : 20.07 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2208 helix: 1.47 (0.17), residues: 924 sheet: 0.32 (0.29), residues: 346 loop : -0.54 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 359 TYR 0.029 0.001 TYR B 340 PHE 0.031 0.002 PHE E 75 TRP 0.013 0.002 TRP C 21 HIS 0.011 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00342 (17882) covalent geometry : angle 0.58582 (24321) hydrogen bonds : bond 0.03860 ( 784) hydrogen bonds : angle 4.45310 ( 2268) metal coordination : bond 0.00428 ( 2) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 423 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 83 TYR cc_start: 0.8890 (m-80) cc_final: 0.8422 (m-80) REVERT: A 84 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7782 (mtm110) REVERT: A 116 ASP cc_start: 0.8132 (m-30) cc_final: 0.7660 (m-30) REVERT: A 117 LEU cc_start: 0.8317 (tp) cc_final: 0.7928 (tt) REVERT: A 120 ASP cc_start: 0.7997 (m-30) cc_final: 0.7748 (m-30) REVERT: A 154 MET cc_start: 0.8845 (mmm) cc_final: 0.8561 (mmp) REVERT: A 214 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8372 (ttp-110) REVERT: A 221 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.8237 (ptp90) REVERT: A 254 GLU cc_start: 0.5789 (mm-30) cc_final: 0.4106 (mm-30) REVERT: A 290 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 309 HIS cc_start: 0.8567 (m170) cc_final: 0.8311 (m170) REVERT: A 388 TRP cc_start: 0.8687 (m-10) cc_final: 0.8040 (m-10) REVERT: A 392 ASP cc_start: 0.8045 (m-30) cc_final: 0.7547 (m-30) REVERT: A 414 GLU cc_start: 0.8079 (mp0) cc_final: 0.7756 (mp0) REVERT: A 417 GLU cc_start: 0.7947 (tt0) cc_final: 0.7734 (mt-10) REVERT: A 420 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 423 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 36 TYR cc_start: 0.8713 (t80) cc_final: 0.8218 (t80) REVERT: B 53 GLU cc_start: 0.8225 (tt0) cc_final: 0.7678 (tm-30) REVERT: B 69 GLU cc_start: 0.7999 (pt0) cc_final: 0.7587 (pm20) REVERT: B 74 ASP cc_start: 0.8218 (t70) cc_final: 0.7946 (OUTLIER) REVERT: B 114 ASP cc_start: 0.8211 (m-30) cc_final: 0.7949 (m-30) REVERT: B 118 ASP cc_start: 0.7926 (m-30) cc_final: 0.7602 (m-30) REVERT: B 123 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7920 (tp30) REVERT: B 127 CYS cc_start: 0.7940 (m) cc_final: 0.7512 (m) REVERT: B 154 LYS cc_start: 0.8935 (mmtp) cc_final: 0.8470 (mtpp) REVERT: B 157 GLU cc_start: 0.8404 (tt0) cc_final: 0.7946 (tm-30) REVERT: B 158 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: B 174 LYS cc_start: 0.8696 (mmpt) cc_final: 0.8241 (mmpt) REVERT: B 175 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8717 (m) REVERT: B 213 ARG cc_start: 0.8879 (ptp-110) cc_final: 0.8621 (ptm160) REVERT: B 216 LYS cc_start: 0.9046 (mmtm) cc_final: 0.8774 (mmmm) REVERT: B 274 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8642 (p) REVERT: B 278 SER cc_start: 0.8639 (m) cc_final: 0.8286 (p) REVERT: B 325 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: B 328 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7375 (OUTLIER) REVERT: B 380 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7501 (mtm180) REVERT: B 383 GLU cc_start: 0.8000 (pp20) cc_final: 0.7610 (pp20) REVERT: B 407 GLU cc_start: 0.8043 (tt0) cc_final: 0.7735 (mt-10) REVERT: B 410 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 414 ASN cc_start: 0.8429 (m110) cc_final: 0.8199 (m110) REVERT: B 415 MET cc_start: 0.8509 (ttp) cc_final: 0.8256 (ttm) REVERT: B 421 GLU cc_start: 0.8253 (tt0) cc_final: 0.8006 (tm-30) REVERT: C 3 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7220 (pm20) REVERT: C 112 LYS cc_start: 0.8445 (pptt) cc_final: 0.8112 (pmtt) REVERT: C 123 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7617 (tpp80) REVERT: C 164 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8885 (mmmm) REVERT: C 196 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: C 207 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: C 214 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8263 (ttp-110) REVERT: C 280 LYS cc_start: 0.8994 (mttp) cc_final: 0.8507 (mmmt) REVERT: C 290 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8336 (mm-30) REVERT: C 308 ARG cc_start: 0.6748 (tpt170) cc_final: 0.5778 (tpt170) REVERT: C 322 ASP cc_start: 0.8135 (t70) cc_final: 0.7892 (t0) REVERT: C 377 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8367 (ttp) REVERT: C 417 GLU cc_start: 0.7903 (mp0) cc_final: 0.7483 (mp0) REVERT: C 420 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 424 ASP cc_start: 0.8128 (t70) cc_final: 0.7883 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8548 (tt0) cc_final: 0.7936 (tm-30) REVERT: C 434 GLU cc_start: 0.8065 (pp20) cc_final: 0.7744 (pp20) REVERT: D 1 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8170 (ttp) REVERT: D 3 GLU cc_start: 0.8027 (mp0) cc_final: 0.7743 (mp0) REVERT: D 22 GLU cc_start: 0.8577 (tt0) cc_final: 0.8288 (tm-30) REVERT: D 45 GLU cc_start: 0.8432 (tt0) cc_final: 0.8033 (tm-30) REVERT: D 57 ASN cc_start: 0.7899 (t0) cc_final: 0.6901 (t0) REVERT: D 64 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9043 (mt) REVERT: D 69 GLU cc_start: 0.7403 (pm20) cc_final: 0.7100 (pm20) REVERT: D 73 MET cc_start: 0.8823 (mpm) cc_final: 0.8588 (mmp) REVERT: D 88 ASP cc_start: 0.8278 (t70) cc_final: 0.7792 (t0) REVERT: D 92 PHE cc_start: 0.8675 (p90) cc_final: 0.8381 (p90) REVERT: D 103 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8636 (mtpm) REVERT: D 121 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8327 (mtm180) REVERT: D 157 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7871 (pp20) REVERT: D 161 ASP cc_start: 0.8612 (p0) cc_final: 0.8340 (p0) REVERT: D 181 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7798 (mt-10) REVERT: D 190 HIS cc_start: 0.7981 (t-90) cc_final: 0.6952 (t70) REVERT: D 203 ASP cc_start: 0.8102 (t0) cc_final: 0.7839 (t70) REVERT: D 251 ARG cc_start: 0.8758 (tpp-160) cc_final: 0.8381 (ttm110) REVERT: D 252 LYS cc_start: 0.8905 (tttt) cc_final: 0.8701 (ttmt) REVERT: D 279 GLN cc_start: 0.8217 (pp30) cc_final: 0.7859 (tm130) REVERT: D 291 GLN cc_start: 0.8504 (pp30) cc_final: 0.8291 (pp30) REVERT: D 318 ARG cc_start: 0.8935 (mmm-85) cc_final: 0.8726 (mmm-85) REVERT: D 325 GLU cc_start: 0.8213 (tp30) cc_final: 0.7790 (tp30) REVERT: D 376 GLU cc_start: 0.7875 (mp0) cc_final: 0.7501 (mp0) REVERT: D 383 GLU cc_start: 0.8367 (tp30) cc_final: 0.8049 (tp30) REVERT: D 391 ARG cc_start: 0.8968 (mmm160) cc_final: 0.7337 (ptm160) REVERT: D 404 ASP cc_start: 0.8411 (m-30) cc_final: 0.7647 (m-30) REVERT: D 407 GLU cc_start: 0.8150 (mp0) cc_final: 0.7527 (mp0) REVERT: D 410 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7807 (tm-30) REVERT: E 21 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8032 (t70) REVERT: E 68 GLU cc_start: 0.8123 (tt0) cc_final: 0.7858 (tt0) REVERT: E 69 ASN cc_start: 0.8353 (t0) cc_final: 0.8014 (t0) REVERT: E 104 GLN cc_start: 0.7697 (mt0) cc_final: 0.7158 (mt0) REVERT: E 129 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7689 (tm-30) REVERT: E 187 ASP cc_start: 0.8311 (t0) cc_final: 0.7663 (t0) REVERT: E 226 GLN cc_start: 0.8639 (mt0) cc_final: 0.8373 (mt0) REVERT: E 314 GLN cc_start: 0.8296 (mp10) cc_final: 0.7990 (mp10) REVERT: E 340 SER cc_start: 0.8087 (t) cc_final: 0.7732 (t) REVERT: E 440 ARG cc_start: 0.8363 (mpp80) cc_final: 0.7823 (mpp80) REVERT: E 444 MET cc_start: 0.8472 (mtm) cc_final: 0.8185 (mtm) REVERT: E 457 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7906 (mm-30) REVERT: E 478 ASN cc_start: 0.8387 (t0) cc_final: 0.7941 (t0) REVERT: E 556 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7605 (mm-30) outliers start: 52 outliers final: 32 residues processed: 452 average time/residue: 0.6551 time to fit residues: 324.0461 Evaluate side-chains 473 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 432 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 221 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 ARG 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 372 GLN Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 LEU 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 15 ASP Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 129 optimal weight: 0.7980 chunk 192 optimal weight: 0.0030 chunk 43 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 159 optimal weight: 0.0060 overall best weight: 0.4806 ------------------------------------------------------------------------------- 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** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088774 restraints weight = 28379.042| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.89 r_work: 0.3175 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17885 Z= 0.127 Angle : 0.592 9.507 24321 Z= 0.299 Chirality : 0.044 0.155 2657 Planarity : 0.004 0.048 3175 Dihedral : 10.564 179.558 2519 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.39 % Allowed : 21.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.18), residues: 2208 helix: 1.53 (0.18), residues: 922 sheet: 0.38 (0.29), residues: 350 loop : -0.56 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 221 TYR 0.021 0.001 TYR B 340 PHE 0.032 0.001 PHE E 75 TRP 0.013 0.001 TRP C 21 HIS 0.010 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00297 (17882) covalent geometry : angle 0.59164 (24321) hydrogen bonds : bond 0.03635 ( 784) hydrogen bonds : angle 4.39345 ( 2268) metal coordination : bond 0.00322 ( 2) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 437 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7655 (mt-10) REVERT: A 84 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7815 (mtm110) REVERT: A 116 ASP cc_start: 0.8117 (m-30) cc_final: 0.7652 (m-30) REVERT: A 117 LEU cc_start: 0.8256 (tp) cc_final: 0.7836 (tt) REVERT: A 120 ASP cc_start: 0.8039 (m-30) cc_final: 0.7747 (m-30) REVERT: A 121 ARG cc_start: 0.7983 (tpp-160) cc_final: 0.7636 (mmm-85) REVERT: A 154 MET cc_start: 0.8826 (mmm) cc_final: 0.8545 (mmp) REVERT: A 214 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8368 (ttp-110) REVERT: A 221 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.8201 (ptp90) REVERT: A 254 GLU cc_start: 0.5720 (mm-30) cc_final: 0.4036 (mm-30) REVERT: A 290 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8217 (mm-30) REVERT: A 309 HIS cc_start: 0.8582 (m170) cc_final: 0.8318 (m170) REVERT: A 326 LYS cc_start: 0.8527 (pttp) cc_final: 0.8177 (ptpt) REVERT: A 388 TRP cc_start: 0.8638 (m-10) cc_final: 0.8039 (m-10) REVERT: A 392 ASP cc_start: 0.8026 (m-30) cc_final: 0.7514 (m-30) REVERT: A 414 GLU cc_start: 0.8077 (mp0) cc_final: 0.7747 (mp0) REVERT: A 417 GLU cc_start: 0.7879 (tt0) cc_final: 0.7677 (mt-10) REVERT: A 420 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 423 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7904 (mm-30) REVERT: B 36 TYR cc_start: 0.8695 (t80) cc_final: 0.8214 (t80) REVERT: B 53 GLU cc_start: 0.8170 (tt0) cc_final: 0.7650 (tm-30) REVERT: B 69 GLU cc_start: 0.7979 (pt0) cc_final: 0.7601 (pm20) REVERT: B 74 ASP cc_start: 0.8204 (t70) cc_final: 0.7941 (OUTLIER) REVERT: B 76 VAL cc_start: 0.8854 (t) cc_final: 0.8640 (p) REVERT: B 84 ILE cc_start: 0.9032 (tt) cc_final: 0.8632 (pt) REVERT: B 114 ASP cc_start: 0.8229 (m-30) cc_final: 0.7919 (m-30) REVERT: B 118 ASP cc_start: 0.7921 (m-30) cc_final: 0.7565 (m-30) REVERT: B 123 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7930 (tp30) REVERT: B 127 CYS cc_start: 0.7914 (m) cc_final: 0.7492 (m) REVERT: B 154 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8626 (mtpp) REVERT: B 157 GLU cc_start: 0.8399 (tt0) cc_final: 0.7940 (tm-30) REVERT: B 174 LYS cc_start: 0.8703 (mmpt) cc_final: 0.8250 (mmpt) REVERT: B 175 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8734 (m) REVERT: B 216 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8767 (mmmm) REVERT: B 274 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8626 (p) REVERT: B 278 SER cc_start: 0.8655 (m) cc_final: 0.8302 (p) REVERT: B 325 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: B 328 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7372 (OUTLIER) REVERT: B 380 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7508 (mtm180) REVERT: B 383 GLU cc_start: 0.7972 (pp20) cc_final: 0.7582 (pp20) REVERT: B 407 GLU cc_start: 0.8058 (tt0) cc_final: 0.7601 (mt-10) REVERT: B 410 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7487 (mm-30) REVERT: B 414 ASN cc_start: 0.8456 (m110) cc_final: 0.8175 (m110) REVERT: C 3 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7230 (pm20) REVERT: C 112 LYS cc_start: 0.8430 (pptt) cc_final: 0.8083 (pmtt) REVERT: C 123 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7556 (tpp80) REVERT: C 196 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: C 207 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: C 214 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8201 (ttp-110) REVERT: C 280 LYS cc_start: 0.8989 (mttp) cc_final: 0.8480 (mmmt) REVERT: C 308 ARG cc_start: 0.6677 (tpt170) cc_final: 0.6149 (tpt170) REVERT: C 322 ASP cc_start: 0.8085 (t70) cc_final: 0.7832 (t0) REVERT: C 377 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8377 (ttp) REVERT: C 417 GLU cc_start: 0.7911 (mp0) cc_final: 0.7453 (mp0) REVERT: C 420 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7520 (mm-30) REVERT: C 423 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7693 (mm-30) REVERT: C 424 ASP cc_start: 0.8055 (t70) cc_final: 0.7811 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8522 (tt0) cc_final: 0.7917 (tm-30) REVERT: C 434 GLU cc_start: 0.8088 (pp20) cc_final: 0.7704 (pp20) REVERT: D 1 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8153 (ttp) REVERT: D 3 GLU cc_start: 0.8038 (mp0) cc_final: 0.7777 (mp0) REVERT: D 22 GLU cc_start: 0.8563 (tt0) cc_final: 0.8240 (tm-30) REVERT: D 45 GLU cc_start: 0.8432 (tt0) cc_final: 0.8016 (tm-30) REVERT: D 57 ASN cc_start: 0.7860 (t0) cc_final: 0.6869 (t0) REVERT: D 64 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9031 (mt) REVERT: D 69 GLU cc_start: 0.7399 (pm20) cc_final: 0.7124 (pm20) REVERT: D 74 ASP cc_start: 0.8076 (m-30) cc_final: 0.7842 (m-30) REVERT: D 88 ASP cc_start: 0.8221 (t70) cc_final: 0.7731 (t0) REVERT: D 92 PHE cc_start: 0.8667 (p90) cc_final: 0.8354 (p90) REVERT: D 103 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8620 (mtpm) REVERT: D 121 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8222 (mtm180) REVERT: D 157 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7865 (pp20) REVERT: D 161 ASP cc_start: 0.8537 (p0) cc_final: 0.8254 (p0) REVERT: D 181 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7796 (mt-10) REVERT: D 190 HIS cc_start: 0.7981 (t-90) cc_final: 0.6954 (t70) REVERT: D 203 ASP cc_start: 0.8076 (t0) cc_final: 0.7867 (t70) REVERT: D 251 ARG cc_start: 0.8741 (tpp-160) cc_final: 0.8358 (ttm110) REVERT: D 279 GLN cc_start: 0.8185 (pp30) cc_final: 0.7787 (tm130) REVERT: D 291 GLN cc_start: 0.8473 (pp30) cc_final: 0.8263 (pp30) REVERT: D 325 GLU cc_start: 0.8176 (tp30) cc_final: 0.7766 (tp30) REVERT: D 376 GLU cc_start: 0.7854 (mp0) cc_final: 0.7456 (mp0) REVERT: D 383 GLU cc_start: 0.8351 (tp30) cc_final: 0.8036 (tp30) REVERT: D 391 ARG cc_start: 0.8940 (mmm160) cc_final: 0.7314 (ptm160) REVERT: D 404 ASP cc_start: 0.8436 (m-30) cc_final: 0.7669 (m-30) REVERT: D 407 GLU cc_start: 0.8118 (mp0) cc_final: 0.7520 (mp0) REVERT: D 410 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7808 (tm-30) REVERT: D 417 ASP cc_start: 0.8440 (m-30) cc_final: 0.8228 (m-30) REVERT: E 68 GLU cc_start: 0.8127 (tt0) cc_final: 0.7863 (tt0) REVERT: E 69 ASN cc_start: 0.8342 (t0) cc_final: 0.7998 (t0) REVERT: E 104 GLN cc_start: 0.7720 (mt0) cc_final: 0.7295 (mt0) REVERT: E 129 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7671 (tm-30) REVERT: E 187 ASP cc_start: 0.8257 (t0) cc_final: 0.7600 (t0) REVERT: E 226 GLN cc_start: 0.8625 (mt0) cc_final: 0.8350 (mt0) REVERT: E 314 GLN cc_start: 0.8223 (mp10) cc_final: 0.7933 (mp10) REVERT: E 340 SER cc_start: 0.8115 (t) cc_final: 0.7770 (t) REVERT: E 440 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8018 (mpp80) REVERT: E 444 MET cc_start: 0.8434 (mtm) cc_final: 0.8131 (ttm) REVERT: E 457 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7903 (mm-30) REVERT: E 478 ASN cc_start: 0.8389 (t0) cc_final: 0.7941 (t0) REVERT: E 556 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7530 (mm-30) outliers start: 44 outliers final: 27 residues processed: 459 average time/residue: 0.7625 time to fit residues: 382.8241 Evaluate side-chains 453 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 419 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 349 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 255 PHE 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 157 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 440 ARG Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 102 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 176 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 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 35 GLN A 256 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 256 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.088205 restraints weight = 28596.436| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.89 r_work: 0.3164 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17885 Z= 0.151 Angle : 0.600 9.919 24321 Z= 0.303 Chirality : 0.044 0.190 2657 Planarity : 0.004 0.048 3175 Dihedral : 10.602 178.318 2519 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.39 % Allowed : 21.48 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.18), residues: 2208 helix: 1.49 (0.17), residues: 924 sheet: 0.36 (0.29), residues: 350 loop : -0.57 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 221 TYR 0.025 0.001 TYR D 36 PHE 0.034 0.002 PHE E 75 TRP 0.013 0.001 TRP C 21 HIS 0.010 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00352 (17882) covalent geometry : angle 0.60022 (24321) hydrogen bonds : bond 0.03839 ( 784) hydrogen bonds : angle 4.43166 ( 2268) metal coordination : bond 0.00433 ( 2) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7007.85 seconds wall clock time: 120 minutes 5.67 seconds (7205.67 seconds total)