Starting phenix.real_space_refine on Tue Aug 6 20:56:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4l_42972/08_2024/8v4l_42972.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4l_42972/08_2024/8v4l_42972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4l_42972/08_2024/8v4l_42972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4l_42972/08_2024/8v4l_42972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4l_42972/08_2024/8v4l_42972.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4l_42972/08_2024/8v4l_42972.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 12 5.49 5 Mg 4 5.21 5 S 117 5.16 5 C 11002 2.51 5 N 3007 2.21 5 O 3320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "C ARG 2": "NH1" <-> "NH2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17463 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3373 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3345 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3363 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3303 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3908 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 35, 'TRANS': 465} Chain breaks: 3 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 14, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 115 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.81, per 1000 atoms: 0.68 Number of scatterers: 17463 At special positions: 0 Unit cell: (134.46, 124.5, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 117 16.00 P 12 15.00 Mg 4 11.99 O 3320 8.00 N 3007 7.00 C 11002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 434 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 252 " 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4146 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 14 sheets defined 48.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.946A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.891A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.718A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.902A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.986A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.718A pdb=" N GLU A 284 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.683A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.545A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.910A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.027A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.126A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.235A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.562A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.879A pdb=" N ILE B 84 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 85' Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.755A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.883A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.525A pdb=" N VAL B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 176 " --> pdb=" O PRO B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.284A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.893A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.545A pdb=" N ARG B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.557A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 299' Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.633A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.541A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.872A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.135A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.961A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.931A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.008A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 85 removed outlier: 4.614A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 127 removed outlier: 4.267A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.479A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.528A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.760A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.988A pdb=" N TYR C 282 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.786A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.550A pdb=" N GLY C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.818A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.999A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.902A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 435 removed outlier: 4.169A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.038A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.587A pdb=" N SER D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.877A pdb=" N GLU D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.640A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.903A pdb=" N SER D 176 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.577A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.856A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.720A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.682A pdb=" N ASN D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 299 " --> pdb=" O ALA D 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 295 through 299' Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.656A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.568A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.900A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.037A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 425 removed outlier: 3.837A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 104 removed outlier: 3.741A pdb=" N GLN E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 256 through 270 removed outlier: 4.023A pdb=" N PHE E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.541A pdb=" N GLN E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 340 removed outlier: 3.543A pdb=" N SER E 340 " --> pdb=" O HIS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 467 removed outlier: 4.558A pdb=" N TYR E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Proline residue: E 462 - end of helix Processing helix chain 'E' and resid 480 through 485 Processing helix chain 'E' and resid 494 through 497 removed outlier: 3.638A pdb=" N GLY E 497 " --> pdb=" O SER E 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 494 through 497' Processing helix chain 'E' and resid 498 through 508 Processing helix chain 'E' and resid 551 through 570 removed outlier: 3.555A pdb=" N MET E 569 " --> pdb=" O ALA E 565 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.930A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.559A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.255A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.708A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.940A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU C 3 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU C 136 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 5 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N SER C 140 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL C 9 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.077A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.552A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.532A pdb=" N ARG E 111 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR E 112 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG E 118 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.463A pdb=" N TYR E 52 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASN E 91 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE E 54 " --> pdb=" O ASN E 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 189 through 198 removed outlier: 7.160A pdb=" N VAL E 205 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE E 245 " --> pdb=" O LYS E 287 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE E 289 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 247 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR E 429 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 216 through 220 removed outlier: 5.236A pdb=" N ARG E 238 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 7.26 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: 97.83 - 105.15: 410 105.15 - 112.48: 8413 112.48 - 119.80: 7106 119.80 - 127.13: 8156 127.13 - 134.45: 236 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: 1.38 - 2.09: 1 2.09 - 2.79: 3982 2.79 - 3.49: 23178 3.49 - 4.20: 43550 4.20 - 4.90: 77416 Nonbonded interactions: 148127 Sorted by model distance: nonbonded pdb=" CD GLU B 503 " pdb=" N GLU B1001 " model vdw 1.385 3.350 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=" OE1 GLU B 503 " pdb=" N GLU B1001 " model vdw 2.288 3.120 ... (remaining 148122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 325 or (resid 326 and (name N or \ name CA or name C or name O or name CB )) or resid 327 through 413 or (resid 41 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 415 through \ 439 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 439 or resid 501 throu \ gh 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 281 or (resid 282 through 284 an \ d (name N or name CA or name C or name O or name CB )) or resid 285 through 287 \ or (resid 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 through 327 or (resid 328 and (name N or name CA or name C or name O or name \ CB )) or resid 329 through 360 or (resid 361 through 362 and (name N or name CA \ or name C or name O or name CB )) or resid 363 through 389 or (resid 390 and (n \ ame N or name CA or name C or name O or name CB )) or resid 391 through 428 or r \ esid 601 through 602)) selection = (chain 'D' and (resid 1 through 278 or (resid 279 and (name N or name CA or name \ C or name O or name CB )) or resid 280 through 428 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 21.080 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: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 53.250 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 17882 Z= 0.426 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 : 1.385 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 2208 helix: -1.63 (0.13), residues: 892 sheet: 0.34 (0.28), residues: 358 loop : -1.12 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 344 HIS 0.009 0.002 HIS A 197 PHE 0.031 0.003 PHE C 255 TYR 0.044 0.003 TYR A 432 ARG 0.014 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 595 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7935 (p90) cc_final: 0.7520 (p90) REVERT: A 55 GLU cc_start: 0.7832 (tt0) cc_final: 0.7231 (tm-30) REVERT: A 83 TYR cc_start: 0.8300 (m-80) cc_final: 0.8035 (m-80) REVERT: A 110 ILE cc_start: 0.8283 (mm) cc_final: 0.8027 (mp) REVERT: A 117 LEU cc_start: 0.6935 (tp) cc_final: 0.6573 (tt) REVERT: A 120 ASP cc_start: 0.7308 (m-30) cc_final: 0.6875 (m-30) REVERT: A 124 LYS cc_start: 0.7498 (mttt) cc_final: 0.7247 (mtmm) REVERT: A 133 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8134 (mm-40) REVERT: A 158 SER cc_start: 0.8720 (t) cc_final: 0.8504 (t) REVERT: A 166 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8106 (mtmm) REVERT: A 199 ASP cc_start: 0.7346 (m-30) cc_final: 0.7124 (m-30) REVERT: A 256 GLN cc_start: 0.7629 (mt0) cc_final: 0.5913 (tm-30) REVERT: A 282 TYR cc_start: 0.8338 (m-80) cc_final: 0.8050 (m-80) REVERT: A 284 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7508 (mt-10) REVERT: A 290 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7318 (mt-10) REVERT: A 304 LYS cc_start: 0.8368 (tptp) cc_final: 0.7918 (ttmt) REVERT: A 322 ASP cc_start: 0.7715 (t0) cc_final: 0.7454 (t0) REVERT: A 324 VAL cc_start: 0.8081 (m) cc_final: 0.7158 (t) REVERT: A 326 LYS cc_start: 0.7735 (pttp) cc_final: 0.7226 (ptpt) REVERT: A 345 ASP cc_start: 0.8340 (p0) cc_final: 0.8121 (p0) REVERT: A 367 ASP cc_start: 0.7728 (p0) cc_final: 0.7280 (p0) REVERT: A 370 LYS cc_start: 0.8373 (tptt) cc_final: 0.8049 (tptt) REVERT: A 388 TRP cc_start: 0.7973 (m-10) cc_final: 0.7721 (m-10) REVERT: A 414 GLU cc_start: 0.7641 (mp0) cc_final: 0.7010 (pm20) REVERT: A 420 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 423 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 434 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7164 (pp20) REVERT: B 19 LYS cc_start: 0.8588 (tptm) cc_final: 0.8263 (tppp) REVERT: B 41 ASP cc_start: 0.8431 (m-30) cc_final: 0.8052 (t0) REVERT: B 48 ASN cc_start: 0.8256 (p0) cc_final: 0.7948 (p0) REVERT: B 53 GLU cc_start: 0.7832 (tt0) cc_final: 0.7531 (pm20) REVERT: B 58 LYS cc_start: 0.7195 (tttt) cc_final: 0.6973 (tttt) REVERT: B 69 GLU cc_start: 0.7732 (tt0) cc_final: 0.7333 (pt0) REVERT: B 103 LYS cc_start: 0.8556 (ttmm) cc_final: 0.7884 (ttmm) REVERT: B 107 THR cc_start: 0.8042 (m) cc_final: 0.7606 (p) REVERT: B 118 ASP cc_start: 0.7409 (m-30) cc_final: 0.6977 (m-30) REVERT: B 123 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7342 (tp30) REVERT: B 127 CYS cc_start: 0.6983 (m) cc_final: 0.6301 (m) REVERT: B 134 GLN cc_start: 0.7990 (mt0) cc_final: 0.7624 (mt0) REVERT: B 164 MET cc_start: 0.8599 (tpp) cc_final: 0.8345 (tpt) REVERT: B 174 LYS cc_start: 0.8377 (mmpt) cc_final: 0.7911 (mmpt) REVERT: B 191 GLN cc_start: 0.8032 (mm110) cc_final: 0.7767 (mp-120) REVERT: B 201 CYS cc_start: 0.8634 (m) cc_final: 0.8282 (m) REVERT: B 203 ASP cc_start: 0.8218 (t70) cc_final: 0.7641 (t0) REVERT: B 205 GLU cc_start: 0.7850 (tt0) cc_final: 0.7629 (tt0) REVERT: B 216 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8187 (mmmm) REVERT: B 252 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8191 (ttpt) REVERT: B 278 SER cc_start: 0.8408 (m) cc_final: 0.7674 (p) REVERT: B 289 LEU cc_start: 0.7435 (mt) cc_final: 0.7127 (mp) REVERT: B 291 GLN cc_start: 0.8152 (pp30) cc_final: 0.7946 (pp30) REVERT: B 309 ARG cc_start: 0.7216 (mtt-85) cc_final: 0.6999 (mtt-85) REVERT: B 328 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6853 (tp30) REVERT: B 361 LEU cc_start: 0.8147 (tp) cc_final: 0.7878 (tt) REVERT: B 362 LYS cc_start: 0.8192 (tttp) cc_final: 0.7944 (tttp) REVERT: B 380 ARG cc_start: 0.7563 (mtt90) cc_final: 0.7064 (mtm-85) REVERT: B 390 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7483 (ptp90) REVERT: B 407 GLU cc_start: 0.7863 (tt0) cc_final: 0.7506 (mt-10) REVERT: B 410 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7083 (mm-30) REVERT: B 412 GLU cc_start: 0.7800 (tp30) cc_final: 0.7527 (tp30) REVERT: B 414 ASN cc_start: 0.7425 (m110) cc_final: 0.7028 (m110) REVERT: B 417 ASP cc_start: 0.7524 (m-30) cc_final: 0.7201 (m-30) REVERT: B 421 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 3 GLU cc_start: 0.7415 (mp0) cc_final: 0.6179 (mp0) REVERT: C 60 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7528 (ttmm) REVERT: C 71 GLU cc_start: 0.7007 (pt0) cc_final: 0.6546 (pm20) REVERT: C 90 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8020 (tp30) REVERT: C 91 GLN cc_start: 0.7991 (mt0) cc_final: 0.7740 (mt0) REVERT: C 112 LYS cc_start: 0.7987 (pttp) cc_final: 0.7777 (pttp) REVERT: C 116 ASP cc_start: 0.7479 (p0) cc_final: 0.7219 (p0) REVERT: C 117 LEU cc_start: 0.7839 (tp) cc_final: 0.7599 (tt) REVERT: C 120 ASP cc_start: 0.7648 (m-30) cc_final: 0.7410 (m-30) REVERT: C 123 ARG cc_start: 0.7347 (tpp-160) cc_final: 0.7016 (tpp80) REVERT: C 155 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7440 (tp30) REVERT: C 158 SER cc_start: 0.8658 (t) cc_final: 0.8435 (t) REVERT: C 245 ASP cc_start: 0.8008 (p0) cc_final: 0.7584 (p0) REVERT: C 280 LYS cc_start: 0.8397 (mttp) cc_final: 0.7314 (mmtt) REVERT: C 308 ARG cc_start: 0.5105 (tpt170) cc_final: 0.3968 (mpp80) REVERT: C 322 ASP cc_start: 0.8028 (t70) cc_final: 0.7708 (t70) REVERT: C 386 GLU cc_start: 0.7714 (mp0) cc_final: 0.6990 (mp0) REVERT: C 411 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7869 (mm-30) REVERT: C 420 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7227 (mp0) REVERT: C 424 ASP cc_start: 0.7723 (m-30) cc_final: 0.7496 (t70) REVERT: C 429 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7803 (mt-10) REVERT: C 433 GLU cc_start: 0.7735 (pt0) cc_final: 0.7062 (tp30) REVERT: C 434 GLU cc_start: 0.7698 (pp20) cc_final: 0.7339 (pp20) REVERT: D 3 GLU cc_start: 0.7571 (mp0) cc_final: 0.6658 (mp0) REVERT: D 19 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8126 (tppp) REVERT: D 22 GLU cc_start: 0.8359 (tt0) cc_final: 0.7403 (tp30) REVERT: D 45 GLU cc_start: 0.8643 (tt0) cc_final: 0.7891 (tm-30) REVERT: D 58 LYS cc_start: 0.8056 (tttt) cc_final: 0.7346 (tttt) REVERT: D 69 GLU cc_start: 0.7568 (pp20) cc_final: 0.7221 (pm20) REVERT: D 88 ASP cc_start: 0.8394 (t70) cc_final: 0.7879 (t0) REVERT: D 108 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 121 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7537 (mtm-85) REVERT: D 123 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7721 (mm-30) REVERT: D 158 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7542 (mm-30) REVERT: D 159 TYR cc_start: 0.7792 (m-80) cc_final: 0.7322 (m-80) REVERT: D 174 LYS cc_start: 0.8346 (mptt) cc_final: 0.8080 (mptt) REVERT: D 175 VAL cc_start: 0.8429 (m) cc_final: 0.7537 (t) REVERT: D 181 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7399 (mt-10) REVERT: D 198 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7962 (mt-10) REVERT: D 203 ASP cc_start: 0.8200 (t0) cc_final: 0.7166 (t70) REVERT: D 205 GLU cc_start: 0.7943 (tt0) cc_final: 0.7386 (mp0) REVERT: D 209 ASP cc_start: 0.7469 (t0) cc_final: 0.7225 (t0) REVERT: D 213 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7887 (mtm-85) REVERT: D 216 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8513 (mmmm) REVERT: D 221 THR cc_start: 0.8638 (p) cc_final: 0.8429 (t) REVERT: D 281 TYR cc_start: 0.7968 (m-80) cc_final: 0.7715 (m-80) REVERT: D 291 GLN cc_start: 0.8104 (pp30) cc_final: 0.7811 (pp30) REVERT: D 325 GLU cc_start: 0.7952 (tp30) cc_final: 0.7508 (tp30) REVERT: D 383 GLU cc_start: 0.8032 (tp30) cc_final: 0.7417 (tp30) REVERT: D 391 ARG cc_start: 0.8335 (mmm160) cc_final: 0.6666 (ptm-80) REVERT: D 404 ASP cc_start: 0.8422 (m-30) cc_final: 0.7705 (m-30) REVERT: D 405 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8085 (tm-30) REVERT: D 407 GLU cc_start: 0.7766 (mp0) cc_final: 0.7106 (mp0) REVERT: D 410 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7433 (tm-30) REVERT: D 417 ASP cc_start: 0.8025 (m-30) cc_final: 0.7785 (m-30) REVERT: D 424 GLN cc_start: 0.8119 (tt0) cc_final: 0.7878 (tt0) REVERT: E 9 LEU cc_start: 0.7928 (tt) cc_final: 0.7480 (tm) REVERT: E 53 GLU cc_start: 0.6580 (mp0) cc_final: 0.6327 (mp0) REVERT: E 69 ASN cc_start: 0.7998 (t0) cc_final: 0.7388 (t0) REVERT: E 93 MET cc_start: 0.8118 (mmp) cc_final: 0.7704 (mmm) REVERT: E 104 GLN cc_start: 0.7333 (mt0) cc_final: 0.7058 (mt0) REVERT: E 120 GLU cc_start: 0.7517 (mp0) cc_final: 0.6947 (mp0) REVERT: E 129 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6812 (tm-30) REVERT: E 187 ASP cc_start: 0.8121 (t0) cc_final: 0.7510 (t0) REVERT: E 193 ARG cc_start: 0.7972 (ttt-90) cc_final: 0.7503 (ttt-90) REVERT: E 278 GLN cc_start: 0.8242 (mt0) cc_final: 0.7984 (mt0) REVERT: E 311 LEU cc_start: 0.7379 (mt) cc_final: 0.7174 (mp) REVERT: E 322 LEU cc_start: 0.8313 (mp) cc_final: 0.8102 (mp) REVERT: E 340 SER cc_start: 0.7772 (t) cc_final: 0.7550 (t) REVERT: E 458 ASN cc_start: 0.8596 (t0) cc_final: 0.8374 (t0) REVERT: E 473 ASP cc_start: 0.7613 (p0) cc_final: 0.7371 (p0) REVERT: E 478 ASN cc_start: 0.7546 (t0) cc_final: 0.7167 (t0) REVERT: E 534 ASP cc_start: 0.7943 (p0) cc_final: 0.7556 (p0) REVERT: E 550 TYR cc_start: 0.8562 (m-80) cc_final: 0.8073 (m-10) REVERT: E 578 ILE cc_start: 0.7834 (tp) cc_final: 0.7534 (tt) outliers start: 1 outliers final: 1 residues processed: 596 average time/residue: 1.4461 time to fit residues: 948.1699 Evaluate side-chains 466 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 465 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 6.9990 chunk 167 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 173 optimal weight: 0.3980 chunk 67 optimal weight: 0.1980 chunk 105 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 35 GLN A 176 GLN A 285 GLN B 227 HIS B 280 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 292 GLN ** D 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17882 Z= 0.185 Angle : 0.583 9.332 24321 Z= 0.301 Chirality : 0.044 0.179 2657 Planarity : 0.005 0.060 3175 Dihedral : 10.612 142.109 2522 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.49 % Allowed : 12.69 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2208 helix: 0.08 (0.16), residues: 921 sheet: 0.42 (0.27), residues: 368 loop : -0.81 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 592 HIS 0.010 0.001 HIS D 190 PHE 0.025 0.001 PHE A 255 TYR 0.012 0.001 TYR A 172 ARG 0.009 0.001 ARG E 80 *********************** 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 522 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 476 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7921 (p90) cc_final: 0.7526 (p90) REVERT: A 50 ASN cc_start: 0.8147 (t0) cc_final: 0.7636 (t0) REVERT: A 83 TYR cc_start: 0.8349 (m-80) cc_final: 0.7989 (m-80) REVERT: A 116 ASP cc_start: 0.7570 (m-30) cc_final: 0.6855 (p0) REVERT: A 117 LEU cc_start: 0.7350 (tp) cc_final: 0.7010 (tt) REVERT: A 120 ASP cc_start: 0.7329 (m-30) cc_final: 0.6999 (m-30) REVERT: A 154 MET cc_start: 0.8254 (mmm) cc_final: 0.8013 (mmp) REVERT: A 245 ASP cc_start: 0.7523 (p0) cc_final: 0.7305 (p0) REVERT: A 254 GLU cc_start: 0.7308 (tt0) cc_final: 0.7091 (mm-30) REVERT: A 284 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7529 (mt-10) REVERT: A 290 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 322 ASP cc_start: 0.7843 (t0) cc_final: 0.7548 (p0) REVERT: A 367 ASP cc_start: 0.7862 (p0) cc_final: 0.7413 (p0) REVERT: A 370 LYS cc_start: 0.8449 (tptt) cc_final: 0.8076 (tptt) REVERT: A 414 GLU cc_start: 0.7735 (mp0) cc_final: 0.7263 (pm20) REVERT: A 417 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7488 (tt0) REVERT: A 420 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 423 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7429 (mm-30) REVERT: A 433 GLU cc_start: 0.7554 (pt0) cc_final: 0.7329 (pt0) REVERT: A 434 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7315 (tm-30) REVERT: B 19 LYS cc_start: 0.8588 (tptm) cc_final: 0.8026 (tppp) REVERT: B 48 ASN cc_start: 0.8304 (p0) cc_final: 0.8051 (p0) REVERT: B 53 GLU cc_start: 0.7945 (tt0) cc_final: 0.7524 (pm20) REVERT: B 58 LYS cc_start: 0.7243 (tttt) cc_final: 0.7034 (tttt) REVERT: B 69 GLU cc_start: 0.7774 (tt0) cc_final: 0.7291 (pm20) REVERT: B 81 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7178 (t80) REVERT: B 94 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8318 (mp-120) REVERT: B 103 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7884 (mtpm) REVERT: B 118 ASP cc_start: 0.7382 (m-30) cc_final: 0.7126 (m-30) REVERT: B 122 LYS cc_start: 0.7680 (ttpt) cc_final: 0.7468 (ttpt) REVERT: B 123 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7328 (tp30) REVERT: B 127 CYS cc_start: 0.7119 (m) cc_final: 0.6433 (m) REVERT: B 134 GLN cc_start: 0.8080 (mt0) cc_final: 0.7729 (mt0) REVERT: B 158 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: B 164 MET cc_start: 0.8579 (tpp) cc_final: 0.8296 (tpt) REVERT: B 174 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8021 (mmpt) REVERT: B 203 ASP cc_start: 0.7986 (t70) cc_final: 0.7208 (t0) REVERT: B 216 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8205 (mmmm) REVERT: B 252 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8124 (ttpt) REVERT: B 278 SER cc_start: 0.8099 (m) cc_final: 0.7548 (p) REVERT: B 291 GLN cc_start: 0.8161 (pp30) cc_final: 0.7791 (pp30) REVERT: B 309 ARG cc_start: 0.7177 (mtt-85) cc_final: 0.6919 (mtt-85) REVERT: B 324 LYS cc_start: 0.7877 (tptm) cc_final: 0.7428 (tppp) REVERT: B 328 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6798 (tp30) REVERT: B 362 LYS cc_start: 0.8305 (tttp) cc_final: 0.8015 (tttp) REVERT: B 391 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.6881 (mtp-110) REVERT: B 407 GLU cc_start: 0.7888 (tt0) cc_final: 0.7456 (mt-10) REVERT: B 410 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7068 (mm-30) REVERT: B 412 GLU cc_start: 0.7701 (tp30) cc_final: 0.7168 (tp30) REVERT: B 414 ASN cc_start: 0.7445 (m110) cc_final: 0.7012 (m110) REVERT: B 417 ASP cc_start: 0.7605 (m-30) cc_final: 0.7018 (m-30) REVERT: B 421 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6956 (mt-10) REVERT: C 3 GLU cc_start: 0.7186 (mp0) cc_final: 0.6894 (mt-10) REVERT: C 50 ASN cc_start: 0.8346 (t0) cc_final: 0.8022 (t0) REVERT: C 82 THR cc_start: 0.9105 (m) cc_final: 0.8857 (p) REVERT: C 90 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7968 (tp30) REVERT: C 91 GLN cc_start: 0.8035 (mt0) cc_final: 0.7823 (mt0) REVERT: C 112 LYS cc_start: 0.7973 (pttp) cc_final: 0.7601 (pttm) REVERT: C 116 ASP cc_start: 0.7625 (p0) cc_final: 0.7403 (p0) REVERT: C 123 ARG cc_start: 0.7393 (tpp-160) cc_final: 0.7035 (tpp80) REVERT: C 158 SER cc_start: 0.8604 (t) cc_final: 0.8350 (t) REVERT: C 211 ASP cc_start: 0.7783 (m-30) cc_final: 0.7413 (p0) REVERT: C 280 LYS cc_start: 0.8486 (mttp) cc_final: 0.6748 (mmtt) REVERT: C 284 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6631 (mp0) REVERT: C 297 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7889 (mm-30) REVERT: C 322 ASP cc_start: 0.8149 (t70) cc_final: 0.7768 (t0) REVERT: C 337 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8241 (p) REVERT: C 370 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8174 (tmmt) REVERT: C 377 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8376 (tpp) REVERT: C 386 GLU cc_start: 0.7649 (mp0) cc_final: 0.7167 (mp0) REVERT: C 392 ASP cc_start: 0.7715 (m-30) cc_final: 0.7505 (m-30) REVERT: C 411 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8091 (mm-30) REVERT: C 423 GLU cc_start: 0.7684 (tp30) cc_final: 0.7202 (mm-30) REVERT: C 424 ASP cc_start: 0.7618 (m-30) cc_final: 0.7417 (t70) REVERT: D 3 GLU cc_start: 0.7820 (mp0) cc_final: 0.6777 (mp0) REVERT: D 19 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8143 (tppp) REVERT: D 22 GLU cc_start: 0.8400 (tt0) cc_final: 0.7553 (tp30) REVERT: D 41 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7755 (p0) REVERT: D 45 GLU cc_start: 0.8579 (tt0) cc_final: 0.7799 (tm-30) REVERT: D 58 LYS cc_start: 0.8154 (tttt) cc_final: 0.7838 (ttmm) REVERT: D 69 GLU cc_start: 0.7551 (pp20) cc_final: 0.7304 (pm20) REVERT: D 88 ASP cc_start: 0.8422 (t70) cc_final: 0.7900 (t0) REVERT: D 95 SER cc_start: 0.7866 (t) cc_final: 0.7572 (p) REVERT: D 103 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8205 (mtpm) REVERT: D 123 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7523 (mm-30) REVERT: D 157 GLU cc_start: 0.7684 (pt0) cc_final: 0.7460 (pp20) REVERT: D 158 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7571 (mm-30) REVERT: D 159 TYR cc_start: 0.8122 (m-80) cc_final: 0.7725 (m-80) REVERT: D 161 ASP cc_start: 0.8221 (p0) cc_final: 0.7961 (p0) REVERT: D 174 LYS cc_start: 0.8481 (mptt) cc_final: 0.8093 (mptt) REVERT: D 181 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7347 (mt-10) REVERT: D 198 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8040 (mt-10) REVERT: D 203 ASP cc_start: 0.8185 (t0) cc_final: 0.7421 (t70) REVERT: D 213 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7981 (mtm180) REVERT: D 216 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8584 (mmmm) REVERT: D 221 THR cc_start: 0.8592 (p) cc_final: 0.8386 (t) REVERT: D 257 MET cc_start: 0.8210 (mmm) cc_final: 0.7937 (mtp) REVERT: D 262 ARG cc_start: 0.8827 (mtm180) cc_final: 0.8582 (mtm180) REVERT: D 291 GLN cc_start: 0.8283 (pp30) cc_final: 0.8003 (pp30) REVERT: D 323 MET cc_start: 0.8061 (mmm) cc_final: 0.7827 (mmm) REVERT: D 325 GLU cc_start: 0.8147 (tp30) cc_final: 0.7607 (tp30) REVERT: D 383 GLU cc_start: 0.7997 (tp30) cc_final: 0.7427 (tp30) REVERT: D 391 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7358 (mtm180) REVERT: D 404 ASP cc_start: 0.8413 (m-30) cc_final: 0.7486 (m-30) REVERT: D 407 GLU cc_start: 0.7695 (mp0) cc_final: 0.7035 (mp0) REVERT: D 410 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7196 (tm-30) REVERT: D 412 GLU cc_start: 0.7964 (tp30) cc_final: 0.7603 (mm-30) REVERT: D 413 SER cc_start: 0.7732 (t) cc_final: 0.7062 (p) REVERT: D 417 ASP cc_start: 0.8076 (m-30) cc_final: 0.7813 (m-30) REVERT: E 9 LEU cc_start: 0.7779 (tt) cc_final: 0.7463 (tm) REVERT: E 69 ASN cc_start: 0.8088 (t0) cc_final: 0.7372 (t0) REVERT: E 95 MET cc_start: 0.7828 (mtp) cc_final: 0.7575 (mtm) REVERT: E 98 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7200 (mp10) REVERT: E 120 GLU cc_start: 0.7280 (mp0) cc_final: 0.6837 (mp0) REVERT: E 129 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6787 (tm-30) REVERT: E 187 ASP cc_start: 0.8212 (t0) cc_final: 0.7516 (t0) REVERT: E 278 GLN cc_start: 0.8148 (mt0) cc_final: 0.7883 (mt0) REVERT: E 291 MET cc_start: 0.8660 (mtm) cc_final: 0.8234 (mtm) REVERT: E 340 SER cc_start: 0.7768 (t) cc_final: 0.7557 (t) REVERT: E 439 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7534 (ttpp) REVERT: E 444 MET cc_start: 0.8140 (mtp) cc_final: 0.7886 (mtm) REVERT: E 457 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7747 (mm-30) REVERT: E 478 ASN cc_start: 0.7739 (t0) cc_final: 0.7274 (t0) REVERT: E 519 TYR cc_start: 0.8568 (m-80) cc_final: 0.8351 (m-10) REVERT: E 534 ASP cc_start: 0.7977 (p0) cc_final: 0.7750 (p0) REVERT: E 550 TYR cc_start: 0.8512 (m-80) cc_final: 0.8121 (m-10) REVERT: E 578 ILE cc_start: 0.7781 (tp) cc_final: 0.7552 (tt) REVERT: E 593 MET cc_start: 0.7536 (tpt) cc_final: 0.7150 (tpp) outliers start: 46 outliers final: 14 residues processed: 496 average time/residue: 1.5492 time to fit residues: 840.6137 Evaluate side-chains 464 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 444 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 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 41 ASP Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 533 HIS Chi-restraints excluded: chain E residue 584 SER Chi-restraints excluded: chain E residue 597 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN B 190 HIS B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 356 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 170 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17882 Z= 0.242 Angle : 0.575 7.792 24321 Z= 0.295 Chirality : 0.045 0.168 2657 Planarity : 0.005 0.052 3175 Dihedral : 10.627 166.197 2519 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.04 % Allowed : 14.86 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2208 helix: 0.77 (0.17), residues: 921 sheet: 0.45 (0.28), residues: 351 loop : -0.62 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 21 HIS 0.010 0.001 HIS D 190 PHE 0.021 0.002 PHE E 75 TYR 0.018 0.001 TYR C 432 ARG 0.009 0.001 ARG E 590 *********************** 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 526 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 470 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7866 (tt0) cc_final: 0.7357 (tp30) REVERT: A 83 TYR cc_start: 0.8472 (m-80) cc_final: 0.8040 (m-80) REVERT: A 114 ILE cc_start: 0.7182 (pt) cc_final: 0.6945 (pp) REVERT: A 116 ASP cc_start: 0.7770 (m-30) cc_final: 0.7022 (p0) REVERT: A 117 LEU cc_start: 0.7467 (tp) cc_final: 0.7000 (tt) REVERT: A 120 ASP cc_start: 0.7450 (m-30) cc_final: 0.7071 (m-30) REVERT: A 154 MET cc_start: 0.8232 (mmm) cc_final: 0.8001 (mmp) REVERT: A 214 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7538 (ttp-110) REVERT: A 241 SER cc_start: 0.8870 (m) cc_final: 0.8534 (t) REVERT: A 245 ASP cc_start: 0.7659 (p0) cc_final: 0.7377 (p0) REVERT: A 254 GLU cc_start: 0.7376 (tt0) cc_final: 0.6812 (tp30) REVERT: A 275 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.7977 (p) REVERT: A 277 SER cc_start: 0.8233 (t) cc_final: 0.7483 (p) REVERT: A 284 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7681 (mt-10) REVERT: A 290 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7608 (mm-30) REVERT: A 322 ASP cc_start: 0.7915 (t0) cc_final: 0.7460 (p0) REVERT: A 338 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7831 (ttpp) REVERT: A 367 ASP cc_start: 0.8000 (p0) cc_final: 0.7575 (p0) REVERT: A 370 LYS cc_start: 0.8424 (tptt) cc_final: 0.8050 (tptt) REVERT: A 414 GLU cc_start: 0.7768 (mp0) cc_final: 0.6938 (mp0) REVERT: A 420 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 423 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 434 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7372 (pp20) REVERT: B 48 ASN cc_start: 0.8325 (p0) cc_final: 0.8002 (p0) REVERT: B 53 GLU cc_start: 0.8021 (tt0) cc_final: 0.7338 (tp30) REVERT: B 58 LYS cc_start: 0.7454 (tttt) cc_final: 0.7021 (ttmm) REVERT: B 69 GLU cc_start: 0.7793 (tt0) cc_final: 0.7277 (pm20) REVERT: B 86 ARG cc_start: 0.8288 (ttm170) cc_final: 0.6276 (tpm170) REVERT: B 94 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8334 (mp-120) REVERT: B 103 LYS cc_start: 0.8286 (ttmm) cc_final: 0.8026 (mtpt) REVERT: B 118 ASP cc_start: 0.7341 (m-30) cc_final: 0.7061 (m-30) REVERT: B 123 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7441 (tp30) REVERT: B 127 CYS cc_start: 0.7363 (m) cc_final: 0.6617 (m) REVERT: B 134 GLN cc_start: 0.8138 (mt0) cc_final: 0.7796 (mt0) REVERT: B 154 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7394 (mttp) REVERT: B 158 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: B 164 MET cc_start: 0.8529 (tpp) cc_final: 0.8214 (tpt) REVERT: B 174 LYS cc_start: 0.8372 (mmpt) cc_final: 0.7903 (mmpt) REVERT: B 194 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: B 203 ASP cc_start: 0.7997 (t70) cc_final: 0.7217 (t0) REVERT: B 216 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8208 (mmmm) REVERT: B 274 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 278 SER cc_start: 0.8034 (m) cc_final: 0.7562 (p) REVERT: B 291 GLN cc_start: 0.8130 (pp30) cc_final: 0.7777 (pp30) REVERT: B 309 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.7069 (mtt90) REVERT: B 324 LYS cc_start: 0.7819 (tptm) cc_final: 0.7495 (tppp) REVERT: B 328 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6804 (tp30) REVERT: B 362 LYS cc_start: 0.8297 (tttp) cc_final: 0.8043 (tttp) REVERT: B 391 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.7025 (mtp-110) REVERT: B 407 GLU cc_start: 0.7894 (tt0) cc_final: 0.7398 (mt-10) REVERT: B 410 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7016 (mm-30) REVERT: B 412 GLU cc_start: 0.7753 (tp30) cc_final: 0.7346 (tp30) REVERT: B 414 ASN cc_start: 0.7531 (m110) cc_final: 0.7112 (m110) REVERT: B 417 ASP cc_start: 0.7678 (m-30) cc_final: 0.7132 (m-30) REVERT: B 421 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6967 (mt-10) REVERT: C 3 GLU cc_start: 0.7034 (mp0) cc_final: 0.6519 (mp0) REVERT: C 50 ASN cc_start: 0.8517 (t0) cc_final: 0.8058 (t0) REVERT: C 77 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8025 (mm-30) REVERT: C 90 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7984 (tp30) REVERT: C 97 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7939 (tt0) REVERT: C 112 LYS cc_start: 0.8146 (pttp) cc_final: 0.7747 (pttm) REVERT: C 123 ARG cc_start: 0.7403 (tpp-160) cc_final: 0.7038 (tpp80) REVERT: C 196 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: C 207 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6597 (mt-10) REVERT: C 211 ASP cc_start: 0.7753 (m-30) cc_final: 0.7362 (p0) REVERT: C 254 GLU cc_start: 0.7515 (tt0) cc_final: 0.7054 (mm-30) REVERT: C 280 LYS cc_start: 0.8450 (mttp) cc_final: 0.7096 (mtpt) REVERT: C 284 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6721 (mp0) REVERT: C 297 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7858 (mm-30) REVERT: C 308 ARG cc_start: 0.5392 (tpt170) cc_final: 0.4945 (tpt170) REVERT: C 322 ASP cc_start: 0.8219 (t70) cc_final: 0.7834 (t0) REVERT: C 337 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8300 (p) REVERT: C 370 LYS cc_start: 0.8392 (ttpp) cc_final: 0.8141 (tmmt) REVERT: C 377 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7941 (tmm) REVERT: C 386 GLU cc_start: 0.7749 (mp0) cc_final: 0.7172 (mp0) REVERT: C 411 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8068 (mm-30) REVERT: C 420 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 423 GLU cc_start: 0.7703 (tp30) cc_final: 0.7222 (mm-30) REVERT: C 424 ASP cc_start: 0.7762 (m-30) cc_final: 0.7467 (t0) REVERT: C 434 GLU cc_start: 0.7810 (pp20) cc_final: 0.7342 (pp20) REVERT: D 3 GLU cc_start: 0.7797 (mp0) cc_final: 0.6939 (mp0) REVERT: D 19 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8224 (tppp) REVERT: D 22 GLU cc_start: 0.8437 (tt0) cc_final: 0.7571 (tp30) REVERT: D 41 ASP cc_start: 0.7998 (m-30) cc_final: 0.7784 (OUTLIER) REVERT: D 45 GLU cc_start: 0.8625 (tt0) cc_final: 0.7788 (tm-30) REVERT: D 69 GLU cc_start: 0.7706 (pp20) cc_final: 0.7345 (pm20) REVERT: D 88 ASP cc_start: 0.8457 (t70) cc_final: 0.7911 (t0) REVERT: D 95 SER cc_start: 0.7870 (t) cc_final: 0.7631 (p) REVERT: D 103 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8213 (mtpm) REVERT: D 158 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7709 (mm-30) REVERT: D 159 TYR cc_start: 0.8413 (m-80) cc_final: 0.8117 (m-80) REVERT: D 161 ASP cc_start: 0.8240 (p0) cc_final: 0.7958 (p0) REVERT: D 162 ARG cc_start: 0.8259 (mmt-90) cc_final: 0.8002 (mmt180) REVERT: D 174 LYS cc_start: 0.8605 (mptt) cc_final: 0.8249 (mptt) REVERT: D 181 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7347 (mt-10) REVERT: D 190 HIS cc_start: 0.7994 (t-90) cc_final: 0.6594 (t-90) REVERT: D 198 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8202 (mt-10) REVERT: D 203 ASP cc_start: 0.8259 (t0) cc_final: 0.7421 (t70) REVERT: D 213 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.8065 (mtm180) REVERT: D 216 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8302 (mmmm) REVERT: D 233 MET cc_start: 0.8726 (mtt) cc_final: 0.8455 (mtp) REVERT: D 251 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7847 (ttm110) REVERT: D 262 ARG cc_start: 0.8879 (mtm180) cc_final: 0.8666 (mtm180) REVERT: D 291 GLN cc_start: 0.8326 (pp30) cc_final: 0.7991 (pp30) REVERT: D 325 GLU cc_start: 0.8121 (tp30) cc_final: 0.7564 (tp30) REVERT: D 383 GLU cc_start: 0.8023 (tp30) cc_final: 0.7415 (tp30) REVERT: D 391 ARG cc_start: 0.8624 (mmm160) cc_final: 0.6827 (ptm160) REVERT: D 404 ASP cc_start: 0.8403 (m-30) cc_final: 0.7393 (m-30) REVERT: D 407 GLU cc_start: 0.7715 (mp0) cc_final: 0.6825 (mp0) REVERT: D 410 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7272 (tm-30) REVERT: D 412 GLU cc_start: 0.8031 (tp30) cc_final: 0.7816 (mm-30) REVERT: E 9 LEU cc_start: 0.7822 (tt) cc_final: 0.7503 (tm) REVERT: E 61 ASP cc_start: 0.7582 (m-30) cc_final: 0.7229 (m-30) REVERT: E 69 ASN cc_start: 0.8120 (t0) cc_final: 0.7458 (t0) REVERT: E 120 GLU cc_start: 0.7146 (mp0) cc_final: 0.6754 (mp0) REVERT: E 129 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6869 (tm-30) REVERT: E 152 PHE cc_start: 0.8258 (m-10) cc_final: 0.7874 (m-10) REVERT: E 187 ASP cc_start: 0.8402 (t0) cc_final: 0.7716 (t0) REVERT: E 237 PHE cc_start: 0.8069 (m-10) cc_final: 0.7858 (m-10) REVERT: E 278 GLN cc_start: 0.8260 (mt0) cc_final: 0.8025 (mt0) REVERT: E 314 GLN cc_start: 0.8420 (mm110) cc_final: 0.8131 (mm110) REVERT: E 340 SER cc_start: 0.7952 (t) cc_final: 0.7527 (t) REVERT: E 444 MET cc_start: 0.8320 (mtp) cc_final: 0.8087 (mtm) REVERT: E 457 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7805 (mm-30) REVERT: E 478 ASN cc_start: 0.7863 (t0) cc_final: 0.7325 (t0) REVERT: E 519 TYR cc_start: 0.8601 (m-80) cc_final: 0.8396 (m-10) REVERT: E 534 ASP cc_start: 0.8022 (p0) cc_final: 0.7797 (p0) REVERT: E 550 TYR cc_start: 0.8540 (m-80) cc_final: 0.8174 (m-10) REVERT: E 556 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7455 (mm-30) REVERT: E 569 MET cc_start: 0.7234 (mtp) cc_final: 0.7032 (mtm) REVERT: E 586 LEU cc_start: 0.7654 (tp) cc_final: 0.7372 (tp) REVERT: E 588 ASN cc_start: 0.8490 (t0) cc_final: 0.8014 (m-40) outliers start: 56 outliers final: 15 residues processed: 496 average time/residue: 1.5789 time to fit residues: 858.9691 Evaluate side-chains 454 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 432 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 275 VAL Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 533 HIS Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 191 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 423 GLN C 101 ASN C 128 GLN C 249 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 416 ASN E 98 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 573 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17882 Z= 0.205 Angle : 0.552 8.527 24321 Z= 0.281 Chirality : 0.044 0.156 2657 Planarity : 0.004 0.052 3175 Dihedral : 10.636 177.117 2519 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.93 % Allowed : 16.11 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2208 helix: 1.16 (0.17), residues: 918 sheet: 0.48 (0.29), residues: 348 loop : -0.58 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 21 HIS 0.010 0.001 HIS E 323 PHE 0.023 0.001 PHE E 75 TYR 0.016 0.001 TYR A 432 ARG 0.015 0.001 ARG E 590 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 445 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7209 (mt-10) REVERT: A 83 TYR cc_start: 0.8511 (m-80) cc_final: 0.8017 (m-80) REVERT: A 114 ILE cc_start: 0.7267 (pt) cc_final: 0.6996 (pp) REVERT: A 116 ASP cc_start: 0.7888 (m-30) cc_final: 0.7241 (p0) REVERT: A 117 LEU cc_start: 0.7496 (tp) cc_final: 0.7004 (tt) REVERT: A 120 ASP cc_start: 0.7401 (m-30) cc_final: 0.7011 (m-30) REVERT: A 154 MET cc_start: 0.8330 (mmm) cc_final: 0.8045 (mmp) REVERT: A 211 ASP cc_start: 0.7829 (m-30) cc_final: 0.7620 (m-30) REVERT: A 214 ARG cc_start: 0.8045 (ttp-110) cc_final: 0.7383 (ttp-110) REVERT: A 233 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7667 (mm-40) REVERT: A 241 SER cc_start: 0.8838 (m) cc_final: 0.8538 (t) REVERT: A 245 ASP cc_start: 0.7736 (p0) cc_final: 0.7427 (p0) REVERT: A 251 ASP cc_start: 0.7256 (m-30) cc_final: 0.6530 (p0) REVERT: A 254 GLU cc_start: 0.7437 (tt0) cc_final: 0.7093 (tp30) REVERT: A 275 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 277 SER cc_start: 0.8313 (t) cc_final: 0.7576 (p) REVERT: A 284 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7661 (mt-10) REVERT: A 290 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 322 ASP cc_start: 0.7936 (t0) cc_final: 0.7377 (p0) REVERT: A 338 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7855 (ttpp) REVERT: A 367 ASP cc_start: 0.8005 (p0) cc_final: 0.7479 (p0) REVERT: A 370 LYS cc_start: 0.8424 (tptt) cc_final: 0.8046 (tptt) REVERT: A 377 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8303 (ttt) REVERT: A 388 TRP cc_start: 0.8183 (m-10) cc_final: 0.7797 (m-10) REVERT: A 414 GLU cc_start: 0.7760 (mp0) cc_final: 0.6985 (mp0) REVERT: A 420 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7406 (mm-30) REVERT: A 423 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 434 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7422 (pp20) REVERT: B 19 LYS cc_start: 0.8461 (tptm) cc_final: 0.8198 (tppt) REVERT: B 36 TYR cc_start: 0.8486 (t80) cc_final: 0.8052 (t80) REVERT: B 48 ASN cc_start: 0.8347 (p0) cc_final: 0.8097 (p0) REVERT: B 53 GLU cc_start: 0.8039 (tt0) cc_final: 0.7404 (tp30) REVERT: B 58 LYS cc_start: 0.7659 (tttt) cc_final: 0.7230 (ttmm) REVERT: B 69 GLU cc_start: 0.7774 (tt0) cc_final: 0.7274 (pm20) REVERT: B 74 ASP cc_start: 0.7403 (t0) cc_final: 0.7016 (t0) REVERT: B 103 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7832 (mtpm) REVERT: B 114 ASP cc_start: 0.7675 (m-30) cc_final: 0.7431 (m-30) REVERT: B 118 ASP cc_start: 0.7339 (m-30) cc_final: 0.7060 (m-30) REVERT: B 123 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7410 (tp30) REVERT: B 127 CYS cc_start: 0.7498 (m) cc_final: 0.6723 (m) REVERT: B 134 GLN cc_start: 0.8076 (mt0) cc_final: 0.7701 (mt0) REVERT: B 158 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 164 MET cc_start: 0.8508 (tpp) cc_final: 0.8193 (tpt) REVERT: B 174 LYS cc_start: 0.8341 (mmpt) cc_final: 0.7889 (mmpt) REVERT: B 175 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8318 (m) REVERT: B 203 ASP cc_start: 0.7922 (t70) cc_final: 0.7144 (t0) REVERT: B 216 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8244 (mmmm) REVERT: B 274 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 278 SER cc_start: 0.8045 (m) cc_final: 0.7617 (p) REVERT: B 291 GLN cc_start: 0.8045 (pp30) cc_final: 0.7744 (pp30) REVERT: B 309 ARG cc_start: 0.7323 (mtt-85) cc_final: 0.6803 (mtp85) REVERT: B 324 LYS cc_start: 0.7866 (tptm) cc_final: 0.7558 (tppp) REVERT: B 325 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 328 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6817 (tp30) REVERT: B 362 LYS cc_start: 0.8213 (tttp) cc_final: 0.7989 (tttp) REVERT: B 407 GLU cc_start: 0.7939 (tt0) cc_final: 0.7409 (mt-10) REVERT: B 410 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7019 (mm-30) REVERT: B 412 GLU cc_start: 0.7757 (tp30) cc_final: 0.7093 (tp30) REVERT: B 414 ASN cc_start: 0.7578 (m110) cc_final: 0.7148 (m110) REVERT: B 417 ASP cc_start: 0.7603 (m-30) cc_final: 0.7190 (m-30) REVERT: C 50 ASN cc_start: 0.8535 (t0) cc_final: 0.8123 (t0) REVERT: C 77 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8046 (mm-30) REVERT: C 90 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7973 (tp30) REVERT: C 96 LYS cc_start: 0.8990 (mmtm) cc_final: 0.8770 (mmtm) REVERT: C 112 LYS cc_start: 0.8206 (pttp) cc_final: 0.7795 (pttm) REVERT: C 123 ARG cc_start: 0.7388 (tpp-160) cc_final: 0.7012 (tpp80) REVERT: C 166 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8220 (mttm) REVERT: C 196 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: C 207 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6795 (mt-10) REVERT: C 245 ASP cc_start: 0.7916 (p0) cc_final: 0.7687 (p0) REVERT: C 251 ASP cc_start: 0.7374 (m-30) cc_final: 0.7041 (t70) REVERT: C 254 GLU cc_start: 0.7596 (tt0) cc_final: 0.7093 (mm-30) REVERT: C 280 LYS cc_start: 0.8444 (mttp) cc_final: 0.7722 (mtpt) REVERT: C 297 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7868 (mm-30) REVERT: C 308 ARG cc_start: 0.5274 (tpt170) cc_final: 0.4991 (tpt170) REVERT: C 322 ASP cc_start: 0.8177 (t70) cc_final: 0.7830 (t0) REVERT: C 337 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8309 (p) REVERT: C 377 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8381 (tpp) REVERT: C 386 GLU cc_start: 0.7723 (mp0) cc_final: 0.7139 (mp0) REVERT: C 411 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8150 (mm-30) REVERT: C 420 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7289 (mm-30) REVERT: C 423 GLU cc_start: 0.7740 (tp30) cc_final: 0.7256 (mm-30) REVERT: C 424 ASP cc_start: 0.7640 (m-30) cc_final: 0.7390 (t0) REVERT: C 434 GLU cc_start: 0.7757 (pp20) cc_final: 0.7226 (pp20) REVERT: D 1 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7705 (ttp) REVERT: D 3 GLU cc_start: 0.7852 (mp0) cc_final: 0.7178 (mp0) REVERT: D 19 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8294 (tppp) REVERT: D 22 GLU cc_start: 0.8483 (tt0) cc_final: 0.7525 (tp30) REVERT: D 41 ASP cc_start: 0.8017 (m-30) cc_final: 0.7778 (p0) REVERT: D 45 GLU cc_start: 0.8614 (tt0) cc_final: 0.7892 (tm-30) REVERT: D 57 ASN cc_start: 0.7536 (t0) cc_final: 0.6264 (t0) REVERT: D 64 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8614 (mt) REVERT: D 69 GLU cc_start: 0.7740 (pp20) cc_final: 0.7385 (pm20) REVERT: D 88 ASP cc_start: 0.8452 (t70) cc_final: 0.7882 (t0) REVERT: D 95 SER cc_start: 0.7959 (t) cc_final: 0.7675 (p) REVERT: D 103 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8192 (mtpm) REVERT: D 123 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7372 (mm-30) REVERT: D 159 TYR cc_start: 0.8471 (m-80) cc_final: 0.8098 (m-80) REVERT: D 161 ASP cc_start: 0.8241 (p0) cc_final: 0.7914 (p0) REVERT: D 162 ARG cc_start: 0.8235 (mmt-90) cc_final: 0.7921 (mmt180) REVERT: D 174 LYS cc_start: 0.8674 (mptt) cc_final: 0.8295 (mptt) REVERT: D 181 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7334 (mt-10) REVERT: D 203 ASP cc_start: 0.8275 (t0) cc_final: 0.7392 (t70) REVERT: D 213 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.8097 (mtm180) REVERT: D 216 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8320 (mmmm) REVERT: D 233 MET cc_start: 0.8780 (mtt) cc_final: 0.8539 (mtp) REVERT: D 251 ARG cc_start: 0.8188 (tpp-160) cc_final: 0.7573 (ttm110) REVERT: D 257 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7881 (mmm) REVERT: D 262 ARG cc_start: 0.8866 (mtm180) cc_final: 0.8644 (mtm180) REVERT: D 291 GLN cc_start: 0.8269 (pp30) cc_final: 0.7958 (pp30) REVERT: D 325 GLU cc_start: 0.8134 (tp30) cc_final: 0.7511 (tp30) REVERT: D 376 GLU cc_start: 0.7583 (mp0) cc_final: 0.7225 (mp0) REVERT: D 383 GLU cc_start: 0.7966 (tp30) cc_final: 0.7351 (tp30) REVERT: D 391 ARG cc_start: 0.8661 (mmm160) cc_final: 0.6862 (ptm160) REVERT: D 404 ASP cc_start: 0.8376 (m-30) cc_final: 0.7345 (m-30) REVERT: D 407 GLU cc_start: 0.7769 (mp0) cc_final: 0.6859 (mp0) REVERT: D 412 GLU cc_start: 0.8076 (tp30) cc_final: 0.7247 (tm-30) REVERT: E 9 LEU cc_start: 0.7788 (tt) cc_final: 0.7487 (tm) REVERT: E 61 ASP cc_start: 0.7512 (m-30) cc_final: 0.7192 (m-30) REVERT: E 68 GLU cc_start: 0.8116 (tt0) cc_final: 0.7591 (tt0) REVERT: E 69 ASN cc_start: 0.8127 (t0) cc_final: 0.7465 (t0) REVERT: E 104 GLN cc_start: 0.7257 (mt0) cc_final: 0.7000 (mt0) REVERT: E 120 GLU cc_start: 0.7166 (mp0) cc_final: 0.6753 (mp0) REVERT: E 129 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6839 (tm-30) REVERT: E 152 PHE cc_start: 0.8319 (m-10) cc_final: 0.8029 (m-10) REVERT: E 181 THR cc_start: 0.6047 (OUTLIER) cc_final: 0.5838 (p) REVERT: E 187 ASP cc_start: 0.8385 (t0) cc_final: 0.7688 (t0) REVERT: E 237 PHE cc_start: 0.8046 (m-10) cc_final: 0.7804 (m-10) REVERT: E 246 PHE cc_start: 0.8561 (t80) cc_final: 0.8290 (t80) REVERT: E 278 GLN cc_start: 0.8262 (mt0) cc_final: 0.8030 (mt0) REVERT: E 291 MET cc_start: 0.8674 (mtp) cc_final: 0.8200 (mtm) REVERT: E 313 ARG cc_start: 0.8509 (mmt90) cc_final: 0.8293 (mmm-85) REVERT: E 314 GLN cc_start: 0.8428 (mm110) cc_final: 0.8222 (mm-40) REVERT: E 340 SER cc_start: 0.7971 (t) cc_final: 0.7523 (t) REVERT: E 439 LYS cc_start: 0.7911 (ttmp) cc_final: 0.7644 (ttmm) REVERT: E 440 ARG cc_start: 0.8128 (mpt-90) cc_final: 0.7596 (mpp80) REVERT: E 444 MET cc_start: 0.8331 (mtp) cc_final: 0.7964 (mtm) REVERT: E 478 ASN cc_start: 0.7944 (t0) cc_final: 0.7370 (t0) REVERT: E 519 TYR cc_start: 0.8556 (m-80) cc_final: 0.8317 (m-10) REVERT: E 534 ASP cc_start: 0.8029 (p0) cc_final: 0.7819 (p0) REVERT: E 550 TYR cc_start: 0.8454 (m-80) cc_final: 0.8213 (m-10) REVERT: E 556 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7407 (mm-30) REVERT: E 588 ASN cc_start: 0.8507 (t0) cc_final: 0.8086 (m-40) outliers start: 54 outliers final: 15 residues processed: 473 average time/residue: 1.5287 time to fit residues: 792.8868 Evaluate side-chains 451 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 423 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 275 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 181 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.0170 chunk 121 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 191 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 128 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17882 Z= 0.188 Angle : 0.539 8.769 24321 Z= 0.273 Chirality : 0.043 0.157 2657 Planarity : 0.004 0.055 3175 Dihedral : 10.648 179.557 2519 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.09 % Allowed : 16.65 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2208 helix: 1.38 (0.17), residues: 912 sheet: 0.53 (0.29), residues: 341 loop : -0.51 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 21 HIS 0.012 0.001 HIS D 190 PHE 0.025 0.001 PHE E 75 TYR 0.010 0.001 TYR A 432 ARG 0.016 0.001 ARG E 590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 441 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7928 (tt0) cc_final: 0.7370 (tp30) REVERT: A 77 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7159 (mt-10) REVERT: A 83 TYR cc_start: 0.8534 (m-80) cc_final: 0.8043 (m-80) REVERT: A 116 ASP cc_start: 0.7910 (m-30) cc_final: 0.7179 (m-30) REVERT: A 117 LEU cc_start: 0.7480 (tp) cc_final: 0.7000 (tt) REVERT: A 120 ASP cc_start: 0.7397 (m-30) cc_final: 0.7021 (m-30) REVERT: A 211 ASP cc_start: 0.7822 (m-30) cc_final: 0.7313 (t70) REVERT: A 241 SER cc_start: 0.8823 (m) cc_final: 0.8533 (t) REVERT: A 251 ASP cc_start: 0.7357 (m-30) cc_final: 0.6986 (t0) REVERT: A 254 GLU cc_start: 0.7434 (tt0) cc_final: 0.7188 (tp30) REVERT: A 277 SER cc_start: 0.8338 (t) cc_final: 0.7612 (p) REVERT: A 284 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7681 (mt-10) REVERT: A 290 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 322 ASP cc_start: 0.7947 (t0) cc_final: 0.7376 (p0) REVERT: A 338 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7844 (ttpp) REVERT: A 367 ASP cc_start: 0.7995 (p0) cc_final: 0.7454 (p0) REVERT: A 370 LYS cc_start: 0.8417 (tptt) cc_final: 0.8044 (tptt) REVERT: A 377 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8289 (ttt) REVERT: A 388 TRP cc_start: 0.8134 (m-10) cc_final: 0.7829 (m-10) REVERT: A 414 GLU cc_start: 0.7798 (mp0) cc_final: 0.6926 (mp0) REVERT: A 420 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 423 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 434 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7524 (pp20) REVERT: B 19 LYS cc_start: 0.8428 (tptm) cc_final: 0.8167 (tppt) REVERT: B 36 TYR cc_start: 0.8547 (t80) cc_final: 0.8205 (t80) REVERT: B 48 ASN cc_start: 0.8348 (p0) cc_final: 0.7989 (p0) REVERT: B 53 GLU cc_start: 0.8052 (tt0) cc_final: 0.7418 (tp30) REVERT: B 58 LYS cc_start: 0.7676 (tttt) cc_final: 0.7251 (ttmm) REVERT: B 69 GLU cc_start: 0.7769 (tt0) cc_final: 0.7249 (pt0) REVERT: B 74 ASP cc_start: 0.7411 (t0) cc_final: 0.7000 (t0) REVERT: B 103 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8091 (mtpt) REVERT: B 114 ASP cc_start: 0.7651 (m-30) cc_final: 0.7400 (m-30) REVERT: B 118 ASP cc_start: 0.7357 (m-30) cc_final: 0.7077 (m-30) REVERT: B 123 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7394 (tp30) REVERT: B 127 CYS cc_start: 0.7505 (m) cc_final: 0.6721 (m) REVERT: B 134 GLN cc_start: 0.8067 (mt0) cc_final: 0.7689 (mt0) REVERT: B 157 GLU cc_start: 0.7967 (tp30) cc_final: 0.7729 (tt0) REVERT: B 158 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: B 164 MET cc_start: 0.8484 (tpp) cc_final: 0.8056 (tpt) REVERT: B 174 LYS cc_start: 0.8336 (mmpt) cc_final: 0.7826 (mmpt) REVERT: B 175 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8320 (m) REVERT: B 194 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7686 (tp30) REVERT: B 203 ASP cc_start: 0.7935 (t70) cc_final: 0.7127 (t0) REVERT: B 216 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8243 (mmmm) REVERT: B 262 ARG cc_start: 0.8752 (mtm180) cc_final: 0.8421 (mtm180) REVERT: B 274 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8293 (p) REVERT: B 278 SER cc_start: 0.8048 (m) cc_final: 0.7613 (p) REVERT: B 291 GLN cc_start: 0.7958 (pp30) cc_final: 0.7683 (pp30) REVERT: B 309 ARG cc_start: 0.7272 (mtt-85) cc_final: 0.6775 (mtp85) REVERT: B 325 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6895 (mm-30) REVERT: B 328 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6815 (tp30) REVERT: B 362 LYS cc_start: 0.8260 (tttp) cc_final: 0.8045 (tttp) REVERT: B 407 GLU cc_start: 0.7888 (tt0) cc_final: 0.7366 (mt-10) REVERT: B 410 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7028 (mm-30) REVERT: B 412 GLU cc_start: 0.7824 (tp30) cc_final: 0.7090 (tp30) REVERT: B 414 ASN cc_start: 0.7611 (m110) cc_final: 0.7193 (m110) REVERT: B 417 ASP cc_start: 0.7577 (m-30) cc_final: 0.7244 (m-30) REVERT: B 421 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7058 (mt-10) REVERT: C 3 GLU cc_start: 0.7168 (mp0) cc_final: 0.6700 (mp0) REVERT: C 50 ASN cc_start: 0.8538 (t0) cc_final: 0.8129 (t0) REVERT: C 77 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8105 (mm-30) REVERT: C 90 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8024 (tp30) REVERT: C 112 LYS cc_start: 0.8210 (pttp) cc_final: 0.7779 (pttm) REVERT: C 123 ARG cc_start: 0.7394 (tpp-160) cc_final: 0.7013 (tpp80) REVERT: C 154 MET cc_start: 0.8719 (mmm) cc_final: 0.8515 (mtm) REVERT: C 196 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: C 199 ASP cc_start: 0.7947 (p0) cc_final: 0.7730 (p0) REVERT: C 218 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8403 (t0) REVERT: C 245 ASP cc_start: 0.7944 (p0) cc_final: 0.7675 (p0) REVERT: C 251 ASP cc_start: 0.7573 (m-30) cc_final: 0.6692 (p0) REVERT: C 254 GLU cc_start: 0.7601 (tt0) cc_final: 0.6900 (mm-30) REVERT: C 277 SER cc_start: 0.8135 (t) cc_final: 0.7701 (p) REVERT: C 280 LYS cc_start: 0.8454 (mttp) cc_final: 0.7642 (mtpt) REVERT: C 308 ARG cc_start: 0.5204 (tpt170) cc_final: 0.4930 (tpt170) REVERT: C 322 ASP cc_start: 0.8179 (t70) cc_final: 0.7827 (t0) REVERT: C 337 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8344 (p) REVERT: C 367 ASP cc_start: 0.7251 (t0) cc_final: 0.6773 (t0) REVERT: C 370 LYS cc_start: 0.8470 (tmmm) cc_final: 0.8251 (tmmt) REVERT: C 377 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8368 (tpp) REVERT: C 411 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8079 (mm-30) REVERT: C 420 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7323 (mm-30) REVERT: C 423 GLU cc_start: 0.7767 (tp30) cc_final: 0.7279 (mm-30) REVERT: C 424 ASP cc_start: 0.7650 (m-30) cc_final: 0.7392 (t0) REVERT: C 434 GLU cc_start: 0.7771 (pp20) cc_final: 0.7287 (pp20) REVERT: D 1 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7713 (ttp) REVERT: D 3 GLU cc_start: 0.7883 (mp0) cc_final: 0.7294 (mp0) REVERT: D 19 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8146 (tppp) REVERT: D 22 GLU cc_start: 0.8471 (tt0) cc_final: 0.7975 (tm-30) REVERT: D 26 ASP cc_start: 0.7553 (m-30) cc_final: 0.7117 (t0) REVERT: D 41 ASP cc_start: 0.8032 (m-30) cc_final: 0.7767 (p0) REVERT: D 45 GLU cc_start: 0.8584 (tt0) cc_final: 0.7792 (tm-30) REVERT: D 57 ASN cc_start: 0.7705 (t0) cc_final: 0.6370 (t0) REVERT: D 69 GLU cc_start: 0.7780 (pp20) cc_final: 0.7367 (pm20) REVERT: D 88 ASP cc_start: 0.8450 (t70) cc_final: 0.7884 (t0) REVERT: D 95 SER cc_start: 0.8011 (t) cc_final: 0.7687 (p) REVERT: D 103 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8171 (mtpm) REVERT: D 123 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7388 (mm-30) REVERT: D 159 TYR cc_start: 0.8471 (m-80) cc_final: 0.8135 (m-80) REVERT: D 161 ASP cc_start: 0.8259 (p0) cc_final: 0.7898 (p0) REVERT: D 162 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7910 (mmt180) REVERT: D 174 LYS cc_start: 0.8670 (mptt) cc_final: 0.8296 (mptt) REVERT: D 181 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7482 (mt-10) REVERT: D 190 HIS cc_start: 0.8156 (t-90) cc_final: 0.6837 (t70) REVERT: D 203 ASP cc_start: 0.8278 (t0) cc_final: 0.7381 (t70) REVERT: D 213 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.8072 (mtm180) REVERT: D 216 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8324 (mmmm) REVERT: D 251 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7593 (ttm110) REVERT: D 262 ARG cc_start: 0.8886 (mtm180) cc_final: 0.8652 (mtm180) REVERT: D 291 GLN cc_start: 0.8265 (pp30) cc_final: 0.7992 (pp30) REVERT: D 325 GLU cc_start: 0.8127 (tp30) cc_final: 0.7462 (tp30) REVERT: D 375 GLN cc_start: 0.8175 (pt0) cc_final: 0.7895 (pt0) REVERT: D 376 GLU cc_start: 0.7551 (mp0) cc_final: 0.7166 (mp0) REVERT: D 383 GLU cc_start: 0.7957 (tp30) cc_final: 0.7447 (tp30) REVERT: D 391 ARG cc_start: 0.8693 (mmm160) cc_final: 0.6839 (ptm160) REVERT: D 404 ASP cc_start: 0.8361 (m-30) cc_final: 0.7594 (m-30) REVERT: D 407 GLU cc_start: 0.7808 (mp0) cc_final: 0.6969 (mp0) REVERT: D 410 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7365 (tm-30) REVERT: D 412 GLU cc_start: 0.8071 (tp30) cc_final: 0.7315 (tm-30) REVERT: E 9 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7465 (tm) REVERT: E 61 ASP cc_start: 0.7501 (m-30) cc_final: 0.7110 (m-30) REVERT: E 68 GLU cc_start: 0.8159 (tt0) cc_final: 0.7659 (tt0) REVERT: E 69 ASN cc_start: 0.8138 (t0) cc_final: 0.7494 (t0) REVERT: E 104 GLN cc_start: 0.7279 (mt0) cc_final: 0.6969 (mt0) REVERT: E 120 GLU cc_start: 0.7173 (mp0) cc_final: 0.6752 (mp0) REVERT: E 129 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6876 (tm-30) REVERT: E 152 PHE cc_start: 0.8197 (m-10) cc_final: 0.7954 (m-10) REVERT: E 187 ASP cc_start: 0.8375 (t0) cc_final: 0.7672 (t0) REVERT: E 246 PHE cc_start: 0.8542 (t80) cc_final: 0.8314 (t80) REVERT: E 278 GLN cc_start: 0.8267 (mt0) cc_final: 0.8052 (mt0) REVERT: E 313 ARG cc_start: 0.8503 (mmt90) cc_final: 0.8259 (mmm-85) REVERT: E 319 ASP cc_start: 0.6984 (t70) cc_final: 0.6782 (t0) REVERT: E 340 SER cc_start: 0.7904 (t) cc_final: 0.7475 (t) REVERT: E 440 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7506 (mpp80) REVERT: E 444 MET cc_start: 0.8271 (mtp) cc_final: 0.8006 (mtm) REVERT: E 457 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7503 (mm-30) REVERT: E 478 ASN cc_start: 0.8080 (t0) cc_final: 0.7472 (t0) REVERT: E 550 TYR cc_start: 0.8442 (m-80) cc_final: 0.8191 (m-10) REVERT: E 556 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7407 (mm-30) REVERT: E 588 ASN cc_start: 0.8503 (t0) cc_final: 0.8101 (m-40) REVERT: E 593 MET cc_start: 0.7983 (tpp) cc_final: 0.7679 (tpp) outliers start: 57 outliers final: 19 residues processed: 470 average time/residue: 1.4992 time to fit residues: 774.1279 Evaluate side-chains 460 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 429 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 234 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 337 THR 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 170 VAL Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 440 ARG Chi-restraints excluded: chain E residue 584 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 213 optimal weight: 0.0770 chunk 177 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 0.0020 chunk 112 optimal weight: 2.9990 overall best weight: 0.5746 ------------------------------------------------------------------------------- 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 264 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 128 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 226 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17882 Z= 0.192 Angle : 0.551 9.120 24321 Z= 0.278 Chirality : 0.044 0.160 2657 Planarity : 0.004 0.063 3175 Dihedral : 10.666 179.103 2519 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.20 % Allowed : 16.97 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2208 helix: 1.46 (0.17), residues: 918 sheet: 0.44 (0.29), residues: 347 loop : -0.53 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 21 HIS 0.011 0.001 HIS D 190 PHE 0.026 0.001 PHE E 75 TYR 0.015 0.001 TYR D 425 ARG 0.016 0.001 ARG E 590 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 430 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7939 (tt0) cc_final: 0.7377 (tp30) REVERT: A 77 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 83 TYR cc_start: 0.8547 (m-80) cc_final: 0.8063 (m-80) REVERT: A 116 ASP cc_start: 0.7814 (m-30) cc_final: 0.7120 (m-30) REVERT: A 117 LEU cc_start: 0.7516 (tp) cc_final: 0.7022 (tt) REVERT: A 120 ASP cc_start: 0.7394 (m-30) cc_final: 0.7065 (m-30) REVERT: A 154 MET cc_start: 0.8333 (mmm) cc_final: 0.8109 (mmp) REVERT: A 211 ASP cc_start: 0.7830 (m-30) cc_final: 0.7105 (t70) REVERT: A 214 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7387 (ttp-110) REVERT: A 241 SER cc_start: 0.8823 (m) cc_final: 0.8540 (t) REVERT: A 251 ASP cc_start: 0.7349 (m-30) cc_final: 0.6968 (t0) REVERT: A 254 GLU cc_start: 0.7447 (tt0) cc_final: 0.7236 (tp30) REVERT: A 277 SER cc_start: 0.8372 (t) cc_final: 0.7661 (p) REVERT: A 284 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7649 (mt-10) REVERT: A 290 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7505 (mm-30) REVERT: A 322 ASP cc_start: 0.7953 (t0) cc_final: 0.7375 (p0) REVERT: A 338 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7824 (ttpp) REVERT: A 367 ASP cc_start: 0.7978 (p0) cc_final: 0.7420 (p0) REVERT: A 370 LYS cc_start: 0.8413 (tptt) cc_final: 0.8041 (tptt) REVERT: A 388 TRP cc_start: 0.8116 (m-10) cc_final: 0.7811 (m-10) REVERT: A 414 GLU cc_start: 0.7787 (mp0) cc_final: 0.6914 (mp0) REVERT: A 420 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 423 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 434 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7560 (pp20) REVERT: B 19 LYS cc_start: 0.8415 (tptm) cc_final: 0.8160 (tppt) REVERT: B 36 TYR cc_start: 0.8577 (t80) cc_final: 0.8141 (t80) REVERT: B 48 ASN cc_start: 0.8339 (p0) cc_final: 0.8084 (p0) REVERT: B 53 GLU cc_start: 0.8074 (tt0) cc_final: 0.7440 (tp30) REVERT: B 58 LYS cc_start: 0.7730 (tttt) cc_final: 0.7286 (ttmm) REVERT: B 69 GLU cc_start: 0.7747 (tt0) cc_final: 0.7255 (pt0) REVERT: B 74 ASP cc_start: 0.7420 (t0) cc_final: 0.7046 (t0) REVERT: B 103 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7952 (mtpm) REVERT: B 114 ASP cc_start: 0.7655 (m-30) cc_final: 0.7400 (m-30) REVERT: B 118 ASP cc_start: 0.7352 (m-30) cc_final: 0.7073 (m-30) REVERT: B 123 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7415 (tp30) REVERT: B 127 CYS cc_start: 0.7533 (m) cc_final: 0.6758 (m) REVERT: B 134 GLN cc_start: 0.8063 (mt0) cc_final: 0.7679 (mt0) REVERT: B 157 GLU cc_start: 0.7986 (tp30) cc_final: 0.7765 (tt0) REVERT: B 158 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: B 164 MET cc_start: 0.8428 (tpp) cc_final: 0.8097 (tpt) REVERT: B 174 LYS cc_start: 0.8385 (mmpt) cc_final: 0.7813 (mmpt) REVERT: B 175 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8334 (m) REVERT: B 194 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7679 (tp30) REVERT: B 203 ASP cc_start: 0.7959 (t70) cc_final: 0.7165 (t0) REVERT: B 216 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8244 (mmmm) REVERT: B 262 ARG cc_start: 0.8753 (mtm180) cc_final: 0.8445 (mtm180) REVERT: B 274 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8303 (p) REVERT: B 278 SER cc_start: 0.8043 (m) cc_final: 0.7615 (p) REVERT: B 291 GLN cc_start: 0.7984 (pp30) cc_final: 0.7709 (pp30) REVERT: B 309 ARG cc_start: 0.7195 (mtt-85) cc_final: 0.6744 (mtp85) REVERT: B 325 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: B 328 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6824 (tp30) REVERT: B 362 LYS cc_start: 0.8198 (tttp) cc_final: 0.7984 (tttp) REVERT: B 380 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7504 (mtm180) REVERT: B 407 GLU cc_start: 0.7807 (tt0) cc_final: 0.7279 (mt-10) REVERT: B 410 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7036 (mm-30) REVERT: B 412 GLU cc_start: 0.7903 (tp30) cc_final: 0.7130 (tp30) REVERT: B 414 ASN cc_start: 0.7616 (m110) cc_final: 0.7232 (m110) REVERT: B 421 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7021 (mt-10) REVERT: C 50 ASN cc_start: 0.8521 (t0) cc_final: 0.8095 (t0) REVERT: C 77 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8117 (mm-30) REVERT: C 90 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7996 (tp30) REVERT: C 112 LYS cc_start: 0.8216 (pttp) cc_final: 0.7786 (pttm) REVERT: C 123 ARG cc_start: 0.7401 (tpp-160) cc_final: 0.7014 (tpp80) REVERT: C 196 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: C 199 ASP cc_start: 0.7945 (p0) cc_final: 0.7720 (p0) REVERT: C 245 ASP cc_start: 0.7963 (p0) cc_final: 0.7689 (p0) REVERT: C 251 ASP cc_start: 0.7566 (m-30) cc_final: 0.7179 (t70) REVERT: C 254 GLU cc_start: 0.7607 (tt0) cc_final: 0.7180 (mm-30) REVERT: C 277 SER cc_start: 0.8146 (t) cc_final: 0.7713 (p) REVERT: C 280 LYS cc_start: 0.8510 (mttp) cc_final: 0.7590 (mmpt) REVERT: C 308 ARG cc_start: 0.5199 (tpt170) cc_final: 0.4868 (tpt170) REVERT: C 322 ASP cc_start: 0.8180 (t70) cc_final: 0.7784 (t0) REVERT: C 337 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8358 (p) REVERT: C 367 ASP cc_start: 0.7249 (t0) cc_final: 0.6766 (t0) REVERT: C 370 LYS cc_start: 0.8469 (tmmm) cc_final: 0.8221 (tmmt) REVERT: C 377 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8300 (ttm) REVERT: C 411 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8062 (mm-30) REVERT: C 420 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7266 (mm-30) REVERT: C 423 GLU cc_start: 0.7821 (tp30) cc_final: 0.7345 (mm-30) REVERT: C 424 ASP cc_start: 0.7596 (m-30) cc_final: 0.7390 (t70) REVERT: C 431 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.6892 (m-30) REVERT: C 433 GLU cc_start: 0.7950 (tt0) cc_final: 0.7211 (tm-30) REVERT: C 434 GLU cc_start: 0.7798 (pp20) cc_final: 0.7246 (pp20) REVERT: D 3 GLU cc_start: 0.7846 (mp0) cc_final: 0.7251 (mp0) REVERT: D 19 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8156 (tppp) REVERT: D 22 GLU cc_start: 0.8478 (tt0) cc_final: 0.7972 (tm-30) REVERT: D 26 ASP cc_start: 0.7557 (m-30) cc_final: 0.7131 (t0) REVERT: D 45 GLU cc_start: 0.8579 (tt0) cc_final: 0.7839 (tm-30) REVERT: D 57 ASN cc_start: 0.7782 (t0) cc_final: 0.6438 (t0) REVERT: D 69 GLU cc_start: 0.7775 (pp20) cc_final: 0.7362 (pm20) REVERT: D 88 ASP cc_start: 0.8409 (t70) cc_final: 0.7851 (t0) REVERT: D 92 PHE cc_start: 0.8492 (p90) cc_final: 0.8184 (p90) REVERT: D 95 SER cc_start: 0.7967 (t) cc_final: 0.7669 (p) REVERT: D 103 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8181 (mtpm) REVERT: D 154 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7097 (mptt) REVERT: D 159 TYR cc_start: 0.8487 (m-80) cc_final: 0.8180 (m-80) REVERT: D 161 ASP cc_start: 0.8260 (p0) cc_final: 0.7885 (p0) REVERT: D 162 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7891 (mmt180) REVERT: D 174 LYS cc_start: 0.8672 (mptt) cc_final: 0.8297 (mptt) REVERT: D 181 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7365 (mt-10) REVERT: D 190 HIS cc_start: 0.8118 (t-90) cc_final: 0.6820 (t70) REVERT: D 203 ASP cc_start: 0.8291 (t0) cc_final: 0.7381 (t70) REVERT: D 213 ARG cc_start: 0.8318 (ttp-110) cc_final: 0.8082 (mtm180) REVERT: D 216 LYS cc_start: 0.8921 (mmtm) cc_final: 0.8328 (mmmm) REVERT: D 251 ARG cc_start: 0.8163 (tpp-160) cc_final: 0.7580 (ttm110) REVERT: D 262 ARG cc_start: 0.8882 (mtm180) cc_final: 0.8642 (mtm180) REVERT: D 291 GLN cc_start: 0.8259 (pp30) cc_final: 0.7929 (pp30) REVERT: D 325 GLU cc_start: 0.8127 (tp30) cc_final: 0.7413 (tp30) REVERT: D 376 GLU cc_start: 0.7623 (mp0) cc_final: 0.7216 (mp0) REVERT: D 383 GLU cc_start: 0.7955 (tp30) cc_final: 0.7451 (tp30) REVERT: D 391 ARG cc_start: 0.8746 (mmm160) cc_final: 0.6984 (ptm160) REVERT: D 404 ASP cc_start: 0.8352 (m-30) cc_final: 0.7295 (m-30) REVERT: D 407 GLU cc_start: 0.7815 (mp0) cc_final: 0.6786 (mp0) REVERT: D 410 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7351 (tm-30) REVERT: D 412 GLU cc_start: 0.8066 (tp30) cc_final: 0.7317 (tm-30) REVERT: D 417 ASP cc_start: 0.8156 (m-30) cc_final: 0.7907 (m-30) REVERT: D 424 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: E 9 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7457 (tm) REVERT: E 61 ASP cc_start: 0.7411 (m-30) cc_final: 0.7149 (m-30) REVERT: E 68 GLU cc_start: 0.8170 (tt0) cc_final: 0.7672 (tt0) REVERT: E 69 ASN cc_start: 0.8129 (t0) cc_final: 0.7518 (t0) REVERT: E 104 GLN cc_start: 0.7282 (mt0) cc_final: 0.6968 (mt0) REVERT: E 120 GLU cc_start: 0.7185 (mp0) cc_final: 0.6756 (mp0) REVERT: E 129 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6880 (tm-30) REVERT: E 152 PHE cc_start: 0.8176 (m-10) cc_final: 0.7961 (m-10) REVERT: E 187 ASP cc_start: 0.8373 (t0) cc_final: 0.7670 (t0) REVERT: E 246 PHE cc_start: 0.8549 (t80) cc_final: 0.8332 (t80) REVERT: E 278 GLN cc_start: 0.8277 (mt0) cc_final: 0.8034 (mt0) REVERT: E 340 SER cc_start: 0.7932 (t) cc_final: 0.7483 (t) REVERT: E 439 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7739 (ttmm) REVERT: E 440 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7480 (mpp80) REVERT: E 444 MET cc_start: 0.8291 (mtp) cc_final: 0.8034 (mtm) REVERT: E 457 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 478 ASN cc_start: 0.8088 (t0) cc_final: 0.7473 (t0) REVERT: E 534 ASP cc_start: 0.7946 (p0) cc_final: 0.7406 (p0) REVERT: E 550 TYR cc_start: 0.8430 (m-80) cc_final: 0.8162 (m-10) REVERT: E 556 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7405 (mm-30) REVERT: E 588 ASN cc_start: 0.8509 (t0) cc_final: 0.8129 (m-40) outliers start: 59 outliers final: 26 residues processed: 457 average time/residue: 1.5075 time to fit residues: 756.8778 Evaluate side-chains 454 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 415 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 154 LYS 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 9 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 439 LYS 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 206 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 213 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 342 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 28 HIS C 128 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 165 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17882 Z= 0.217 Angle : 0.560 9.446 24321 Z= 0.282 Chirality : 0.044 0.163 2657 Planarity : 0.004 0.053 3175 Dihedral : 10.724 178.235 2519 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.25 % Allowed : 17.57 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2208 helix: 1.49 (0.17), residues: 920 sheet: 0.38 (0.29), residues: 341 loop : -0.51 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 21 HIS 0.011 0.001 HIS D 190 PHE 0.027 0.001 PHE E 75 TYR 0.014 0.001 TYR D 425 ARG 0.014 0.001 ARG E 590 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 433 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7482 (mtm180) cc_final: 0.7182 (ptp90) REVERT: A 55 GLU cc_start: 0.7909 (tt0) cc_final: 0.7400 (tp30) REVERT: A 77 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 83 TYR cc_start: 0.8569 (m-80) cc_final: 0.8046 (m-80) REVERT: A 116 ASP cc_start: 0.7830 (m-30) cc_final: 0.7143 (m-30) REVERT: A 117 LEU cc_start: 0.7571 (tp) cc_final: 0.7091 (tt) REVERT: A 120 ASP cc_start: 0.7412 (m-30) cc_final: 0.7072 (m-30) REVERT: A 154 MET cc_start: 0.8340 (mmm) cc_final: 0.7977 (mmp) REVERT: A 211 ASP cc_start: 0.7846 (m-30) cc_final: 0.7632 (m-30) REVERT: A 218 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: A 221 ARG cc_start: 0.8061 (ptp-110) cc_final: 0.7840 (ptp90) REVERT: A 241 SER cc_start: 0.8678 (m) cc_final: 0.8410 (t) REVERT: A 242 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 251 ASP cc_start: 0.7401 (m-30) cc_final: 0.6950 (t0) REVERT: A 254 GLU cc_start: 0.7471 (tt0) cc_final: 0.7215 (tp30) REVERT: A 277 SER cc_start: 0.8380 (t) cc_final: 0.7698 (p) REVERT: A 284 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7653 (mt-10) REVERT: A 290 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 322 ASP cc_start: 0.7961 (t0) cc_final: 0.7360 (p0) REVERT: A 326 LYS cc_start: 0.7984 (pttp) cc_final: 0.7551 (ptpt) REVERT: A 338 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7802 (ttpp) REVERT: A 370 LYS cc_start: 0.8407 (tptt) cc_final: 0.8047 (tptt) REVERT: A 388 TRP cc_start: 0.8110 (m-10) cc_final: 0.7421 (m-10) REVERT: A 392 ASP cc_start: 0.8274 (m-30) cc_final: 0.7584 (m-30) REVERT: A 414 GLU cc_start: 0.7766 (mp0) cc_final: 0.7133 (mp0) REVERT: A 420 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7429 (mm-30) REVERT: A 423 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 434 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7582 (pp20) REVERT: B 19 LYS cc_start: 0.8407 (tptm) cc_final: 0.8153 (tppt) REVERT: B 36 TYR cc_start: 0.8561 (t80) cc_final: 0.8129 (t80) REVERT: B 48 ASN cc_start: 0.8329 (p0) cc_final: 0.7986 (p0) REVERT: B 53 GLU cc_start: 0.8070 (tt0) cc_final: 0.7493 (tp30) REVERT: B 58 LYS cc_start: 0.7746 (tttt) cc_final: 0.7310 (ttmm) REVERT: B 69 GLU cc_start: 0.7719 (tt0) cc_final: 0.7234 (pt0) REVERT: B 74 ASP cc_start: 0.7474 (t0) cc_final: 0.7139 (t0) REVERT: B 114 ASP cc_start: 0.7665 (m-30) cc_final: 0.7390 (m-30) REVERT: B 118 ASP cc_start: 0.7342 (m-30) cc_final: 0.7058 (m-30) REVERT: B 123 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7459 (tp30) REVERT: B 127 CYS cc_start: 0.7521 (m) cc_final: 0.6803 (m) REVERT: B 134 GLN cc_start: 0.8074 (mt0) cc_final: 0.7688 (mt0) REVERT: B 154 LYS cc_start: 0.7793 (mmtp) cc_final: 0.7504 (mttp) REVERT: B 157 GLU cc_start: 0.8033 (tp30) cc_final: 0.7831 (tt0) REVERT: B 158 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: B 164 MET cc_start: 0.8432 (tpp) cc_final: 0.8103 (tpt) REVERT: B 174 LYS cc_start: 0.8278 (mmpt) cc_final: 0.7683 (mmpt) REVERT: B 175 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8345 (m) REVERT: B 203 ASP cc_start: 0.8141 (t70) cc_final: 0.7360 (t0) REVERT: B 213 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.8127 (ptm160) REVERT: B 216 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8243 (mmmm) REVERT: B 262 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8470 (mtm180) REVERT: B 274 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8344 (p) REVERT: B 278 SER cc_start: 0.8140 (m) cc_final: 0.7697 (p) REVERT: B 291 GLN cc_start: 0.8009 (pp30) cc_final: 0.7726 (pp30) REVERT: B 309 ARG cc_start: 0.7194 (mtt-85) cc_final: 0.6791 (mtp85) REVERT: B 325 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7017 (tp30) REVERT: B 328 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6866 (tp30) REVERT: B 343 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7819 (mp0) REVERT: B 407 GLU cc_start: 0.7851 (tt0) cc_final: 0.7315 (mt-10) REVERT: B 410 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7037 (mm-30) REVERT: B 412 GLU cc_start: 0.7906 (tp30) cc_final: 0.7097 (tp30) REVERT: B 414 ASN cc_start: 0.7641 (m110) cc_final: 0.7248 (m110) REVERT: B 421 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6886 (mt-10) REVERT: C 3 GLU cc_start: 0.7203 (mp0) cc_final: 0.6722 (mp0) REVERT: C 50 ASN cc_start: 0.8506 (t0) cc_final: 0.8124 (t0) REVERT: C 77 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8082 (mm-30) REVERT: C 90 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8011 (tp30) REVERT: C 112 LYS cc_start: 0.8243 (pttp) cc_final: 0.7813 (pttm) REVERT: C 123 ARG cc_start: 0.7357 (tpp-160) cc_final: 0.6947 (tpp80) REVERT: C 128 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: C 196 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: C 199 ASP cc_start: 0.7953 (p0) cc_final: 0.7716 (p0) REVERT: C 245 ASP cc_start: 0.7949 (p0) cc_final: 0.7660 (p0) REVERT: C 251 ASP cc_start: 0.7595 (m-30) cc_final: 0.7193 (t70) REVERT: C 254 GLU cc_start: 0.7629 (tt0) cc_final: 0.7155 (mm-30) REVERT: C 277 SER cc_start: 0.8238 (t) cc_final: 0.7829 (p) REVERT: C 280 LYS cc_start: 0.8523 (mttp) cc_final: 0.7407 (mmpt) REVERT: C 308 ARG cc_start: 0.5159 (tpt170) cc_final: 0.4831 (tpt170) REVERT: C 322 ASP cc_start: 0.8182 (t70) cc_final: 0.7853 (t0) REVERT: C 337 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8367 (p) REVERT: C 367 ASP cc_start: 0.7277 (t0) cc_final: 0.6979 (t0) REVERT: C 370 LYS cc_start: 0.8502 (tmmm) cc_final: 0.8254 (tmmt) REVERT: C 377 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8298 (ttm) REVERT: C 411 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8049 (mm-30) REVERT: C 420 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7350 (mm-30) REVERT: C 423 GLU cc_start: 0.7831 (tp30) cc_final: 0.7356 (mm-30) REVERT: C 424 ASP cc_start: 0.7611 (m-30) cc_final: 0.7342 (t0) REVERT: C 433 GLU cc_start: 0.7993 (tt0) cc_final: 0.7235 (tm-30) REVERT: D 3 GLU cc_start: 0.7876 (mp0) cc_final: 0.7306 (mp0) REVERT: D 19 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8150 (tppp) REVERT: D 22 GLU cc_start: 0.8361 (tt0) cc_final: 0.7878 (tm-30) REVERT: D 26 ASP cc_start: 0.7558 (m-30) cc_final: 0.7168 (t0) REVERT: D 41 ASP cc_start: 0.8059 (m-30) cc_final: 0.7796 (p0) REVERT: D 45 GLU cc_start: 0.8610 (tt0) cc_final: 0.7823 (tm-30) REVERT: D 57 ASN cc_start: 0.7870 (t0) cc_final: 0.6544 (t0) REVERT: D 69 GLU cc_start: 0.7786 (pp20) cc_final: 0.7354 (pm20) REVERT: D 88 ASP cc_start: 0.8460 (t70) cc_final: 0.7911 (t0) REVERT: D 92 PHE cc_start: 0.8556 (p90) cc_final: 0.8218 (p90) REVERT: D 95 SER cc_start: 0.7979 (t) cc_final: 0.7670 (p) REVERT: D 103 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8159 (mtpm) REVERT: D 123 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7327 (mm-30) REVERT: D 154 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7009 (mptt) REVERT: D 159 TYR cc_start: 0.8467 (m-80) cc_final: 0.8151 (m-80) REVERT: D 161 ASP cc_start: 0.8247 (p0) cc_final: 0.7917 (p0) REVERT: D 162 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7904 (mmt-90) REVERT: D 174 LYS cc_start: 0.8615 (mptt) cc_final: 0.8249 (mptt) REVERT: D 181 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7497 (mt-10) REVERT: D 190 HIS cc_start: 0.8212 (t-90) cc_final: 0.7289 (t70) REVERT: D 203 ASP cc_start: 0.8263 (t0) cc_final: 0.7378 (t70) REVERT: D 213 ARG cc_start: 0.8345 (ttp-110) cc_final: 0.8097 (mtm180) REVERT: D 216 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8393 (mmmm) REVERT: D 251 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7590 (ttm110) REVERT: D 291 GLN cc_start: 0.8254 (pp30) cc_final: 0.7931 (pp30) REVERT: D 325 GLU cc_start: 0.8150 (tp30) cc_final: 0.7429 (tp30) REVERT: D 376 GLU cc_start: 0.7638 (mp0) cc_final: 0.7192 (mp0) REVERT: D 383 GLU cc_start: 0.7981 (tp30) cc_final: 0.7472 (tp30) REVERT: D 391 ARG cc_start: 0.8822 (mmm160) cc_final: 0.6972 (ptm160) REVERT: D 404 ASP cc_start: 0.8280 (m-30) cc_final: 0.7116 (m-30) REVERT: D 407 GLU cc_start: 0.7840 (mp0) cc_final: 0.6832 (mp0) REVERT: D 410 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7311 (tm-30) REVERT: D 412 GLU cc_start: 0.8018 (tp30) cc_final: 0.7241 (tm-30) REVERT: D 417 ASP cc_start: 0.8166 (m-30) cc_final: 0.7878 (m-30) REVERT: D 424 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: E 9 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7439 (tm) REVERT: E 21 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.7819 (t70) REVERT: E 61 ASP cc_start: 0.7442 (m-30) cc_final: 0.7220 (m-30) REVERT: E 68 GLU cc_start: 0.8130 (tt0) cc_final: 0.7860 (tt0) REVERT: E 69 ASN cc_start: 0.8140 (t0) cc_final: 0.7527 (t0) REVERT: E 104 GLN cc_start: 0.7098 (mt0) cc_final: 0.6816 (mt0) REVERT: E 120 GLU cc_start: 0.7203 (mp0) cc_final: 0.6766 (mp0) REVERT: E 129 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6956 (tm-30) REVERT: E 152 PHE cc_start: 0.8159 (m-10) cc_final: 0.7932 (m-10) REVERT: E 187 ASP cc_start: 0.8385 (t0) cc_final: 0.7510 (t0) REVERT: E 314 GLN cc_start: 0.8232 (mp10) cc_final: 0.7989 (mp10) REVERT: E 340 SER cc_start: 0.7993 (t) cc_final: 0.7537 (t) REVERT: E 440 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7367 (mpp80) REVERT: E 444 MET cc_start: 0.8312 (mtp) cc_final: 0.8040 (mtm) REVERT: E 478 ASN cc_start: 0.8083 (t0) cc_final: 0.7446 (t0) REVERT: E 534 ASP cc_start: 0.7955 (p0) cc_final: 0.7382 (p0) REVERT: E 550 TYR cc_start: 0.8434 (m-80) cc_final: 0.8161 (m-10) REVERT: E 556 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7412 (mm-30) REVERT: E 588 ASN cc_start: 0.8571 (t0) cc_final: 0.8234 (m-40) outliers start: 60 outliers final: 26 residues processed: 461 average time/residue: 1.4728 time to fit residues: 746.1626 Evaluate side-chains 468 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 426 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 262 ARG 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 128 GLN Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 337 THR 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 65 LEU Chi-restraints excluded: chain D residue 154 LYS 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 9 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 128 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 292 GLN E 226 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17882 Z= 0.272 Angle : 0.585 9.647 24321 Z= 0.297 Chirality : 0.045 0.164 2657 Planarity : 0.004 0.051 3175 Dihedral : 10.745 173.650 2519 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.36 % Allowed : 18.38 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 2208 helix: 1.49 (0.17), residues: 918 sheet: 0.36 (0.29), residues: 341 loop : -0.53 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 21 HIS 0.012 0.001 HIS D 190 PHE 0.028 0.002 PHE E 75 TYR 0.016 0.001 TYR D 425 ARG 0.012 0.001 ARG E 590 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 430 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7549 (mtm180) cc_final: 0.6947 (ptp90) REVERT: A 55 GLU cc_start: 0.7976 (tt0) cc_final: 0.7420 (tp30) REVERT: A 77 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7135 (mt-10) REVERT: A 83 TYR cc_start: 0.8574 (m-80) cc_final: 0.8086 (m-80) REVERT: A 84 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7504 (mtm110) REVERT: A 116 ASP cc_start: 0.7846 (m-30) cc_final: 0.7201 (m-30) REVERT: A 117 LEU cc_start: 0.7754 (tp) cc_final: 0.7245 (tt) REVERT: A 120 ASP cc_start: 0.7363 (m-30) cc_final: 0.6959 (m-30) REVERT: A 154 MET cc_start: 0.8359 (mmm) cc_final: 0.8090 (mmp) REVERT: A 218 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: A 241 SER cc_start: 0.8709 (m) cc_final: 0.8444 (t) REVERT: A 242 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8347 (tt) REVERT: A 251 ASP cc_start: 0.7442 (m-30) cc_final: 0.6989 (t0) REVERT: A 254 GLU cc_start: 0.7535 (tt0) cc_final: 0.7314 (tp30) REVERT: A 277 SER cc_start: 0.8433 (t) cc_final: 0.7925 (p) REVERT: A 284 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7650 (mt-10) REVERT: A 290 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 322 ASP cc_start: 0.7996 (t0) cc_final: 0.7350 (p0) REVERT: A 326 LYS cc_start: 0.7997 (pttp) cc_final: 0.7633 (ptpt) REVERT: A 338 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7794 (ttpp) REVERT: A 370 LYS cc_start: 0.8480 (tptt) cc_final: 0.8129 (tptt) REVERT: A 388 TRP cc_start: 0.8118 (m-10) cc_final: 0.7436 (m-10) REVERT: A 392 ASP cc_start: 0.8271 (m-30) cc_final: 0.7582 (m-30) REVERT: A 414 GLU cc_start: 0.7785 (mp0) cc_final: 0.7225 (mp0) REVERT: A 420 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7425 (mm-30) REVERT: A 423 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 434 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7640 (pp20) REVERT: B 36 TYR cc_start: 0.8550 (t80) cc_final: 0.8188 (t80) REVERT: B 48 ASN cc_start: 0.8371 (p0) cc_final: 0.8117 (p0) REVERT: B 53 GLU cc_start: 0.8092 (tt0) cc_final: 0.7494 (tp30) REVERT: B 58 LYS cc_start: 0.7737 (tttt) cc_final: 0.7313 (ttmm) REVERT: B 69 GLU cc_start: 0.7722 (tt0) cc_final: 0.7193 (pt0) REVERT: B 74 ASP cc_start: 0.7479 (t0) cc_final: 0.7157 (t0) REVERT: B 114 ASP cc_start: 0.7653 (m-30) cc_final: 0.7387 (m-30) REVERT: B 118 ASP cc_start: 0.7342 (m-30) cc_final: 0.7064 (m-30) REVERT: B 123 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7403 (tp30) REVERT: B 127 CYS cc_start: 0.7467 (m) cc_final: 0.6793 (m) REVERT: B 134 GLN cc_start: 0.8102 (mt0) cc_final: 0.7721 (mt0) REVERT: B 157 GLU cc_start: 0.8032 (tp30) cc_final: 0.7830 (tt0) REVERT: B 158 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: B 164 MET cc_start: 0.8448 (tpp) cc_final: 0.8113 (tpt) REVERT: B 174 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7694 (mmpt) REVERT: B 175 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8359 (m) REVERT: B 203 ASP cc_start: 0.8107 (t70) cc_final: 0.7426 (t0) REVERT: B 216 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8238 (mmmm) REVERT: B 274 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 278 SER cc_start: 0.8183 (m) cc_final: 0.7715 (p) REVERT: B 291 GLN cc_start: 0.8056 (pp30) cc_final: 0.7794 (pp30) REVERT: B 325 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: B 328 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6879 (OUTLIER) REVERT: B 407 GLU cc_start: 0.7924 (tt0) cc_final: 0.7438 (mt-10) REVERT: B 410 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7107 (mm-30) REVERT: B 414 ASN cc_start: 0.7659 (m110) cc_final: 0.7273 (m110) REVERT: C 77 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8098 (mm-30) REVERT: C 90 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7949 (tp30) REVERT: C 97 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7850 (tt0) REVERT: C 112 LYS cc_start: 0.8260 (pttp) cc_final: 0.7840 (pttm) REVERT: C 123 ARG cc_start: 0.7400 (tpp-160) cc_final: 0.6993 (tpp80) REVERT: C 196 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: C 199 ASP cc_start: 0.7971 (p0) cc_final: 0.7742 (p0) REVERT: C 245 ASP cc_start: 0.7957 (p0) cc_final: 0.7657 (p0) REVERT: C 251 ASP cc_start: 0.7614 (m-30) cc_final: 0.7211 (t70) REVERT: C 254 GLU cc_start: 0.7654 (tt0) cc_final: 0.7159 (mm-30) REVERT: C 277 SER cc_start: 0.8285 (t) cc_final: 0.7906 (p) REVERT: C 280 LYS cc_start: 0.8397 (mttp) cc_final: 0.7527 (mmpt) REVERT: C 322 ASP cc_start: 0.8211 (t70) cc_final: 0.7846 (t0) REVERT: C 337 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8373 (p) REVERT: C 370 LYS cc_start: 0.8517 (tmmm) cc_final: 0.8260 (tmmt) REVERT: C 377 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8301 (ttm) REVERT: C 386 GLU cc_start: 0.7705 (mp0) cc_final: 0.7086 (mp0) REVERT: C 411 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 420 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 423 GLU cc_start: 0.7853 (tp30) cc_final: 0.7359 (mm-30) REVERT: C 424 ASP cc_start: 0.7579 (m-30) cc_final: 0.7306 (t0) REVERT: C 433 GLU cc_start: 0.8024 (tt0) cc_final: 0.7242 (tm-30) REVERT: C 434 GLU cc_start: 0.7887 (pp20) cc_final: 0.7370 (pp20) REVERT: D 1 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7831 (ttp) REVERT: D 3 GLU cc_start: 0.7922 (mp0) cc_final: 0.7367 (mp0) REVERT: D 22 GLU cc_start: 0.8328 (tt0) cc_final: 0.7853 (tm-30) REVERT: D 26 ASP cc_start: 0.7716 (m-30) cc_final: 0.7316 (t0) REVERT: D 41 ASP cc_start: 0.8080 (m-30) cc_final: 0.7814 (p0) REVERT: D 45 GLU cc_start: 0.8628 (tt0) cc_final: 0.7880 (tm-30) REVERT: D 57 ASN cc_start: 0.7947 (t0) cc_final: 0.6643 (t0) REVERT: D 69 GLU cc_start: 0.7920 (pp20) cc_final: 0.7445 (pm20) REVERT: D 88 ASP cc_start: 0.8468 (t70) cc_final: 0.7920 (t0) REVERT: D 92 PHE cc_start: 0.8588 (p90) cc_final: 0.8211 (p90) REVERT: D 95 SER cc_start: 0.7985 (t) cc_final: 0.7730 (p) REVERT: D 103 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8017 (mtpm) REVERT: D 108 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7580 (mp0) REVERT: D 154 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7089 (mptt) REVERT: D 159 TYR cc_start: 0.8496 (m-80) cc_final: 0.8151 (m-80) REVERT: D 161 ASP cc_start: 0.8218 (p0) cc_final: 0.7836 (p0) REVERT: D 162 ARG cc_start: 0.8260 (mmt-90) cc_final: 0.7888 (mmt-90) REVERT: D 174 LYS cc_start: 0.8622 (mptt) cc_final: 0.8249 (mptt) REVERT: D 181 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7492 (mt-10) REVERT: D 190 HIS cc_start: 0.8244 (t-90) cc_final: 0.7334 (t70) REVERT: D 203 ASP cc_start: 0.8193 (t0) cc_final: 0.7372 (t70) REVERT: D 213 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.8070 (mtm180) REVERT: D 216 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8384 (mmmm) REVERT: D 251 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7753 (ttm110) REVERT: D 279 GLN cc_start: 0.7829 (pp30) cc_final: 0.7502 (pp30) REVERT: D 289 LEU cc_start: 0.8017 (mp) cc_final: 0.7804 (mp) REVERT: D 291 GLN cc_start: 0.8256 (pp30) cc_final: 0.7952 (pp30) REVERT: D 309 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7768 (mtp85) REVERT: D 324 LYS cc_start: 0.8315 (tptp) cc_final: 0.7913 (ttpp) REVERT: D 325 GLU cc_start: 0.8176 (tp30) cc_final: 0.7439 (tp30) REVERT: D 376 GLU cc_start: 0.7631 (mp0) cc_final: 0.7180 (mp0) REVERT: D 383 GLU cc_start: 0.7979 (tp30) cc_final: 0.7458 (tp30) REVERT: D 391 ARG cc_start: 0.8852 (mmm160) cc_final: 0.6917 (ptm160) REVERT: D 404 ASP cc_start: 0.8239 (m-30) cc_final: 0.7064 (m-30) REVERT: D 407 GLU cc_start: 0.7835 (mp0) cc_final: 0.6813 (mp0) REVERT: D 410 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7325 (tm-30) REVERT: D 412 GLU cc_start: 0.7969 (tp30) cc_final: 0.7126 (tm-30) REVERT: D 417 ASP cc_start: 0.8142 (m-30) cc_final: 0.7885 (m-30) REVERT: D 424 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: E 9 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7443 (tm) REVERT: E 21 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.7832 (t70) REVERT: E 61 ASP cc_start: 0.7478 (m-30) cc_final: 0.7257 (m-30) REVERT: E 69 ASN cc_start: 0.8190 (t0) cc_final: 0.7582 (t0) REVERT: E 80 ARG cc_start: 0.7302 (ttp80) cc_final: 0.6945 (ttp80) REVERT: E 120 GLU cc_start: 0.7234 (mp0) cc_final: 0.6779 (mp0) REVERT: E 129 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6903 (tm-30) REVERT: E 152 PHE cc_start: 0.8144 (m-10) cc_final: 0.7933 (m-10) REVERT: E 187 ASP cc_start: 0.8306 (t0) cc_final: 0.7698 (t0) REVERT: E 226 GLN cc_start: 0.8818 (mt0) cc_final: 0.8422 (mt0) REVERT: E 314 GLN cc_start: 0.8196 (mp10) cc_final: 0.7940 (mp10) REVERT: E 340 SER cc_start: 0.7990 (t) cc_final: 0.7529 (t) REVERT: E 440 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7781 (mpt-90) REVERT: E 444 MET cc_start: 0.8337 (mtp) cc_final: 0.8071 (mtm) REVERT: E 457 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7473 (mm-30) REVERT: E 478 ASN cc_start: 0.8066 (t0) cc_final: 0.7414 (t0) REVERT: E 534 ASP cc_start: 0.7991 (p0) cc_final: 0.7774 (p0) REVERT: E 550 TYR cc_start: 0.8438 (m-80) cc_final: 0.8171 (m-10) REVERT: E 556 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7421 (mm-30) REVERT: E 588 ASN cc_start: 0.8584 (t0) cc_final: 0.8275 (m-40) outliers start: 62 outliers final: 30 residues processed: 461 average time/residue: 1.4851 time to fit residues: 753.9680 Evaluate side-chains 477 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 433 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 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 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 337 THR 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 65 LEU Chi-restraints excluded: chain D residue 154 LYS 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 9 LEU Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 197 optimal weight: 0.0060 chunk 130 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17882 Z= 0.223 Angle : 0.578 9.709 24321 Z= 0.292 Chirality : 0.044 0.159 2657 Planarity : 0.004 0.052 3175 Dihedral : 10.684 175.349 2519 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.82 % Allowed : 19.20 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2208 helix: 1.52 (0.17), residues: 919 sheet: 0.27 (0.29), residues: 342 loop : -0.56 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.011 0.001 HIS D 190 PHE 0.029 0.001 PHE E 75 TYR 0.015 0.001 TYR D 425 ARG 0.011 0.001 ARG E 590 *********************** 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 485 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 433 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7509 (mtm180) cc_final: 0.6960 (ptp90) REVERT: A 55 GLU cc_start: 0.7957 (tt0) cc_final: 0.7434 (tp30) REVERT: A 83 TYR cc_start: 0.8566 (m-80) cc_final: 0.8004 (m-80) REVERT: A 84 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7542 (mtm110) REVERT: A 114 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6617 (pt) REVERT: A 116 ASP cc_start: 0.7830 (m-30) cc_final: 0.7282 (m-30) REVERT: A 117 LEU cc_start: 0.7754 (tp) cc_final: 0.7281 (tt) REVERT: A 120 ASP cc_start: 0.7358 (m-30) cc_final: 0.7057 (m-30) REVERT: A 154 MET cc_start: 0.8360 (mmm) cc_final: 0.8044 (mmp) REVERT: A 214 ARG cc_start: 0.8160 (ttp-110) cc_final: 0.7949 (ttp-110) REVERT: A 241 SER cc_start: 0.8704 (m) cc_final: 0.8326 (t) REVERT: A 251 ASP cc_start: 0.7429 (m-30) cc_final: 0.6974 (t0) REVERT: A 254 GLU cc_start: 0.7541 (tt0) cc_final: 0.7307 (tp30) REVERT: A 277 SER cc_start: 0.8388 (t) cc_final: 0.7956 (p) REVERT: A 284 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7610 (mt-10) REVERT: A 290 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 322 ASP cc_start: 0.7999 (t0) cc_final: 0.7346 (p0) REVERT: A 326 LYS cc_start: 0.7981 (pttp) cc_final: 0.7626 (ptpt) REVERT: A 338 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7868 (mtpp) REVERT: A 342 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7460 (mm-40) REVERT: A 370 LYS cc_start: 0.8476 (tptt) cc_final: 0.8126 (tptt) REVERT: A 388 TRP cc_start: 0.8149 (m-10) cc_final: 0.7479 (m-10) REVERT: A 392 ASP cc_start: 0.8269 (m-30) cc_final: 0.7569 (m-30) REVERT: A 414 GLU cc_start: 0.7741 (mp0) cc_final: 0.7216 (mp0) REVERT: A 420 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7444 (mm-30) REVERT: A 423 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 434 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7645 (pp20) REVERT: B 36 TYR cc_start: 0.8551 (t80) cc_final: 0.8189 (t80) REVERT: B 48 ASN cc_start: 0.8363 (p0) cc_final: 0.8106 (p0) REVERT: B 53 GLU cc_start: 0.8041 (tt0) cc_final: 0.7455 (tp30) REVERT: B 58 LYS cc_start: 0.7729 (tttt) cc_final: 0.7313 (ttmm) REVERT: B 69 GLU cc_start: 0.7701 (tt0) cc_final: 0.7113 (pt0) REVERT: B 74 ASP cc_start: 0.7496 (t0) cc_final: 0.7164 (t0) REVERT: B 114 ASP cc_start: 0.7643 (m-30) cc_final: 0.7362 (m-30) REVERT: B 118 ASP cc_start: 0.7328 (m-30) cc_final: 0.7050 (m-30) REVERT: B 123 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7420 (tp30) REVERT: B 127 CYS cc_start: 0.7490 (m) cc_final: 0.6819 (m) REVERT: B 134 GLN cc_start: 0.8080 (mt0) cc_final: 0.7693 (mt0) REVERT: B 154 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7525 (mttp) REVERT: B 157 GLU cc_start: 0.8027 (tp30) cc_final: 0.7824 (tt0) REVERT: B 158 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: B 164 MET cc_start: 0.8446 (tpp) cc_final: 0.8106 (tpt) REVERT: B 174 LYS cc_start: 0.8237 (mmpt) cc_final: 0.7677 (mmpt) REVERT: B 175 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8355 (m) REVERT: B 203 ASP cc_start: 0.8084 (t70) cc_final: 0.7399 (t0) REVERT: B 213 ARG cc_start: 0.8464 (ptp-110) cc_final: 0.8139 (ptm160) REVERT: B 216 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8247 (mmmm) REVERT: B 274 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8388 (p) REVERT: B 278 SER cc_start: 0.8189 (m) cc_final: 0.7721 (p) REVERT: B 291 GLN cc_start: 0.8105 (pp30) cc_final: 0.7868 (pp30) REVERT: B 325 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: B 328 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6882 (OUTLIER) REVERT: B 391 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.6956 (mtm180) REVERT: B 407 GLU cc_start: 0.7905 (tt0) cc_final: 0.7420 (mt-10) REVERT: B 410 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7103 (mm-30) REVERT: B 414 ASN cc_start: 0.7577 (m110) cc_final: 0.7347 (m110) REVERT: B 421 GLU cc_start: 0.7980 (tt0) cc_final: 0.7371 (tm-30) REVERT: C 77 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8072 (mm-30) REVERT: C 90 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7963 (tp30) REVERT: C 112 LYS cc_start: 0.8248 (pttp) cc_final: 0.7825 (pttm) REVERT: C 123 ARG cc_start: 0.7411 (tpp-160) cc_final: 0.7003 (tpp80) REVERT: C 196 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: C 199 ASP cc_start: 0.7978 (p0) cc_final: 0.7759 (p0) REVERT: C 245 ASP cc_start: 0.7951 (p0) cc_final: 0.7433 (p0) REVERT: C 251 ASP cc_start: 0.7607 (m-30) cc_final: 0.7241 (t70) REVERT: C 254 GLU cc_start: 0.7643 (tt0) cc_final: 0.7193 (mm-30) REVERT: C 277 SER cc_start: 0.8332 (t) cc_final: 0.7962 (p) REVERT: C 280 LYS cc_start: 0.8343 (mttp) cc_final: 0.7501 (mmtt) REVERT: C 308 ARG cc_start: 0.5714 (tpt170) cc_final: 0.5332 (tpt170) REVERT: C 322 ASP cc_start: 0.8187 (t70) cc_final: 0.7839 (t0) REVERT: C 370 LYS cc_start: 0.8512 (tmmm) cc_final: 0.8237 (tmmt) REVERT: C 377 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8305 (ttm) REVERT: C 411 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8027 (mm-30) REVERT: C 420 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7271 (mm-30) REVERT: C 423 GLU cc_start: 0.7840 (tp30) cc_final: 0.7397 (mm-30) REVERT: C 424 ASP cc_start: 0.7581 (m-30) cc_final: 0.7309 (OUTLIER) REVERT: C 433 GLU cc_start: 0.8049 (tt0) cc_final: 0.7248 (tm-30) REVERT: C 434 GLU cc_start: 0.7861 (pp20) cc_final: 0.7383 (pp20) REVERT: D 1 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7845 (ttp) REVERT: D 3 GLU cc_start: 0.7941 (mp0) cc_final: 0.7410 (mp0) REVERT: D 19 LYS cc_start: 0.8438 (tppp) cc_final: 0.8030 (tppp) REVERT: D 22 GLU cc_start: 0.8339 (tt0) cc_final: 0.7811 (tm-30) REVERT: D 26 ASP cc_start: 0.7693 (m-30) cc_final: 0.7318 (t0) REVERT: D 41 ASP cc_start: 0.8076 (m-30) cc_final: 0.7818 (OUTLIER) REVERT: D 45 GLU cc_start: 0.8632 (tt0) cc_final: 0.7881 (tm-30) REVERT: D 57 ASN cc_start: 0.7998 (t0) cc_final: 0.6720 (t0) REVERT: D 69 GLU cc_start: 0.7906 (pp20) cc_final: 0.7453 (pm20) REVERT: D 88 ASP cc_start: 0.8402 (t70) cc_final: 0.7852 (t0) REVERT: D 92 PHE cc_start: 0.8591 (p90) cc_final: 0.8215 (p90) REVERT: D 95 SER cc_start: 0.7987 (t) cc_final: 0.7699 (p) REVERT: D 103 LYS cc_start: 0.8508 (mtpt) cc_final: 0.7998 (mtpm) REVERT: D 108 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7671 (mp0) REVERT: D 154 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.6908 (mptt) REVERT: D 157 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: D 159 TYR cc_start: 0.8499 (m-80) cc_final: 0.8195 (m-80) REVERT: D 161 ASP cc_start: 0.8219 (p0) cc_final: 0.7835 (p0) REVERT: D 162 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7895 (mmt-90) REVERT: D 174 LYS cc_start: 0.8615 (mptt) cc_final: 0.8243 (mptt) REVERT: D 181 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7378 (mt-10) REVERT: D 190 HIS cc_start: 0.8218 (t-90) cc_final: 0.7317 (t70) REVERT: D 203 ASP cc_start: 0.8198 (t0) cc_final: 0.7369 (t70) REVERT: D 213 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.8063 (mtm180) REVERT: D 216 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8381 (mmmm) REVERT: D 251 ARG cc_start: 0.8182 (tpp-160) cc_final: 0.7759 (ttm110) REVERT: D 279 GLN cc_start: 0.7779 (pp30) cc_final: 0.7497 (tm130) REVERT: D 291 GLN cc_start: 0.8248 (pp30) cc_final: 0.7947 (pp30) REVERT: D 309 ARG cc_start: 0.8145 (mmm-85) cc_final: 0.7749 (mtp85) REVERT: D 325 GLU cc_start: 0.8169 (tp30) cc_final: 0.7457 (tp30) REVERT: D 376 GLU cc_start: 0.7625 (mp0) cc_final: 0.7152 (mp0) REVERT: D 383 GLU cc_start: 0.7976 (tp30) cc_final: 0.7455 (tp30) REVERT: D 391 ARG cc_start: 0.8859 (mmm160) cc_final: 0.6912 (ptm160) REVERT: D 404 ASP cc_start: 0.8239 (m-30) cc_final: 0.7309 (m-30) REVERT: D 407 GLU cc_start: 0.7834 (mp0) cc_final: 0.6970 (mp0) REVERT: D 410 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7311 (tm-30) REVERT: D 412 GLU cc_start: 0.7974 (tp30) cc_final: 0.7148 (tm-30) REVERT: E 9 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7358 (tm) REVERT: E 21 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.7848 (t70) REVERT: E 68 GLU cc_start: 0.8191 (tt0) cc_final: 0.7660 (tt0) REVERT: E 69 ASN cc_start: 0.8197 (t0) cc_final: 0.7596 (t0) REVERT: E 80 ARG cc_start: 0.7280 (ttp80) cc_final: 0.6930 (ttp80) REVERT: E 104 GLN cc_start: 0.7498 (mt0) cc_final: 0.7097 (mt0) REVERT: E 120 GLU cc_start: 0.7240 (mp0) cc_final: 0.6774 (mp0) REVERT: E 129 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6926 (tm-30) REVERT: E 187 ASP cc_start: 0.8300 (t0) cc_final: 0.7740 (t0) REVERT: E 314 GLN cc_start: 0.8133 (mp10) cc_final: 0.7879 (mp10) REVERT: E 340 SER cc_start: 0.7962 (t) cc_final: 0.7531 (t) REVERT: E 440 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7540 (mpp80) REVERT: E 457 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7480 (mm-30) REVERT: E 478 ASN cc_start: 0.8067 (t0) cc_final: 0.7420 (t0) REVERT: E 550 TYR cc_start: 0.8432 (m-80) cc_final: 0.8168 (m-10) REVERT: E 556 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7413 (mm-30) REVERT: E 588 ASN cc_start: 0.8580 (t0) cc_final: 0.8287 (m-40) outliers start: 52 outliers final: 30 residues processed: 457 average time/residue: 1.5227 time to fit residues: 763.9151 Evaluate side-chains 459 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 419 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 THR 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 362 LYS 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 219 ILE 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 65 LEU Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 440 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 135 optimal weight: 0.7980 chunk 107 optimal weight: 0.0370 chunk 139 optimal weight: 1.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 88 HIS A 256 GLN B 227 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 128 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17882 Z= 0.184 Angle : 0.568 9.850 24321 Z= 0.286 Chirality : 0.043 0.155 2657 Planarity : 0.004 0.049 3175 Dihedral : 10.571 179.553 2519 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.49 % Allowed : 20.07 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2208 helix: 1.57 (0.18), residues: 921 sheet: 0.44 (0.29), residues: 343 loop : -0.56 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 21 HIS 0.009 0.001 HIS D 190 PHE 0.030 0.001 PHE E 75 TYR 0.027 0.001 TYR D 36 ARG 0.010 0.001 ARG E 590 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 424 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7484 (mtm180) cc_final: 0.7015 (ptp90) REVERT: A 83 TYR cc_start: 0.8562 (m-80) cc_final: 0.8023 (m-80) REVERT: A 84 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7654 (mtm110) REVERT: A 116 ASP cc_start: 0.7966 (m-30) cc_final: 0.7418 (m-30) REVERT: A 117 LEU cc_start: 0.7730 (tp) cc_final: 0.7297 (tt) REVERT: A 120 ASP cc_start: 0.7367 (m-30) cc_final: 0.7041 (m-30) REVERT: A 141 PHE cc_start: 0.8405 (m-80) cc_final: 0.8064 (m-80) REVERT: A 154 MET cc_start: 0.8339 (mmm) cc_final: 0.7976 (mmp) REVERT: A 218 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: A 241 SER cc_start: 0.8679 (m) cc_final: 0.8339 (t) REVERT: A 251 ASP cc_start: 0.7397 (m-30) cc_final: 0.7031 (t0) REVERT: A 254 GLU cc_start: 0.7487 (tt0) cc_final: 0.7169 (tp30) REVERT: A 277 SER cc_start: 0.8515 (t) cc_final: 0.8071 (p) REVERT: A 284 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7611 (mt-10) REVERT: A 290 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7528 (mm-30) REVERT: A 322 ASP cc_start: 0.7967 (t0) cc_final: 0.7352 (p0) REVERT: A 326 LYS cc_start: 0.7962 (pttp) cc_final: 0.7617 (ptpt) REVERT: A 338 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7861 (mtpp) REVERT: A 370 LYS cc_start: 0.8471 (tptt) cc_final: 0.8123 (tptt) REVERT: A 388 TRP cc_start: 0.8127 (m-10) cc_final: 0.7418 (m-10) REVERT: A 392 ASP cc_start: 0.8270 (m-30) cc_final: 0.7551 (m-30) REVERT: A 414 GLU cc_start: 0.7739 (mp0) cc_final: 0.7207 (mp0) REVERT: A 420 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 423 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 434 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7642 (pp20) REVERT: B 36 TYR cc_start: 0.8546 (t80) cc_final: 0.8189 (t80) REVERT: B 48 ASN cc_start: 0.8356 (p0) cc_final: 0.7992 (p0) REVERT: B 53 GLU cc_start: 0.7995 (tt0) cc_final: 0.7424 (tp30) REVERT: B 58 LYS cc_start: 0.7718 (tttt) cc_final: 0.7316 (ttmm) REVERT: B 69 GLU cc_start: 0.7688 (tt0) cc_final: 0.7081 (pt0) REVERT: B 74 ASP cc_start: 0.7471 (t0) cc_final: 0.7174 (OUTLIER) REVERT: B 76 VAL cc_start: 0.7744 (t) cc_final: 0.7508 (p) REVERT: B 84 ILE cc_start: 0.8741 (tt) cc_final: 0.8209 (pt) REVERT: B 114 ASP cc_start: 0.7640 (m-30) cc_final: 0.7365 (m-30) REVERT: B 118 ASP cc_start: 0.7330 (m-30) cc_final: 0.7040 (m-30) REVERT: B 123 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7460 (tp30) REVERT: B 127 CYS cc_start: 0.7606 (m) cc_final: 0.6866 (m) REVERT: B 134 GLN cc_start: 0.8058 (mt0) cc_final: 0.7672 (mt0) REVERT: B 154 LYS cc_start: 0.7814 (mmtp) cc_final: 0.7519 (mttp) REVERT: B 157 GLU cc_start: 0.8024 (tp30) cc_final: 0.7821 (tt0) REVERT: B 158 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 164 MET cc_start: 0.8410 (tpp) cc_final: 0.8092 (tpt) REVERT: B 174 LYS cc_start: 0.8252 (mmpt) cc_final: 0.7669 (mmpt) REVERT: B 175 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8357 (m) REVERT: B 203 ASP cc_start: 0.8073 (t70) cc_final: 0.7362 (t0) REVERT: B 274 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 278 SER cc_start: 0.8168 (m) cc_final: 0.7729 (p) REVERT: B 325 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: B 328 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6875 (OUTLIER) REVERT: B 391 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.6859 (mtm110) REVERT: B 407 GLU cc_start: 0.7858 (tt0) cc_final: 0.7362 (mt-10) REVERT: B 410 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7056 (mm-30) REVERT: B 414 ASN cc_start: 0.7653 (m110) cc_final: 0.7337 (m110) REVERT: C 77 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8072 (mm-30) REVERT: C 90 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7965 (tp30) REVERT: C 112 LYS cc_start: 0.8222 (pttp) cc_final: 0.7783 (pttm) REVERT: C 123 ARG cc_start: 0.7408 (tpp-160) cc_final: 0.6998 (tpp80) REVERT: C 196 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: C 199 ASP cc_start: 0.7980 (p0) cc_final: 0.7753 (p0) REVERT: C 245 ASP cc_start: 0.7781 (p0) cc_final: 0.7399 (p0) REVERT: C 251 ASP cc_start: 0.7600 (m-30) cc_final: 0.7220 (t70) REVERT: C 254 GLU cc_start: 0.7634 (tt0) cc_final: 0.7195 (mm-30) REVERT: C 277 SER cc_start: 0.8336 (t) cc_final: 0.7983 (p) REVERT: C 280 LYS cc_start: 0.8403 (mttp) cc_final: 0.7684 (mmtt) REVERT: C 308 ARG cc_start: 0.5708 (tpt170) cc_final: 0.5339 (tpt170) REVERT: C 322 ASP cc_start: 0.8184 (t70) cc_final: 0.7863 (t0) REVERT: C 337 THR cc_start: 0.8648 (t) cc_final: 0.8420 (p) REVERT: C 367 ASP cc_start: 0.7431 (t0) cc_final: 0.7144 (m-30) REVERT: C 370 LYS cc_start: 0.8512 (tmmm) cc_final: 0.8239 (tmmt) REVERT: C 377 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8319 (ttm) REVERT: C 411 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7994 (mm-30) REVERT: C 420 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7259 (mm-30) REVERT: C 423 GLU cc_start: 0.7842 (tp30) cc_final: 0.7412 (mm-30) REVERT: C 424 ASP cc_start: 0.7630 (m-30) cc_final: 0.7365 (t0) REVERT: C 433 GLU cc_start: 0.8043 (tt0) cc_final: 0.7257 (tm-30) REVERT: C 434 GLU cc_start: 0.7857 (pp20) cc_final: 0.7359 (pp20) REVERT: D 1 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7846 (ttp) REVERT: D 3 GLU cc_start: 0.7932 (mp0) cc_final: 0.7414 (mp0) REVERT: D 19 LYS cc_start: 0.8426 (tppp) cc_final: 0.8165 (tppp) REVERT: D 22 GLU cc_start: 0.8359 (tt0) cc_final: 0.7901 (tm-30) REVERT: D 26 ASP cc_start: 0.7624 (m-30) cc_final: 0.7304 (t0) REVERT: D 27 GLU cc_start: 0.8181 (pt0) cc_final: 0.7957 (tm-30) REVERT: D 41 ASP cc_start: 0.8072 (m-30) cc_final: 0.7817 (OUTLIER) REVERT: D 45 GLU cc_start: 0.8625 (tt0) cc_final: 0.7866 (tm-30) REVERT: D 57 ASN cc_start: 0.7989 (t0) cc_final: 0.6725 (t0) REVERT: D 69 GLU cc_start: 0.7881 (pp20) cc_final: 0.7462 (pm20) REVERT: D 88 ASP cc_start: 0.8403 (t70) cc_final: 0.7854 (t0) REVERT: D 92 PHE cc_start: 0.8616 (p90) cc_final: 0.8224 (p90) REVERT: D 95 SER cc_start: 0.7975 (t) cc_final: 0.7683 (p) REVERT: D 103 LYS cc_start: 0.8498 (mtpt) cc_final: 0.7985 (mtpm) REVERT: D 108 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7552 (mp0) REVERT: D 154 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.6865 (mptt) REVERT: D 157 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7445 (pp20) REVERT: D 159 TYR cc_start: 0.8510 (m-80) cc_final: 0.8229 (m-80) REVERT: D 161 ASP cc_start: 0.8219 (p0) cc_final: 0.7852 (p0) REVERT: D 162 ARG cc_start: 0.8271 (mmt-90) cc_final: 0.7929 (mmt-90) REVERT: D 174 LYS cc_start: 0.8605 (mptt) cc_final: 0.8014 (mppt) REVERT: D 181 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7396 (mt-10) REVERT: D 190 HIS cc_start: 0.8113 (t-90) cc_final: 0.7202 (t70) REVERT: D 203 ASP cc_start: 0.8202 (t0) cc_final: 0.7354 (t70) REVERT: D 213 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.8058 (mtm180) REVERT: D 216 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8374 (mmmm) REVERT: D 251 ARG cc_start: 0.8157 (tpp-160) cc_final: 0.7402 (ttm110) REVERT: D 279 GLN cc_start: 0.7765 (pp30) cc_final: 0.7454 (tm130) REVERT: D 291 GLN cc_start: 0.8171 (pp30) cc_final: 0.7888 (pp30) REVERT: D 309 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.7738 (mtp85) REVERT: D 325 GLU cc_start: 0.8135 (tp30) cc_final: 0.7452 (tp30) REVERT: D 376 GLU cc_start: 0.7603 (mp0) cc_final: 0.7109 (mp0) REVERT: D 383 GLU cc_start: 0.7964 (tp30) cc_final: 0.7450 (tp30) REVERT: D 391 ARG cc_start: 0.8845 (mmm160) cc_final: 0.6930 (ptm160) REVERT: D 404 ASP cc_start: 0.8252 (m-30) cc_final: 0.7339 (m-30) REVERT: D 407 GLU cc_start: 0.7842 (mp0) cc_final: 0.7023 (mp0) REVERT: D 410 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7289 (tm-30) REVERT: D 412 GLU cc_start: 0.7959 (tp30) cc_final: 0.7150 (tm-30) REVERT: D 417 ASP cc_start: 0.8164 (m-30) cc_final: 0.7813 (m-30) REVERT: E 9 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7423 (tm) REVERT: E 68 GLU cc_start: 0.8177 (tt0) cc_final: 0.7633 (tt0) REVERT: E 69 ASN cc_start: 0.8202 (t0) cc_final: 0.7625 (t0) REVERT: E 104 GLN cc_start: 0.7476 (mt0) cc_final: 0.7084 (mt0) REVERT: E 120 GLU cc_start: 0.7211 (mp0) cc_final: 0.6749 (mp0) REVERT: E 129 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6917 (tm-30) REVERT: E 187 ASP cc_start: 0.8259 (t0) cc_final: 0.7660 (t0) REVERT: E 226 GLN cc_start: 0.8788 (mt0) cc_final: 0.8466 (mt0) REVERT: E 314 GLN cc_start: 0.8098 (mp10) cc_final: 0.7851 (mp10) REVERT: E 340 SER cc_start: 0.7991 (t) cc_final: 0.7582 (t) REVERT: E 440 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7567 (mpp80) REVERT: E 444 MET cc_start: 0.8331 (mtm) cc_final: 0.8047 (ttm) REVERT: E 457 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7494 (mm-30) REVERT: E 478 ASN cc_start: 0.8088 (t0) cc_final: 0.7439 (t0) REVERT: E 534 ASP cc_start: 0.7871 (p0) cc_final: 0.7559 (p0) REVERT: E 550 TYR cc_start: 0.8428 (m-80) cc_final: 0.8165 (m-10) REVERT: E 556 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7386 (mm-30) REVERT: E 588 ASN cc_start: 0.8580 (t0) cc_final: 0.8269 (m-40) outliers start: 46 outliers final: 29 residues processed: 447 average time/residue: 1.4758 time to fit residues: 727.8393 Evaluate side-chains 453 residues out of total 1914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 415 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 ASP 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 196 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LYS 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 219 ILE 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 65 LEU Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 184 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS B 307 HIS ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 128 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.088642 restraints weight = 28633.638| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.89 r_work: 0.3174 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17882 Z= 0.189 Angle : 0.571 10.197 24321 Z= 0.287 Chirality : 0.043 0.156 2657 Planarity : 0.004 0.049 3175 Dihedral : 10.444 176.583 2519 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.66 % Allowed : 19.85 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2208 helix: 1.56 (0.18), residues: 926 sheet: 0.37 (0.29), residues: 341 loop : -0.59 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.009 0.001 HIS D 190 PHE 0.030 0.001 PHE E 75 TYR 0.012 0.001 TYR D 425 ARG 0.010 0.001 ARG E 590 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10639.98 seconds wall clock time: 185 minutes 22.63 seconds (11122.63 seconds total)