Starting phenix.real_space_refine on Tue Aug 6 20:36:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4m_42973/08_2024/8v4m_42973.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4m_42973/08_2024/8v4m_42973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4m_42973/08_2024/8v4m_42973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4m_42973/08_2024/8v4m_42973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4m_42973/08_2024/8v4m_42973.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4m_42973/08_2024/8v4m_42973.cif" } resolution = 3.0 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 115 5.16 5 C 10984 2.51 5 N 2999 2.21 5 O 3316 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 PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 265": "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: 17431 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3372 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 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: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3877 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 35, 'TRANS': 463} Chain breaks: 3 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 14, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 119 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: 11.21, per 1000 atoms: 0.64 Number of scatterers: 17431 At special positions: 0 Unit cell: (130.725, 125.745, 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 115 16.00 P 12 15.00 Mg 4 11.99 O 3316 8.00 N 2999 7.00 C 10984 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: 6.59 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 252 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 434 " 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 15 sheets defined 48.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.978A 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 127 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.677A 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: 3.906A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.950A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.959A 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: 3.745A pdb=" N GLU A 284 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.678A 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: 3.553A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.979A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.143A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.079A 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 40 through 44 removed outlier: 3.652A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.717A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 70 through 78 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: 3.506A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.878A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.510A pdb=" N VAL B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.747A 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: 4.273A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.730A 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: 3.895A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.531A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.598A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.651A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.544A 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: 4.004A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.168A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.062A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.928A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.040A 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: 4.630A 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 128 removed outlier: 4.277A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.460A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.551A 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: 3.763A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.910A pdb=" N TYR C 282 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.805A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.819A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.983A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.930A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 435 removed outlier: 4.130A 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: 3.984A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.973A 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: 3.697A 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: 3.934A pdb=" N GLU D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.678A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.929A pdb=" N SER D 176 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.613A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.853A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.767A 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: 3.695A pdb=" N ASN D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.756A 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 322 through 337 removed outlier: 3.695A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.585A 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: 3.908A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.066A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 removed outlier: 7.408A pdb=" N ASP D 404 " --> pdb=" O GLU D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 405 through 425 removed outlier: 3.841A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 104 removed outlier: 4.044A 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: 3.901A pdb=" N PHE E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 282 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.589A pdb=" N GLN E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 340 removed outlier: 3.568A pdb=" N SER E 340 " --> pdb=" O HIS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 467 removed outlier: 4.477A 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 484 Processing helix chain 'E' and resid 494 through 497 removed outlier: 3.660A 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: 4.184A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 581 removed outlier: 3.660A pdb=" N LEU E 580 " --> pdb=" O ARG E 577 " (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: 7.943A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.552A 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: 8.179A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.661A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.021A 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: 7.948A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.436A 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 268 through 273 Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.096A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.654A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER D 364 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE D 317 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR D 366 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA D 315 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE D 368 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL D 313 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN D 370 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.604A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.587A pdb=" N ARG E 111 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR E 112 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 5.876A 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 23 removed outlier: 3.534A pdb=" N HIS E 21 " --> pdb=" O TRP E 57 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 89 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'E' and resid 189 through 198 removed outlier: 7.153A pdb=" N VAL E 205 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER E 212 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N PHE E 284 " --> pdb=" O SER E 212 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG E 243 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS E 287 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE E 245 " --> pdb=" O LYS E 287 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE E 289 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU E 247 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE E 244 " --> pdb=" O TYR E 429 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N VAL E 431 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE E 246 " --> pdb=" O VAL E 431 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU E 433 " --> pdb=" O PHE E 246 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER E 248 " --> pdb=" O LEU E 433 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N GLY E 435 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 216 through 220 removed outlier: 5.916A pdb=" N ASP E 219 " --> pdb=" O ARG E 238 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2259 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: 5.76 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2906 1.31 - 1.44: 4943 1.44 - 1.57: 9797 1.57 - 1.70: 20 1.70 - 1.82: 183 Bond restraints: 17849 Sorted by residual: bond pdb=" O3B G2P B 602 " pdb=" PG G2P B 602 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" O3B G2P D 502 " pdb=" PG G2P D 502 " ideal model delta sigma weight residual 1.716 1.612 0.104 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 1.390 -0.055 1.51e-02 4.39e+03 1.34e+01 bond pdb=" O5' G2P D 502 " pdb=" PA G2P D 502 " ideal model delta sigma weight residual 1.656 1.586 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" O5' G2P B 602 " pdb=" PA G2P B 602 " ideal model delta sigma weight residual 1.656 1.588 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 17844 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.42: 341 104.42 - 111.82: 7554 111.82 - 119.23: 6880 119.23 - 126.63: 9216 126.63 - 134.03: 285 Bond angle restraints: 24276 Sorted by residual: angle pdb=" N PRO E 114 " pdb=" CA PRO E 114 " pdb=" C PRO E 114 " ideal model delta sigma weight residual 114.03 120.18 -6.15 1.23e+00 6.61e-01 2.50e+01 angle pdb=" N THR E 256 " pdb=" CA THR E 256 " pdb=" C THR E 256 " ideal model delta sigma weight residual 109.81 120.13 -10.32 2.21e+00 2.05e-01 2.18e+01 angle pdb=" C CYS E 532 " pdb=" N HIS E 533 " pdb=" CA HIS E 533 " ideal model delta sigma weight residual 122.82 129.27 -6.45 1.42e+00 4.96e-01 2.06e+01 angle pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " pdb=" PB GTP A 502 " ideal model delta sigma weight residual 120.50 133.94 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C PHE B 260 " pdb=" CA PHE B 260 " pdb=" CB PHE B 260 " ideal model delta sigma weight residual 108.88 115.50 -6.62 1.50e+00 4.44e-01 1.95e+01 ... (remaining 24271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 10249 28.04 - 56.09: 301 56.09 - 84.13: 35 84.13 - 112.18: 7 112.18 - 140.22: 8 Dihedral angle restraints: 10600 sinusoidal: 4152 harmonic: 6448 Sorted by residual: 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 -35.63 140.22 1 2.00e+01 2.50e-03 4.24e+01 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 -32.76 137.35 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2G GTP C 502 " pdb=" O3B GTP C 502 " pdb=" PG GTP C 502 " pdb=" PB GTP C 502 " ideal model delta sinusoidal sigma weight residual 177.30 40.97 136.33 1 2.00e+01 2.50e-03 4.14e+01 ... (remaining 10597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1919 0.059 - 0.118: 581 0.118 - 0.176: 125 0.176 - 0.235: 19 0.235 - 0.294: 7 Chirality restraints: 2651 Sorted by residual: 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 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB ILE C 265 " pdb=" CA ILE C 265 " pdb=" CG1 ILE C 265 " pdb=" CG2 ILE C 265 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR E 256 " pdb=" N THR E 256 " pdb=" C THR E 256 " pdb=" CB THR E 256 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2648 not shown) Planarity restraints: 3170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 432 " -0.019 2.00e-02 2.50e+03 2.20e-02 9.65e+00 pdb=" CG TYR A 432 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 432 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 432 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 432 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 432 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 432 " 0.003 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 MET D 267 " -0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO D 268 " 0.131 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=" C PHE E 546 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO E 547 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 547 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 547 " -0.041 5.00e-02 4.00e+02 ... (remaining 3167 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 1 2.08 - 2.79: 3730 2.79 - 3.49: 23174 3.49 - 4.20: 43482 4.20 - 4.90: 77339 Nonbonded interactions: 147726 Sorted by model distance: nonbonded pdb=" CD GLU B 503 " pdb=" N GLU B1001 " model vdw 1.380 3.350 nonbonded pdb=" OE1 GLU B 503 " pdb="ZN ZN E 701 " model vdw 2.137 2.230 nonbonded pdb=" OE2 GLU E 255 " pdb="ZN ZN E 701 " model vdw 2.164 2.230 nonbonded pdb="MG MG A 501 " pdb=" O2B GTP A 502 " model vdw 2.210 2.170 nonbonded pdb=" OE1 GLU B 503 " pdb=" N GLU B1001 " model vdw 2.285 3.120 ... (remaining 147721 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 \ 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) or re \ sid 431 through 439 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 439 or resid 501 throu \ gh 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 281 or (resid 282 through 284 an \ d (name N or name CA or name C or name O or name CB )) or resid 285 through 287 \ or (resid 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 through 327 or (resid 328 and (name N or name CA or name C or name O or name \ CB )) or resid 329 through 360 or (resid 361 through 362 and (name N or name CA \ or name C or name O or name CB )) or resid 363 through 389 or (resid 390 and (n \ ame N or name CA or name C or name O or name CB )) or resid 391 through 428 or r \ esid 601 through 602)) selection = (chain 'D' and (resid 1 through 278 or (resid 279 and (name N or name CA or name \ C or name O or name CB )) or resid 280 through 428 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.380 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 51.780 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 0.105 17849 Z= 0.401 Angle : 1.034 13.435 24276 Z= 0.567 Chirality : 0.060 0.294 2651 Planarity : 0.009 0.106 3170 Dihedral : 14.316 140.220 6460 Min Nonbonded Distance : 1.380 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -1.91 (0.15), residues: 2205 helix: -1.73 (0.13), residues: 882 sheet: 0.30 (0.29), residues: 326 loop : -1.23 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 346 HIS 0.010 0.002 HIS A 197 PHE 0.036 0.003 PHE C 255 TYR 0.048 0.003 TYR A 432 ARG 0.015 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 596 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7657 (ptt-90) REVERT: A 47 ASP cc_start: 0.7249 (p0) cc_final: 0.6720 (p0) REVERT: A 50 ASN cc_start: 0.7862 (t0) cc_final: 0.7219 (t0) REVERT: A 114 ILE cc_start: 0.7936 (pt) cc_final: 0.7716 (pt) REVERT: A 124 LYS cc_start: 0.8301 (mttt) cc_final: 0.7923 (ttmm) REVERT: A 128 GLN cc_start: 0.7646 (pt0) cc_final: 0.7310 (tm-30) REVERT: A 155 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 158 SER cc_start: 0.8568 (t) cc_final: 0.8251 (t) REVERT: A 196 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 209 ILE cc_start: 0.7197 (mt) cc_final: 0.6882 (mt) REVERT: A 227 LEU cc_start: 0.7890 (mp) cc_final: 0.7676 (mt) REVERT: A 241 SER cc_start: 0.8650 (m) cc_final: 0.8186 (p) REVERT: A 254 GLU cc_start: 0.7187 (tt0) cc_final: 0.6426 (mm-30) REVERT: A 284 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 322 ASP cc_start: 0.7533 (t0) cc_final: 0.7196 (t70) REVERT: A 414 GLU cc_start: 0.8362 (mp0) cc_final: 0.7980 (mp0) REVERT: A 415 GLU cc_start: 0.7757 (tt0) cc_final: 0.7316 (tm-30) REVERT: A 423 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 424 ASP cc_start: 0.8047 (m-30) cc_final: 0.7635 (t0) REVERT: B 3 GLU cc_start: 0.8100 (mp0) cc_final: 0.7241 (mp0) REVERT: B 19 LYS cc_start: 0.8315 (tptm) cc_final: 0.8066 (tptt) REVERT: B 41 ASP cc_start: 0.8342 (m-30) cc_final: 0.7863 (p0) REVERT: B 45 GLU cc_start: 0.7858 (pt0) cc_final: 0.7589 (pt0) REVERT: B 48 ASN cc_start: 0.8386 (p0) cc_final: 0.7950 (p0) REVERT: B 53 GLU cc_start: 0.7734 (tt0) cc_final: 0.7458 (tt0) REVERT: B 58 LYS cc_start: 0.7221 (tttt) cc_final: 0.6645 (pttt) REVERT: B 88 ASP cc_start: 0.8491 (t0) cc_final: 0.8149 (t0) REVERT: B 103 LYS cc_start: 0.8595 (tttt) cc_final: 0.8069 (mtpp) REVERT: B 181 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7719 (tt0) REVERT: B 201 CYS cc_start: 0.8603 (m) cc_final: 0.8354 (m) REVERT: B 212 PHE cc_start: 0.7868 (m-10) cc_final: 0.7545 (m-10) REVERT: B 213 ARG cc_start: 0.7656 (ptp90) cc_final: 0.7324 (ttp-110) REVERT: B 216 LYS cc_start: 0.8793 (mmtm) cc_final: 0.8342 (mmmm) REVERT: B 252 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8452 (ttpt) REVERT: B 278 SER cc_start: 0.8534 (m) cc_final: 0.7803 (p) REVERT: B 282 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7206 (ptm-80) REVERT: B 288 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7310 (tm-30) REVERT: B 300 MET cc_start: 0.8108 (mtm) cc_final: 0.7902 (mtm) REVERT: B 324 LYS cc_start: 0.7911 (tptm) cc_final: 0.7678 (tptp) REVERT: B 350 LYS cc_start: 0.8638 (tptt) cc_final: 0.8253 (tptm) REVERT: B 356 ILE cc_start: 0.8624 (mm) cc_final: 0.8312 (mp) REVERT: B 362 LYS cc_start: 0.8261 (tptp) cc_final: 0.7833 (tptp) REVERT: B 383 GLU cc_start: 0.7990 (tp30) cc_final: 0.7669 (tp30) REVERT: B 425 TYR cc_start: 0.8478 (m-80) cc_final: 0.7717 (m-80) REVERT: C 2 ARG cc_start: 0.7835 (mtm180) cc_final: 0.7606 (mtm180) REVERT: C 22 GLU cc_start: 0.8215 (tt0) cc_final: 0.7978 (tt0) REVERT: C 47 ASP cc_start: 0.7944 (p0) cc_final: 0.7511 (t0) REVERT: C 60 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7728 (ttmm) REVERT: C 91 GLN cc_start: 0.8401 (mt0) cc_final: 0.8158 (mt0) REVERT: C 97 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7666 (tt0) REVERT: C 123 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7295 (tpp80) REVERT: C 124 LYS cc_start: 0.8286 (mtpp) cc_final: 0.8069 (ttmm) REVERT: C 154 MET cc_start: 0.8163 (mmm) cc_final: 0.7921 (mtt) REVERT: C 168 GLU cc_start: 0.8347 (pp20) cc_final: 0.8114 (pp20) REVERT: C 207 GLU cc_start: 0.7040 (tt0) cc_final: 0.5732 (tm-30) REVERT: C 218 ASP cc_start: 0.8147 (m-30) cc_final: 0.7414 (t0) REVERT: C 219 ILE cc_start: 0.8283 (mm) cc_final: 0.8010 (mp) REVERT: C 254 GLU cc_start: 0.7081 (tt0) cc_final: 0.6535 (mm-30) REVERT: C 280 LYS cc_start: 0.8607 (mttp) cc_final: 0.7369 (mmtt) REVERT: C 287 SER cc_start: 0.8042 (t) cc_final: 0.7840 (p) REVERT: C 304 LYS cc_start: 0.7771 (tppp) cc_final: 0.5933 (tttp) REVERT: C 308 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7046 (tmt-80) REVERT: C 322 ASP cc_start: 0.8179 (t0) cc_final: 0.7734 (t0) REVERT: C 338 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8473 (mtpp) REVERT: C 349 THR cc_start: 0.8369 (p) cc_final: 0.8130 (p) REVERT: C 352 LYS cc_start: 0.8382 (tptm) cc_final: 0.6773 (tppt) REVERT: C 411 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 413 MET cc_start: 0.8050 (mtp) cc_final: 0.7797 (ttm) REVERT: C 420 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6950 (mp0) REVERT: C 433 GLU cc_start: 0.7695 (pt0) cc_final: 0.7478 (tp30) REVERT: D 19 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8090 (tptm) REVERT: D 44 LEU cc_start: 0.8300 (tp) cc_final: 0.7991 (tm) REVERT: D 45 GLU cc_start: 0.8320 (tt0) cc_final: 0.7684 (tm-30) REVERT: D 69 GLU cc_start: 0.7348 (pp20) cc_final: 0.6665 (pm20) REVERT: D 81 PHE cc_start: 0.8123 (m-80) cc_final: 0.6328 (m-80) REVERT: D 88 ASP cc_start: 0.8256 (t70) cc_final: 0.7875 (t0) REVERT: D 103 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8217 (mtpp) REVERT: D 118 ASP cc_start: 0.7930 (m-30) cc_final: 0.7648 (m-30) REVERT: D 121 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7383 (ptp-110) REVERT: D 122 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7797 (ttmm) REVERT: D 129 CYS cc_start: 0.8126 (t) cc_final: 0.7790 (t) REVERT: D 201 CYS cc_start: 0.8741 (m) cc_final: 0.8349 (m) REVERT: D 203 ASP cc_start: 0.7873 (t0) cc_final: 0.7410 (t70) REVERT: D 216 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8597 (mmmm) REVERT: D 252 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8244 (ttpt) REVERT: D 262 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7729 (ttm110) REVERT: D 289 LEU cc_start: 0.7721 (mp) cc_final: 0.7339 (mt) REVERT: D 299 MET cc_start: 0.7773 (mmp) cc_final: 0.7551 (mpp) REVERT: D 300 MET cc_start: 0.8012 (mtm) cc_final: 0.7742 (mtm) REVERT: D 304 ASP cc_start: 0.7408 (t70) cc_final: 0.6959 (t0) REVERT: D 325 GLU cc_start: 0.8258 (tp30) cc_final: 0.7618 (tm-30) REVERT: D 376 GLU cc_start: 0.7767 (mp0) cc_final: 0.7128 (mp0) REVERT: D 383 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7661 (tm-30) REVERT: D 391 ARG cc_start: 0.7706 (mmm160) cc_final: 0.7229 (mtm180) REVERT: D 404 ASP cc_start: 0.8316 (m-30) cc_final: 0.7886 (t0) REVERT: D 407 GLU cc_start: 0.7785 (mp0) cc_final: 0.7119 (mp0) REVERT: D 410 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7390 (mm-30) REVERT: D 413 SER cc_start: 0.7908 (t) cc_final: 0.7660 (p) REVERT: D 421 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7795 (mt-10) REVERT: E 11 SER cc_start: 0.7418 (t) cc_final: 0.7010 (p) REVERT: E 15 ASP cc_start: 0.8304 (t0) cc_final: 0.7843 (t0) REVERT: E 53 GLU cc_start: 0.7052 (tp30) cc_final: 0.6825 (tp30) REVERT: E 68 GLU cc_start: 0.7904 (tt0) cc_final: 0.7578 (tm-30) REVERT: E 71 ASN cc_start: 0.8468 (m110) cc_final: 0.7890 (m-40) REVERT: E 87 LEU cc_start: 0.7350 (tt) cc_final: 0.7115 (pp) REVERT: E 111 ARG cc_start: 0.6292 (ptt180) cc_final: 0.6044 (ptt-90) REVERT: E 262 PHE cc_start: 0.7618 (t80) cc_final: 0.7358 (t80) REVERT: E 289 ILE cc_start: 0.7270 (mt) cc_final: 0.7022 (tt) REVERT: E 294 PRO cc_start: 0.8209 (Cg_endo) cc_final: 0.7983 (Cg_exo) REVERT: E 295 ASP cc_start: 0.7473 (p0) cc_final: 0.5606 (p0) REVERT: E 330 LYS cc_start: 0.7502 (mtpt) cc_final: 0.7250 (mtpt) REVERT: E 341 ARG cc_start: 0.7006 (mtm-85) cc_final: 0.6409 (mtt-85) REVERT: E 434 HIS cc_start: 0.7932 (m-70) cc_final: 0.7504 (m170) REVERT: E 436 HIS cc_start: 0.7772 (t-90) cc_final: 0.7308 (t-90) REVERT: E 459 MET cc_start: 0.7948 (mtm) cc_final: 0.7263 (mtm) REVERT: E 504 TYR cc_start: 0.8077 (t80) cc_final: 0.7871 (t80) REVERT: E 534 ASP cc_start: 0.7349 (p0) cc_final: 0.6836 (p0) REVERT: E 584 SER cc_start: 0.7298 (m) cc_final: 0.6790 (t) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 1.4773 time to fit residues: 966.9526 Evaluate side-chains 454 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.2980 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 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 28 HIS A 35 GLN A 91 GLN A 256 GLN A 356 ASN B 11 GLN B 190 HIS B 292 GLN B 416 ASN C 91 GLN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN D 292 GLN D 332 ASN D 334 GLN D 416 ASN E 71 ASN ** E 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 ASN E 557 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17849 Z= 0.223 Angle : 0.598 10.528 24276 Z= 0.313 Chirality : 0.045 0.155 2651 Planarity : 0.005 0.063 3170 Dihedral : 10.809 143.372 2517 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.61 % Allowed : 13.61 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2205 helix: 0.09 (0.16), residues: 912 sheet: 0.11 (0.28), residues: 342 loop : -0.76 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 21 HIS 0.007 0.001 HIS A 197 PHE 0.019 0.002 PHE A 255 TYR 0.012 0.001 TYR D 340 ARG 0.009 0.001 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 484 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7709 (ptp90) REVERT: A 50 ASN cc_start: 0.7976 (t0) cc_final: 0.7338 (t0) REVERT: A 123 ARG cc_start: 0.7597 (tpp-160) cc_final: 0.7256 (tpp80) REVERT: A 124 LYS cc_start: 0.8252 (mttt) cc_final: 0.7938 (ttmm) REVERT: A 207 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 253 THR cc_start: 0.7528 (p) cc_final: 0.7295 (m) REVERT: A 254 GLU cc_start: 0.7685 (tt0) cc_final: 0.7050 (mm-30) REVERT: A 280 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8043 (ptmt) REVERT: A 284 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7116 (mm-30) REVERT: A 322 ASP cc_start: 0.7790 (t0) cc_final: 0.7356 (t70) REVERT: A 414 GLU cc_start: 0.8398 (mp0) cc_final: 0.7900 (mp0) REVERT: A 415 GLU cc_start: 0.8075 (tt0) cc_final: 0.7479 (tm-30) REVERT: A 417 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6815 (tt0) REVERT: A 420 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7402 (mt-10) REVERT: A 423 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 433 GLU cc_start: 0.8309 (tp30) cc_final: 0.7847 (tp30) REVERT: B 19 LYS cc_start: 0.8259 (tptm) cc_final: 0.7884 (tptt) REVERT: B 22 GLU cc_start: 0.8075 (tp30) cc_final: 0.7707 (mt-10) REVERT: B 42 LEU cc_start: 0.8174 (mt) cc_final: 0.7582 (mm) REVERT: B 45 GLU cc_start: 0.7936 (pt0) cc_final: 0.7625 (pt0) REVERT: B 48 ASN cc_start: 0.8462 (p0) cc_final: 0.7942 (p0) REVERT: B 58 LYS cc_start: 0.7290 (tttt) cc_final: 0.6733 (pttt) REVERT: B 81 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: B 88 ASP cc_start: 0.8588 (t0) cc_final: 0.8302 (t0) REVERT: B 103 LYS cc_start: 0.8548 (tttt) cc_final: 0.8046 (mtpp) REVERT: B 121 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7153 (mtt-85) REVERT: B 122 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7480 (ttmm) REVERT: B 158 GLU cc_start: 0.8363 (tp30) cc_final: 0.7874 (tp30) REVERT: B 181 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 205 GLU cc_start: 0.7666 (tt0) cc_final: 0.7220 (mt-10) REVERT: B 216 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8314 (mmmm) REVERT: B 252 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8264 (ttpt) REVERT: B 257 MET cc_start: 0.8467 (mmm) cc_final: 0.8085 (mmm) REVERT: B 278 SER cc_start: 0.8731 (m) cc_final: 0.8015 (p) REVERT: B 282 ARG cc_start: 0.7560 (ttt-90) cc_final: 0.6279 (ptm-80) REVERT: B 299 MET cc_start: 0.7974 (mmp) cc_final: 0.7605 (tpp) REVERT: B 304 ASP cc_start: 0.7516 (t70) cc_final: 0.6949 (t70) REVERT: B 306 ARG cc_start: 0.8484 (mpt-90) cc_final: 0.8010 (mpt-90) REVERT: B 340 TYR cc_start: 0.7753 (m-10) cc_final: 0.7503 (m-80) REVERT: B 350 LYS cc_start: 0.8621 (tptt) cc_final: 0.8230 (tptm) REVERT: B 362 LYS cc_start: 0.8334 (tptp) cc_final: 0.7878 (tptp) REVERT: B 363 MET cc_start: 0.8237 (mtm) cc_final: 0.6999 (mtm) REVERT: B 391 ARG cc_start: 0.7950 (mmm160) cc_final: 0.6107 (mtm110) REVERT: B 404 ASP cc_start: 0.7816 (m-30) cc_final: 0.7262 (m-30) REVERT: B 407 GLU cc_start: 0.7236 (mp0) cc_final: 0.6648 (mp0) REVERT: B 421 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: B 425 TYR cc_start: 0.8487 (m-80) cc_final: 0.8167 (m-80) REVERT: C 2 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7916 (mtm180) REVERT: C 3 GLU cc_start: 0.8204 (mp0) cc_final: 0.7671 (mt-10) REVERT: C 36 MET cc_start: 0.8760 (ttp) cc_final: 0.8413 (ttp) REVERT: C 47 ASP cc_start: 0.8125 (p0) cc_final: 0.7407 (t0) REVERT: C 50 ASN cc_start: 0.8469 (t0) cc_final: 0.7678 (t160) REVERT: C 77 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8001 (mm-30) REVERT: C 123 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7254 (tpp80) REVERT: C 124 LYS cc_start: 0.8263 (mtpp) cc_final: 0.8025 (ttmm) REVERT: C 203 MET cc_start: 0.8524 (tpp) cc_final: 0.8248 (mmm) REVERT: C 218 ASP cc_start: 0.8176 (m-30) cc_final: 0.7598 (t0) REVERT: C 254 GLU cc_start: 0.7537 (tt0) cc_final: 0.7212 (tp30) REVERT: C 285 GLN cc_start: 0.8585 (mt0) cc_final: 0.8178 (mm110) REVERT: C 287 SER cc_start: 0.8280 (t) cc_final: 0.7902 (p) REVERT: C 308 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7220 (tmm160) REVERT: C 313 MET cc_start: 0.8558 (mtp) cc_final: 0.8350 (mtp) REVERT: C 322 ASP cc_start: 0.8322 (t0) cc_final: 0.7964 (t0) REVERT: C 337 THR cc_start: 0.8245 (m) cc_final: 0.7839 (p) REVERT: C 349 THR cc_start: 0.8322 (p) cc_final: 0.8114 (p) REVERT: C 392 ASP cc_start: 0.7683 (m-30) cc_final: 0.7365 (m-30) REVERT: C 423 GLU cc_start: 0.7951 (tp30) cc_final: 0.7689 (tm-30) REVERT: C 433 GLU cc_start: 0.7783 (pt0) cc_final: 0.7560 (tp30) REVERT: C 434 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7718 (pp20) REVERT: D 19 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7732 (mmmt) REVERT: D 44 LEU cc_start: 0.8347 (tp) cc_final: 0.8081 (tm) REVERT: D 45 GLU cc_start: 0.8301 (tt0) cc_final: 0.7690 (tm-30) REVERT: D 58 LYS cc_start: 0.8462 (tttt) cc_final: 0.7945 (mtpp) REVERT: D 88 ASP cc_start: 0.8399 (t70) cc_final: 0.7990 (t0) REVERT: D 103 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8307 (mtpm) REVERT: D 118 ASP cc_start: 0.7828 (m-30) cc_final: 0.7454 (m-30) REVERT: D 121 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7430 (ptp-110) REVERT: D 122 LYS cc_start: 0.8308 (ttpt) cc_final: 0.7912 (ttmm) REVERT: D 126 SER cc_start: 0.7893 (t) cc_final: 0.7606 (p) REVERT: D 201 CYS cc_start: 0.8823 (m) cc_final: 0.8466 (m) REVERT: D 203 ASP cc_start: 0.8083 (t0) cc_final: 0.7475 (t0) REVERT: D 212 PHE cc_start: 0.8148 (m-10) cc_final: 0.7840 (m-10) REVERT: D 213 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.8047 (ttm-80) REVERT: D 216 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8595 (mmmm) REVERT: D 233 MET cc_start: 0.8231 (ttm) cc_final: 0.7933 (mtp) REVERT: D 252 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8239 (ttpt) REVERT: D 257 MET cc_start: 0.8057 (mmm) cc_final: 0.7831 (mtp) REVERT: D 304 ASP cc_start: 0.7682 (t70) cc_final: 0.6743 (t0) REVERT: D 306 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7650 (mtm180) REVERT: D 309 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7655 (mtp85) REVERT: D 324 LYS cc_start: 0.8675 (tptm) cc_final: 0.8404 (tppt) REVERT: D 325 GLU cc_start: 0.8484 (tp30) cc_final: 0.7757 (tp30) REVERT: D 329 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6796 (mm-40) REVERT: D 332 ASN cc_start: 0.7974 (t0) cc_final: 0.7594 (m-40) REVERT: D 376 GLU cc_start: 0.7718 (mp0) cc_final: 0.6941 (mp0) REVERT: D 383 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7837 (tm-30) REVERT: D 391 ARG cc_start: 0.7876 (mmm160) cc_final: 0.7118 (mtm180) REVERT: D 404 ASP cc_start: 0.8147 (m-30) cc_final: 0.7844 (t0) REVERT: D 407 GLU cc_start: 0.7695 (mp0) cc_final: 0.7229 (mp0) REVERT: D 410 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7421 (mm-30) REVERT: D 424 GLN cc_start: 0.7844 (tt0) cc_final: 0.7639 (tt0) REVERT: E 11 SER cc_start: 0.8108 (t) cc_final: 0.7749 (p) REVERT: E 15 ASP cc_start: 0.8411 (t0) cc_final: 0.8014 (t0) REVERT: E 61 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: E 68 GLU cc_start: 0.8113 (tt0) cc_final: 0.7700 (tm-30) REVERT: E 94 ASN cc_start: 0.7302 (t0) cc_final: 0.6134 (t0) REVERT: E 111 ARG cc_start: 0.6559 (ptt180) cc_final: 0.6068 (ptt-90) REVERT: E 113 LEU cc_start: 0.7652 (mm) cc_final: 0.7246 (mm) REVERT: E 120 GLU cc_start: 0.7388 (tt0) cc_final: 0.7008 (tt0) REVERT: E 136 VAL cc_start: 0.7986 (t) cc_final: 0.7735 (t) REVERT: E 169 ASN cc_start: 0.7431 (m-40) cc_final: 0.6694 (m-40) REVERT: E 191 TYR cc_start: 0.8081 (t80) cc_final: 0.7744 (OUTLIER) REVERT: E 206 ASP cc_start: 0.8636 (p0) cc_final: 0.8372 (p0) REVERT: E 246 PHE cc_start: 0.8221 (t80) cc_final: 0.7926 (t80) REVERT: E 289 ILE cc_start: 0.7374 (mt) cc_final: 0.7061 (tt) REVERT: E 291 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6988 (mtm) REVERT: E 314 GLN cc_start: 0.6494 (mp10) cc_final: 0.5896 (mp10) REVERT: E 327 TYR cc_start: 0.7677 (t80) cc_final: 0.6841 (t80) REVERT: E 444 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7151 (mtp) REVERT: E 457 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7754 (mm-30) REVERT: E 534 ASP cc_start: 0.7470 (p0) cc_final: 0.7185 (p0) REVERT: E 550 TYR cc_start: 0.8051 (m-10) cc_final: 0.7654 (m-10) REVERT: E 584 SER cc_start: 0.7166 (m) cc_final: 0.6723 (t) REVERT: E 590 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7613 (ttm170) outliers start: 48 outliers final: 12 residues processed: 501 average time/residue: 1.5319 time to fit residues: 843.7716 Evaluate side-chains 435 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 418 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 444 MET Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 200 optimal weight: 0.0060 chunk 216 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 292 GLN B 307 HIS B 334 GLN B 416 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 104 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17849 Z= 0.246 Angle : 0.577 9.294 24276 Z= 0.297 Chirality : 0.045 0.191 2651 Planarity : 0.005 0.059 3170 Dihedral : 10.771 162.486 2517 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.67 % Allowed : 15.51 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.09 (0.17), residues: 2205 helix: 0.85 (0.17), residues: 909 sheet: 0.11 (0.29), residues: 335 loop : -0.65 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 21 HIS 0.013 0.001 HIS B 307 PHE 0.014 0.002 PHE C 49 TYR 0.011 0.001 TYR A 83 ARG 0.010 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 458 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7487 (p0) cc_final: 0.7271 (t0) REVERT: A 50 ASN cc_start: 0.8067 (t0) cc_final: 0.7305 (t0) REVERT: A 76 ASP cc_start: 0.8166 (m-30) cc_final: 0.7315 (m-30) REVERT: A 123 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7332 (tpp80) REVERT: A 124 LYS cc_start: 0.8157 (mttt) cc_final: 0.7787 (ttmm) REVERT: A 221 ARG cc_start: 0.7628 (ptp-110) cc_final: 0.7307 (ptp-110) REVERT: A 230 LEU cc_start: 0.8194 (mp) cc_final: 0.7922 (mm) REVERT: A 254 GLU cc_start: 0.7925 (tt0) cc_final: 0.7162 (mm-30) REVERT: A 280 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8104 (ptpt) REVERT: A 284 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 297 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6947 (tp30) REVERT: A 322 ASP cc_start: 0.7858 (t0) cc_final: 0.7384 (t70) REVERT: A 414 GLU cc_start: 0.8326 (mp0) cc_final: 0.7339 (mp0) REVERT: A 415 GLU cc_start: 0.8066 (tt0) cc_final: 0.7549 (tm-30) REVERT: A 417 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6711 (mp0) REVERT: A 420 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7453 (mt-10) REVERT: A 423 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 433 GLU cc_start: 0.8411 (tp30) cc_final: 0.7877 (tp30) REVERT: B 19 LYS cc_start: 0.8238 (tptm) cc_final: 0.8011 (tptt) REVERT: B 22 GLU cc_start: 0.8188 (tp30) cc_final: 0.7572 (mm-30) REVERT: B 42 LEU cc_start: 0.8216 (mt) cc_final: 0.7498 (mm) REVERT: B 45 GLU cc_start: 0.8035 (pt0) cc_final: 0.7537 (pm20) REVERT: B 48 ASN cc_start: 0.8450 (p0) cc_final: 0.8030 (p0) REVERT: B 58 LYS cc_start: 0.7630 (tttt) cc_final: 0.7015 (pttt) REVERT: B 81 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: B 88 ASP cc_start: 0.8638 (t0) cc_final: 0.8286 (t0) REVERT: B 103 LYS cc_start: 0.8624 (tttt) cc_final: 0.8047 (mtpp) REVERT: B 121 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7521 (mtm-85) REVERT: B 122 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7692 (ttpt) REVERT: B 157 GLU cc_start: 0.8345 (tp30) cc_final: 0.7775 (tm-30) REVERT: B 158 GLU cc_start: 0.8419 (tp30) cc_final: 0.8118 (tp30) REVERT: B 205 GLU cc_start: 0.7714 (tt0) cc_final: 0.7297 (mt-10) REVERT: B 213 ARG cc_start: 0.8020 (ttp-110) cc_final: 0.7751 (ttp-110) REVERT: B 216 LYS cc_start: 0.8692 (mmtm) cc_final: 0.8282 (mmmm) REVERT: B 278 SER cc_start: 0.8730 (m) cc_final: 0.8007 (p) REVERT: B 299 MET cc_start: 0.8282 (mmp) cc_final: 0.7884 (tpp) REVERT: B 340 TYR cc_start: 0.7873 (m-10) cc_final: 0.7616 (m-80) REVERT: B 350 LYS cc_start: 0.8590 (tptt) cc_final: 0.8289 (tptm) REVERT: B 362 LYS cc_start: 0.8364 (tptp) cc_final: 0.7725 (tptp) REVERT: B 363 MET cc_start: 0.8511 (mtm) cc_final: 0.7563 (mtp) REVERT: B 391 ARG cc_start: 0.8105 (mmm160) cc_final: 0.6327 (mtm180) REVERT: B 404 ASP cc_start: 0.7920 (m-30) cc_final: 0.7490 (p0) REVERT: B 407 GLU cc_start: 0.7465 (mp0) cc_final: 0.7246 (tt0) REVERT: B 421 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: B 425 TYR cc_start: 0.8502 (m-80) cc_final: 0.8246 (m-80) REVERT: C 2 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7936 (mtm180) REVERT: C 36 MET cc_start: 0.8678 (ttp) cc_final: 0.8307 (ttp) REVERT: C 47 ASP cc_start: 0.8168 (p0) cc_final: 0.7485 (t0) REVERT: C 50 ASN cc_start: 0.8472 (t0) cc_final: 0.7524 (t0) REVERT: C 71 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7248 (pt0) REVERT: C 77 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 91 GLN cc_start: 0.8168 (mt0) cc_final: 0.7844 (pt0) REVERT: C 123 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7278 (tpp80) REVERT: C 124 LYS cc_start: 0.8272 (mtpp) cc_final: 0.8064 (ttmm) REVERT: C 176 GLN cc_start: 0.8646 (mm110) cc_final: 0.8437 (mm-40) REVERT: C 207 GLU cc_start: 0.7038 (tt0) cc_final: 0.6624 (mt-10) REVERT: C 218 ASP cc_start: 0.8158 (m-30) cc_final: 0.7617 (t0) REVERT: C 221 ARG cc_start: 0.8036 (pmm-80) cc_final: 0.7713 (pmm-80) REVERT: C 254 GLU cc_start: 0.7856 (tt0) cc_final: 0.7339 (tp30) REVERT: C 284 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7558 (mm-30) REVERT: C 285 GLN cc_start: 0.8642 (mt0) cc_final: 0.8244 (mm110) REVERT: C 287 SER cc_start: 0.8184 (t) cc_final: 0.7748 (p) REVERT: C 290 GLU cc_start: 0.7647 (mp0) cc_final: 0.7138 (mp0) REVERT: C 297 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7693 (tp30) REVERT: C 302 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7968 (mtm) REVERT: C 308 ARG cc_start: 0.8036 (mtm180) cc_final: 0.6967 (tmt-80) REVERT: C 322 ASP cc_start: 0.8377 (t0) cc_final: 0.8010 (t0) REVERT: C 337 THR cc_start: 0.8419 (m) cc_final: 0.7983 (p) REVERT: C 377 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7888 (tmm) REVERT: C 386 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7742 (mt-10) REVERT: C 392 ASP cc_start: 0.7766 (m-30) cc_final: 0.7457 (m-30) REVERT: C 411 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8381 (mm-30) REVERT: C 417 GLU cc_start: 0.7028 (mp0) cc_final: 0.6747 (mp0) REVERT: C 423 GLU cc_start: 0.8015 (tp30) cc_final: 0.7427 (mm-30) REVERT: C 433 GLU cc_start: 0.7768 (pt0) cc_final: 0.7476 (tp30) REVERT: D 19 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7702 (tppt) REVERT: D 45 GLU cc_start: 0.8382 (tt0) cc_final: 0.7756 (tm-30) REVERT: D 57 ASN cc_start: 0.8373 (m-40) cc_final: 0.8057 (m-40) REVERT: D 88 ASP cc_start: 0.8460 (t70) cc_final: 0.8015 (t0) REVERT: D 103 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8205 (mtpm) REVERT: D 118 ASP cc_start: 0.7800 (m-30) cc_final: 0.7361 (m-30) REVERT: D 121 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7573 (ptp-110) REVERT: D 122 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8065 (ttmm) REVERT: D 126 SER cc_start: 0.7911 (t) cc_final: 0.7648 (p) REVERT: D 154 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (mptp) REVERT: D 201 CYS cc_start: 0.8862 (m) cc_final: 0.8507 (m) REVERT: D 203 ASP cc_start: 0.8224 (t0) cc_final: 0.7507 (t70) REVERT: D 216 LYS cc_start: 0.8902 (mmtm) cc_final: 0.8591 (mmmm) REVERT: D 233 MET cc_start: 0.8531 (ttm) cc_final: 0.8297 (mtp) REVERT: D 247 ASN cc_start: 0.7978 (m110) cc_final: 0.7685 (m-40) REVERT: D 304 ASP cc_start: 0.7803 (t70) cc_final: 0.6879 (t0) REVERT: D 309 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7842 (mtp85) REVERT: D 324 LYS cc_start: 0.8687 (tptm) cc_final: 0.8390 (tppt) REVERT: D 325 GLU cc_start: 0.8479 (tp30) cc_final: 0.7729 (tp30) REVERT: D 329 GLN cc_start: 0.7535 (mm-40) cc_final: 0.6995 (mm-40) REVERT: D 332 ASN cc_start: 0.8219 (t0) cc_final: 0.7956 (m-40) REVERT: D 377 LEU cc_start: 0.8113 (mt) cc_final: 0.7795 (mp) REVERT: D 380 ARG cc_start: 0.8538 (ptp90) cc_final: 0.8324 (ptp90) REVERT: D 391 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7221 (mtm180) REVERT: D 404 ASP cc_start: 0.8077 (m-30) cc_final: 0.7697 (t0) REVERT: D 407 GLU cc_start: 0.7690 (mp0) cc_final: 0.7226 (mp0) REVERT: D 410 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7210 (mm-30) REVERT: D 414 ASN cc_start: 0.7914 (t0) cc_final: 0.7549 (m110) REVERT: E 15 ASP cc_start: 0.8452 (t0) cc_final: 0.7944 (t0) REVERT: E 61 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: E 67 PHE cc_start: 0.8241 (m-10) cc_final: 0.7953 (m-10) REVERT: E 68 GLU cc_start: 0.8095 (tt0) cc_final: 0.7856 (tm-30) REVERT: E 94 ASN cc_start: 0.7662 (t0) cc_final: 0.6731 (t0) REVERT: E 113 LEU cc_start: 0.7836 (mm) cc_final: 0.7504 (mm) REVERT: E 120 GLU cc_start: 0.7286 (tt0) cc_final: 0.6932 (tt0) REVERT: E 136 VAL cc_start: 0.8117 (t) cc_final: 0.7863 (t) REVERT: E 152 PHE cc_start: 0.6921 (m-10) cc_final: 0.6715 (m-10) REVERT: E 191 TYR cc_start: 0.8096 (t80) cc_final: 0.7800 (OUTLIER) REVERT: E 206 ASP cc_start: 0.8671 (p0) cc_final: 0.8240 (p0) REVERT: E 244 ILE cc_start: 0.7954 (mp) cc_final: 0.7554 (tt) REVERT: E 246 PHE cc_start: 0.8286 (t80) cc_final: 0.8022 (t80) REVERT: E 314 GLN cc_start: 0.6694 (mp10) cc_final: 0.6075 (mp10) REVERT: E 327 TYR cc_start: 0.7913 (t80) cc_final: 0.7214 (t80) REVERT: E 341 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6640 (mtt90) REVERT: E 452 GLU cc_start: 0.7192 (pt0) cc_final: 0.6752 (pt0) REVERT: E 483 ASN cc_start: 0.7127 (t0) cc_final: 0.6416 (t0) REVERT: E 534 ASP cc_start: 0.7587 (p0) cc_final: 0.7285 (p0) REVERT: E 550 TYR cc_start: 0.8188 (m-10) cc_final: 0.7889 (m-10) REVERT: E 584 SER cc_start: 0.7230 (m) cc_final: 0.6644 (t) outliers start: 49 outliers final: 17 residues processed: 480 average time/residue: 1.4033 time to fit residues: 742.9682 Evaluate side-chains 444 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 420 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 416 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 334 GLN D 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17849 Z= 0.213 Angle : 0.557 9.556 24276 Z= 0.285 Chirality : 0.044 0.164 2651 Planarity : 0.004 0.049 3170 Dihedral : 10.727 170.075 2517 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.67 % Allowed : 16.71 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.39 (0.18), residues: 2205 helix: 1.23 (0.17), residues: 906 sheet: 0.21 (0.29), residues: 341 loop : -0.62 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.005 0.001 HIS A 197 PHE 0.025 0.001 PHE E 262 TYR 0.018 0.001 TYR E 52 ARG 0.011 0.001 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 444 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7492 (p0) cc_final: 0.7243 (t0) REVERT: A 50 ASN cc_start: 0.8092 (t0) cc_final: 0.7406 (t0) REVERT: A 71 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: A 123 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.7322 (tpp80) REVERT: A 124 LYS cc_start: 0.8164 (mttt) cc_final: 0.7834 (ttmm) REVERT: A 203 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8188 (mmm) REVERT: A 221 ARG cc_start: 0.7737 (ptp-110) cc_final: 0.7403 (ptp-110) REVERT: A 254 GLU cc_start: 0.7923 (tt0) cc_final: 0.7231 (mm-30) REVERT: A 255 PHE cc_start: 0.8275 (p90) cc_final: 0.7964 (p90) REVERT: A 280 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8147 (ptpp) REVERT: A 284 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7063 (mm-30) REVERT: A 297 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6884 (tp30) REVERT: A 322 ASP cc_start: 0.7875 (t0) cc_final: 0.7336 (t70) REVERT: A 414 GLU cc_start: 0.8315 (mp0) cc_final: 0.7300 (mp0) REVERT: A 415 GLU cc_start: 0.8090 (tt0) cc_final: 0.7565 (tm-30) REVERT: A 417 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6749 (mp0) REVERT: A 420 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7450 (mt-10) REVERT: A 423 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 433 GLU cc_start: 0.8398 (tp30) cc_final: 0.7856 (tp30) REVERT: B 19 LYS cc_start: 0.8207 (tptm) cc_final: 0.7987 (tptt) REVERT: B 22 GLU cc_start: 0.8199 (tp30) cc_final: 0.7965 (mm-30) REVERT: B 41 ASP cc_start: 0.8233 (m-30) cc_final: 0.7932 (m-30) REVERT: B 45 GLU cc_start: 0.8072 (pt0) cc_final: 0.7715 (pt0) REVERT: B 48 ASN cc_start: 0.8444 (p0) cc_final: 0.8059 (p0) REVERT: B 58 LYS cc_start: 0.7652 (tttt) cc_final: 0.7181 (pttt) REVERT: B 81 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: B 86 ARG cc_start: 0.8389 (ttm170) cc_final: 0.6688 (mmp-170) REVERT: B 88 ASP cc_start: 0.8665 (t0) cc_final: 0.8285 (t0) REVERT: B 103 LYS cc_start: 0.8586 (tttt) cc_final: 0.7700 (ttmm) REVERT: B 121 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7477 (mtt-85) REVERT: B 122 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7666 (ttmm) REVERT: B 154 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7926 (mttm) REVERT: B 157 GLU cc_start: 0.8374 (tp30) cc_final: 0.7751 (tm-30) REVERT: B 205 GLU cc_start: 0.7707 (tt0) cc_final: 0.7226 (mt-10) REVERT: B 213 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7624 (ttp80) REVERT: B 267 MET cc_start: 0.8557 (mtp) cc_final: 0.8314 (mtm) REVERT: B 278 SER cc_start: 0.8572 (m) cc_final: 0.8282 (m) REVERT: B 285 THR cc_start: 0.7682 (t) cc_final: 0.7401 (p) REVERT: B 304 ASP cc_start: 0.7691 (t70) cc_final: 0.7263 (OUTLIER) REVERT: B 318 ARG cc_start: 0.8436 (mtt-85) cc_final: 0.8034 (mmm160) REVERT: B 332 ASN cc_start: 0.7370 (t0) cc_final: 0.7144 (t0) REVERT: B 335 ASN cc_start: 0.7987 (m-40) cc_final: 0.7756 (m-40) REVERT: B 340 TYR cc_start: 0.7904 (m-10) cc_final: 0.7647 (m-80) REVERT: B 350 LYS cc_start: 0.8588 (tptt) cc_final: 0.8287 (tptm) REVERT: B 362 LYS cc_start: 0.8395 (tptp) cc_final: 0.7744 (tptp) REVERT: B 363 MET cc_start: 0.8571 (mtm) cc_final: 0.7700 (mtp) REVERT: B 391 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7129 (mtp180) REVERT: B 404 ASP cc_start: 0.7912 (m-30) cc_final: 0.7491 (p0) REVERT: B 407 GLU cc_start: 0.7522 (mp0) cc_final: 0.7279 (tt0) REVERT: B 410 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7106 (mm-30) REVERT: B 414 ASN cc_start: 0.7972 (t0) cc_final: 0.7636 (m110) REVERT: B 421 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: B 425 TYR cc_start: 0.8516 (m-80) cc_final: 0.8239 (m-80) REVERT: C 2 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7850 (mtm180) REVERT: C 47 ASP cc_start: 0.8157 (p0) cc_final: 0.7463 (t0) REVERT: C 50 ASN cc_start: 0.8442 (t0) cc_final: 0.7377 (t0) REVERT: C 71 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: C 76 ASP cc_start: 0.8129 (m-30) cc_final: 0.7678 (m-30) REVERT: C 77 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7862 (mt-10) REVERT: C 123 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7295 (tpp80) REVERT: C 124 LYS cc_start: 0.8280 (mtpp) cc_final: 0.8062 (ttmm) REVERT: C 160 ASP cc_start: 0.7934 (t0) cc_final: 0.7671 (t0) REVERT: C 176 GLN cc_start: 0.8664 (mm110) cc_final: 0.8455 (mm-40) REVERT: C 207 GLU cc_start: 0.7116 (tt0) cc_final: 0.6703 (mt-10) REVERT: C 218 ASP cc_start: 0.8225 (m-30) cc_final: 0.7677 (t0) REVERT: C 221 ARG cc_start: 0.8091 (pmm-80) cc_final: 0.7737 (pmm-80) REVERT: C 254 GLU cc_start: 0.7942 (tt0) cc_final: 0.7367 (tp30) REVERT: C 265 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7790 (mp) REVERT: C 284 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 285 GLN cc_start: 0.8611 (mt0) cc_final: 0.8220 (mm110) REVERT: C 287 SER cc_start: 0.8213 (t) cc_final: 0.7689 (p) REVERT: C 290 GLU cc_start: 0.7671 (mp0) cc_final: 0.7121 (mp0) REVERT: C 308 ARG cc_start: 0.8085 (mtm180) cc_final: 0.6872 (tmt-80) REVERT: C 322 ASP cc_start: 0.8385 (t0) cc_final: 0.8025 (t0) REVERT: C 337 THR cc_start: 0.8451 (m) cc_final: 0.8007 (p) REVERT: C 377 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8133 (tpp) REVERT: C 386 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7680 (mt-10) REVERT: C 392 ASP cc_start: 0.7768 (m-30) cc_final: 0.7459 (m-30) REVERT: C 411 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8411 (mm-30) REVERT: C 415 GLU cc_start: 0.8210 (mm-30) cc_final: 0.8005 (mm-30) REVERT: C 417 GLU cc_start: 0.7225 (mp0) cc_final: 0.6799 (mp0) REVERT: C 420 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6856 (mm-30) REVERT: C 433 GLU cc_start: 0.7751 (pt0) cc_final: 0.7540 (tp30) REVERT: D 19 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7662 (mmmt) REVERT: D 45 GLU cc_start: 0.8407 (tt0) cc_final: 0.7747 (tm-30) REVERT: D 57 ASN cc_start: 0.8443 (m-40) cc_final: 0.8167 (m-40) REVERT: D 88 ASP cc_start: 0.8475 (t70) cc_final: 0.8164 (t70) REVERT: D 103 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8301 (mtpm) REVERT: D 118 ASP cc_start: 0.7799 (m-30) cc_final: 0.7289 (m-30) REVERT: D 121 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7597 (ptp-110) REVERT: D 122 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8065 (ttmm) REVERT: D 126 SER cc_start: 0.7946 (t) cc_final: 0.7684 (p) REVERT: D 128 ASP cc_start: 0.8759 (t0) cc_final: 0.8310 (t70) REVERT: D 154 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8054 (mptp) REVERT: D 201 CYS cc_start: 0.8880 (m) cc_final: 0.8560 (m) REVERT: D 203 ASP cc_start: 0.8293 (t0) cc_final: 0.7495 (t0) REVERT: D 213 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8149 (ttm-80) REVERT: D 216 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8606 (mmmm) REVERT: D 252 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8269 (ttpt) REVERT: D 304 ASP cc_start: 0.8052 (t70) cc_final: 0.7073 (t0) REVERT: D 306 ARG cc_start: 0.8182 (mtm180) cc_final: 0.7625 (mtm180) REVERT: D 309 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8032 (mtp85) REVERT: D 324 LYS cc_start: 0.8669 (tptm) cc_final: 0.8391 (tppt) REVERT: D 325 GLU cc_start: 0.8419 (tp30) cc_final: 0.7667 (tp30) REVERT: D 332 ASN cc_start: 0.8254 (t0) cc_final: 0.7984 (m-40) REVERT: D 380 ARG cc_start: 0.8371 (ptp90) cc_final: 0.8138 (ptp90) REVERT: D 391 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7146 (mtm180) REVERT: D 404 ASP cc_start: 0.8077 (m-30) cc_final: 0.7679 (t0) REVERT: D 407 GLU cc_start: 0.7686 (mp0) cc_final: 0.7188 (mp0) REVERT: D 410 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7118 (mm-30) REVERT: D 414 ASN cc_start: 0.7916 (t0) cc_final: 0.7485 (m-40) REVERT: D 425 TYR cc_start: 0.7402 (m-10) cc_final: 0.7200 (m-10) REVERT: E 3 LEU cc_start: 0.8280 (mt) cc_final: 0.8072 (mp) REVERT: E 15 ASP cc_start: 0.8493 (t0) cc_final: 0.7959 (t0) REVERT: E 53 GLU cc_start: 0.6604 (tm-30) cc_final: 0.5924 (tm-30) REVERT: E 61 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: E 67 PHE cc_start: 0.8304 (m-10) cc_final: 0.7957 (m-10) REVERT: E 68 GLU cc_start: 0.8101 (tt0) cc_final: 0.7724 (tm-30) REVERT: E 94 ASN cc_start: 0.7814 (t0) cc_final: 0.7224 (t0) REVERT: E 113 LEU cc_start: 0.7912 (mm) cc_final: 0.7574 (mm) REVERT: E 120 GLU cc_start: 0.7267 (tt0) cc_final: 0.6922 (tt0) REVERT: E 163 ASP cc_start: 0.7875 (m-30) cc_final: 0.7662 (m-30) REVERT: E 206 ASP cc_start: 0.8674 (p0) cc_final: 0.8191 (p0) REVERT: E 221 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6369 (mm-30) REVERT: E 244 ILE cc_start: 0.7954 (mp) cc_final: 0.7584 (tt) REVERT: E 246 PHE cc_start: 0.8320 (t80) cc_final: 0.8055 (t80) REVERT: E 314 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6394 (mp10) REVERT: E 327 TYR cc_start: 0.7973 (t80) cc_final: 0.7270 (t80) REVERT: E 341 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6966 (mtm110) REVERT: E 483 ASN cc_start: 0.7188 (t0) cc_final: 0.6500 (t0) REVERT: E 534 ASP cc_start: 0.7644 (p0) cc_final: 0.7368 (p0) REVERT: E 550 TYR cc_start: 0.8207 (m-10) cc_final: 0.7886 (m-10) REVERT: E 584 SER cc_start: 0.7037 (m) cc_final: 0.6396 (t) outliers start: 49 outliers final: 20 residues processed: 469 average time/residue: 1.5744 time to fit residues: 808.7983 Evaluate side-chains 442 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 411 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS B 190 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 307 HIS B 347 ASN B 348 ASN B 416 ASN C 28 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 535 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 17849 Z= 0.344 Angle : 0.625 11.428 24276 Z= 0.319 Chirality : 0.047 0.193 2651 Planarity : 0.005 0.067 3170 Dihedral : 11.111 177.815 2517 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.97 % Allowed : 16.60 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.34 (0.18), residues: 2205 helix: 1.15 (0.17), residues: 909 sheet: 0.20 (0.29), residues: 341 loop : -0.60 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 21 HIS 0.007 0.001 HIS A 197 PHE 0.020 0.002 PHE A 255 TYR 0.020 0.002 TYR E 429 ARG 0.012 0.001 ARG E 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 444 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8171 (t0) cc_final: 0.7421 (t0) REVERT: A 71 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: A 113 GLU cc_start: 0.7506 (mp0) cc_final: 0.6968 (mp0) REVERT: A 121 ARG cc_start: 0.7309 (tpp-160) cc_final: 0.7083 (tpp80) REVERT: A 123 ARG cc_start: 0.7551 (tpp-160) cc_final: 0.7232 (tpp80) REVERT: A 124 LYS cc_start: 0.8165 (mttt) cc_final: 0.7766 (ttmm) REVERT: A 203 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8318 (mmm) REVERT: A 221 ARG cc_start: 0.7780 (ptp-110) cc_final: 0.7439 (ptp-110) REVERT: A 254 GLU cc_start: 0.8041 (tt0) cc_final: 0.7341 (mm-30) REVERT: A 255 PHE cc_start: 0.8304 (p90) cc_final: 0.8012 (p90) REVERT: A 280 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8213 (ptpp) REVERT: A 284 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6959 (mm-30) REVERT: A 322 ASP cc_start: 0.7936 (t0) cc_final: 0.7319 (t70) REVERT: A 326 LYS cc_start: 0.4282 (tppt) cc_final: 0.3735 (mmmm) REVERT: A 414 GLU cc_start: 0.8315 (mp0) cc_final: 0.7790 (mp0) REVERT: A 415 GLU cc_start: 0.8110 (tt0) cc_final: 0.7594 (tm-30) REVERT: A 420 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7477 (mt-10) REVERT: A 423 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 433 GLU cc_start: 0.8371 (tp30) cc_final: 0.7836 (tp30) REVERT: B 19 LYS cc_start: 0.8209 (tptm) cc_final: 0.7990 (tptt) REVERT: B 22 GLU cc_start: 0.8237 (tp30) cc_final: 0.7957 (mm-30) REVERT: B 41 ASP cc_start: 0.8186 (m-30) cc_final: 0.7852 (m-30) REVERT: B 45 GLU cc_start: 0.8234 (pt0) cc_final: 0.7905 (pt0) REVERT: B 48 ASN cc_start: 0.8477 (p0) cc_final: 0.8093 (p0) REVERT: B 58 LYS cc_start: 0.7714 (tttt) cc_final: 0.7228 (pttt) REVERT: B 81 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: B 84 ILE cc_start: 0.8723 (tt) cc_final: 0.8288 (pt) REVERT: B 88 ASP cc_start: 0.8686 (t0) cc_final: 0.8313 (t0) REVERT: B 103 LYS cc_start: 0.8601 (tttt) cc_final: 0.7457 (mtpm) REVERT: B 122 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7821 (ttpt) REVERT: B 154 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7879 (mttm) REVERT: B 157 GLU cc_start: 0.8390 (tp30) cc_final: 0.7829 (tm-30) REVERT: B 203 ASP cc_start: 0.7866 (t0) cc_final: 0.7519 (t0) REVERT: B 205 GLU cc_start: 0.7754 (tt0) cc_final: 0.7085 (mt-10) REVERT: B 278 SER cc_start: 0.8404 (m) cc_final: 0.8157 (m) REVERT: B 299 MET cc_start: 0.8544 (mmp) cc_final: 0.8283 (mmt) REVERT: B 327 ASP cc_start: 0.7598 (m-30) cc_final: 0.7390 (m-30) REVERT: B 332 ASN cc_start: 0.7576 (t0) cc_final: 0.7328 (t0) REVERT: B 340 TYR cc_start: 0.7950 (m-10) cc_final: 0.7732 (m-80) REVERT: B 350 LYS cc_start: 0.8562 (tptt) cc_final: 0.8233 (tptm) REVERT: B 363 MET cc_start: 0.8683 (mtm) cc_final: 0.8312 (mtp) REVERT: B 383 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7830 (tt0) REVERT: B 391 ARG cc_start: 0.8292 (mmm160) cc_final: 0.6510 (mtm180) REVERT: B 404 ASP cc_start: 0.7894 (m-30) cc_final: 0.6829 (m-30) REVERT: B 407 GLU cc_start: 0.7480 (mp0) cc_final: 0.6482 (mp0) REVERT: B 410 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7117 (mm-30) REVERT: B 414 ASN cc_start: 0.8060 (t0) cc_final: 0.7760 (m110) REVERT: B 421 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: B 425 TYR cc_start: 0.8518 (m-80) cc_final: 0.8301 (m-80) REVERT: C 2 ARG cc_start: 0.8177 (mtm180) cc_final: 0.7872 (mtm180) REVERT: C 3 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7203 (mp0) REVERT: C 36 MET cc_start: 0.8639 (ttp) cc_final: 0.8380 (ttp) REVERT: C 47 ASP cc_start: 0.8042 (p0) cc_final: 0.7234 (t0) REVERT: C 50 ASN cc_start: 0.8449 (t0) cc_final: 0.7478 (t0) REVERT: C 71 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: C 84 ARG cc_start: 0.8642 (ptp90) cc_final: 0.8423 (ptp90) REVERT: C 121 ARG cc_start: 0.6928 (tpp80) cc_final: 0.6708 (tpp80) REVERT: C 124 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8099 (ttmm) REVERT: C 158 SER cc_start: 0.8709 (t) cc_final: 0.8384 (t) REVERT: C 218 ASP cc_start: 0.8236 (m-30) cc_final: 0.7723 (t0) REVERT: C 221 ARG cc_start: 0.8186 (pmm-80) cc_final: 0.7885 (pmm-80) REVERT: C 254 GLU cc_start: 0.8097 (tt0) cc_final: 0.7610 (tp30) REVERT: C 265 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7826 (mp) REVERT: C 284 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7855 (mm-30) REVERT: C 285 GLN cc_start: 0.8662 (mt0) cc_final: 0.8260 (mm110) REVERT: C 297 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7723 (mm-30) REVERT: C 302 MET cc_start: 0.8282 (mtt) cc_final: 0.8062 (mtt) REVERT: C 308 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7046 (tmt-80) REVERT: C 322 ASP cc_start: 0.8385 (t0) cc_final: 0.8005 (t0) REVERT: C 377 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7773 (tmm) REVERT: C 392 ASP cc_start: 0.7743 (m-30) cc_final: 0.7419 (m-30) REVERT: C 415 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8067 (mm-30) REVERT: C 417 GLU cc_start: 0.7385 (mp0) cc_final: 0.6840 (mp0) REVERT: C 420 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6997 (mm-30) REVERT: C 423 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: C 434 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7692 (pp20) REVERT: D 19 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7762 (mmmt) REVERT: D 45 GLU cc_start: 0.8462 (tt0) cc_final: 0.7814 (tm-30) REVERT: D 57 ASN cc_start: 0.8621 (m-40) cc_final: 0.8383 (m-40) REVERT: D 88 ASP cc_start: 0.8470 (t70) cc_final: 0.8200 (t70) REVERT: D 103 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8242 (mtpm) REVERT: D 121 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7659 (ptp-110) REVERT: D 122 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8243 (ttmm) REVERT: D 126 SER cc_start: 0.7875 (t) cc_final: 0.7605 (p) REVERT: D 128 ASP cc_start: 0.8751 (t0) cc_final: 0.8261 (t0) REVERT: D 201 CYS cc_start: 0.8874 (m) cc_final: 0.8499 (m) REVERT: D 203 ASP cc_start: 0.8235 (t0) cc_final: 0.7568 (t0) REVERT: D 213 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.8201 (ttm-80) REVERT: D 216 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8598 (mmmm) REVERT: D 252 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8231 (ttpt) REVERT: D 304 ASP cc_start: 0.7372 (t70) cc_final: 0.6452 (t0) REVERT: D 306 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7713 (mtm180) REVERT: D 309 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7976 (mtp85) REVERT: D 323 MET cc_start: 0.8146 (mmm) cc_final: 0.7874 (mmm) REVERT: D 324 LYS cc_start: 0.8585 (tptm) cc_final: 0.8351 (tppt) REVERT: D 325 GLU cc_start: 0.8421 (tp30) cc_final: 0.7760 (tp30) REVERT: D 332 ASN cc_start: 0.8261 (t0) cc_final: 0.7951 (m-40) REVERT: D 391 ARG cc_start: 0.8593 (mmm160) cc_final: 0.7127 (mtm110) REVERT: D 404 ASP cc_start: 0.8021 (m-30) cc_final: 0.7407 (t0) REVERT: D 407 GLU cc_start: 0.7692 (mp0) cc_final: 0.6959 (mp0) REVERT: D 410 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7162 (mm-30) REVERT: D 414 ASN cc_start: 0.7937 (t0) cc_final: 0.7489 (m-40) REVERT: D 425 TYR cc_start: 0.7509 (m-10) cc_final: 0.7184 (m-10) REVERT: E 15 ASP cc_start: 0.8490 (t0) cc_final: 0.7967 (t0) REVERT: E 53 GLU cc_start: 0.6467 (tm-30) cc_final: 0.5835 (tm-30) REVERT: E 61 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: E 67 PHE cc_start: 0.8333 (m-10) cc_final: 0.7185 (m-10) REVERT: E 68 GLU cc_start: 0.8011 (tt0) cc_final: 0.7708 (tm-30) REVERT: E 72 ARG cc_start: 0.7824 (ptt-90) cc_final: 0.6970 (ptp90) REVERT: E 94 ASN cc_start: 0.8310 (t0) cc_final: 0.7148 (t0) REVERT: E 113 LEU cc_start: 0.8166 (mm) cc_final: 0.7825 (mm) REVERT: E 120 GLU cc_start: 0.7285 (tt0) cc_final: 0.6936 (tt0) REVERT: E 129 GLU cc_start: 0.8210 (pm20) cc_final: 0.7980 (pm20) REVERT: E 152 PHE cc_start: 0.6888 (m-10) cc_final: 0.6654 (m-10) REVERT: E 206 ASP cc_start: 0.8666 (p0) cc_final: 0.8152 (p0) REVERT: E 213 CYS cc_start: 0.7387 (m) cc_final: 0.6704 (m) REVERT: E 244 ILE cc_start: 0.8058 (mp) cc_final: 0.7673 (tt) REVERT: E 246 PHE cc_start: 0.8311 (t80) cc_final: 0.8074 (t80) REVERT: E 307 ARG cc_start: 0.7767 (mmm160) cc_final: 0.6902 (mmm160) REVERT: E 314 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6529 (mp10) REVERT: E 327 TYR cc_start: 0.8107 (t80) cc_final: 0.7494 (t80) REVERT: E 341 ARG cc_start: 0.7252 (mtm-85) cc_final: 0.6902 (mtm110) REVERT: E 483 ASN cc_start: 0.7319 (t0) cc_final: 0.6545 (t0) REVERT: E 534 ASP cc_start: 0.7812 (p0) cc_final: 0.7481 (p0) REVERT: E 550 TYR cc_start: 0.8336 (m-10) cc_final: 0.8047 (m-10) REVERT: E 556 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7066 (mm-30) REVERT: E 584 SER cc_start: 0.7274 (m) cc_final: 0.6763 (t) REVERT: E 593 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6840 (tpp) outliers start: 73 outliers final: 27 residues processed: 488 average time/residue: 1.4988 time to fit residues: 802.6669 Evaluate side-chains 470 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 430 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 593 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.0770 chunk 111 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 307 HIS B 329 GLN B 416 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 HIS E 599 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17849 Z= 0.207 Angle : 0.591 10.959 24276 Z= 0.299 Chirality : 0.044 0.174 2651 Planarity : 0.005 0.065 3170 Dihedral : 11.072 178.192 2517 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.94 % Allowed : 18.78 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2205 helix: 1.31 (0.17), residues: 907 sheet: 0.28 (0.29), residues: 341 loop : -0.59 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.008 0.001 HIS B 307 PHE 0.019 0.001 PHE A 255 TYR 0.021 0.001 TYR B 36 ARG 0.010 0.001 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 461 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.8020 (mpp-170) REVERT: A 50 ASN cc_start: 0.8130 (t0) cc_final: 0.7430 (t0) REVERT: A 71 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: A 76 ASP cc_start: 0.8251 (m-30) cc_final: 0.7428 (m-30) REVERT: A 113 GLU cc_start: 0.7481 (mp0) cc_final: 0.6955 (mp0) REVERT: A 123 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7310 (tpp80) REVERT: A 124 LYS cc_start: 0.8171 (mttt) cc_final: 0.7748 (ttmm) REVERT: A 203 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8303 (mmm) REVERT: A 221 ARG cc_start: 0.7772 (ptp-110) cc_final: 0.7454 (ptp-110) REVERT: A 254 GLU cc_start: 0.8044 (tt0) cc_final: 0.7347 (mm-30) REVERT: A 255 PHE cc_start: 0.8272 (p90) cc_final: 0.7984 (p90) REVERT: A 256 GLN cc_start: 0.8260 (mt0) cc_final: 0.7982 (mt0) REVERT: A 280 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8247 (ptpp) REVERT: A 284 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6825 (mm-30) REVERT: A 306 ASP cc_start: 0.8067 (t0) cc_final: 0.7478 (t0) REVERT: A 322 ASP cc_start: 0.7916 (t0) cc_final: 0.7564 (t0) REVERT: A 358 GLN cc_start: 0.8895 (tp40) cc_final: 0.8626 (mm-40) REVERT: A 399 TYR cc_start: 0.8701 (t80) cc_final: 0.8191 (t80) REVERT: A 414 GLU cc_start: 0.8330 (mp0) cc_final: 0.7266 (mp0) REVERT: A 415 GLU cc_start: 0.8063 (tt0) cc_final: 0.7539 (tm-30) REVERT: A 417 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6858 (mp0) REVERT: A 420 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7472 (mt-10) REVERT: A 423 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7903 (mm-30) REVERT: A 433 GLU cc_start: 0.8346 (tp30) cc_final: 0.7800 (tp30) REVERT: B 45 GLU cc_start: 0.8184 (pt0) cc_final: 0.7796 (pt0) REVERT: B 48 ASN cc_start: 0.8424 (p0) cc_final: 0.8043 (p0) REVERT: B 53 GLU cc_start: 0.8205 (tt0) cc_final: 0.7668 (mm-30) REVERT: B 57 ASN cc_start: 0.8110 (m-40) cc_final: 0.7877 (m-40) REVERT: B 58 LYS cc_start: 0.7667 (tttt) cc_final: 0.7163 (pttt) REVERT: B 84 ILE cc_start: 0.8683 (tt) cc_final: 0.8327 (pt) REVERT: B 88 ASP cc_start: 0.8656 (t0) cc_final: 0.8325 (t0) REVERT: B 122 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7779 (ttpt) REVERT: B 154 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8081 (mptm) REVERT: B 157 GLU cc_start: 0.8387 (tp30) cc_final: 0.7824 (tm-30) REVERT: B 197 ASP cc_start: 0.8420 (m-30) cc_final: 0.8148 (m-30) REVERT: B 205 GLU cc_start: 0.7748 (tt0) cc_final: 0.7165 (mt-10) REVERT: B 267 MET cc_start: 0.8566 (mtp) cc_final: 0.8314 (mtm) REVERT: B 278 SER cc_start: 0.8424 (m) cc_final: 0.8182 (m) REVERT: B 282 ARG cc_start: 0.7290 (ptm-80) cc_final: 0.6714 (tmm160) REVERT: B 324 LYS cc_start: 0.8267 (tptp) cc_final: 0.8035 (tppt) REVERT: B 327 ASP cc_start: 0.7589 (m-30) cc_final: 0.7384 (m-30) REVERT: B 332 ASN cc_start: 0.7437 (t0) cc_final: 0.7209 (t0) REVERT: B 340 TYR cc_start: 0.7964 (m-10) cc_final: 0.7657 (m-80) REVERT: B 350 LYS cc_start: 0.8616 (tptt) cc_final: 0.8294 (tptm) REVERT: B 363 MET cc_start: 0.8646 (mtm) cc_final: 0.8306 (mtp) REVERT: B 383 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7792 (tt0) REVERT: B 391 ARG cc_start: 0.8247 (mmm160) cc_final: 0.6668 (mtm180) REVERT: B 404 ASP cc_start: 0.7917 (m-30) cc_final: 0.7222 (m-30) REVERT: B 407 GLU cc_start: 0.7507 (mp0) cc_final: 0.6778 (mp0) REVERT: B 410 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7121 (mm-30) REVERT: B 414 ASN cc_start: 0.7999 (t0) cc_final: 0.7669 (m110) REVERT: B 421 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: B 425 TYR cc_start: 0.8515 (m-80) cc_final: 0.8284 (m-80) REVERT: C 2 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7755 (mtm180) REVERT: C 47 ASP cc_start: 0.8013 (p0) cc_final: 0.7252 (t0) REVERT: C 50 ASN cc_start: 0.8385 (t0) cc_final: 0.7377 (t0) REVERT: C 71 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: C 77 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7907 (mt-10) REVERT: C 84 ARG cc_start: 0.8642 (ptp90) cc_final: 0.8426 (ptp90) REVERT: C 158 SER cc_start: 0.8687 (t) cc_final: 0.8376 (t) REVERT: C 196 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: C 203 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8153 (mmm) REVERT: C 207 GLU cc_start: 0.7255 (tt0) cc_final: 0.6909 (mt-10) REVERT: C 218 ASP cc_start: 0.8243 (m-30) cc_final: 0.7639 (t0) REVERT: C 221 ARG cc_start: 0.8182 (pmm-80) cc_final: 0.7873 (pmm-80) REVERT: C 254 GLU cc_start: 0.8031 (tt0) cc_final: 0.7716 (tp30) REVERT: C 265 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7772 (mp) REVERT: C 269 LEU cc_start: 0.8367 (mp) cc_final: 0.8151 (mp) REVERT: C 280 LYS cc_start: 0.8639 (mttp) cc_final: 0.7277 (mmtt) REVERT: C 284 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7498 (mm-30) REVERT: C 285 GLN cc_start: 0.8642 (mt0) cc_final: 0.8285 (mm110) REVERT: C 290 GLU cc_start: 0.7726 (mp0) cc_final: 0.7140 (mp0) REVERT: C 297 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7787 (tp30) REVERT: C 308 ARG cc_start: 0.8205 (mtm180) cc_final: 0.7013 (tmt-80) REVERT: C 322 ASP cc_start: 0.8376 (t0) cc_final: 0.8030 (t0) REVERT: C 377 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7769 (tmm) REVERT: C 386 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7766 (mt-10) REVERT: C 392 ASP cc_start: 0.7724 (m-30) cc_final: 0.7382 (m-30) REVERT: C 415 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8054 (mm-30) REVERT: C 417 GLU cc_start: 0.7369 (mp0) cc_final: 0.6858 (mp0) REVERT: C 420 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7079 (mm-30) REVERT: D 19 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7748 (mmmt) REVERT: D 45 GLU cc_start: 0.8443 (tt0) cc_final: 0.7810 (tm-30) REVERT: D 57 ASN cc_start: 0.8644 (m-40) cc_final: 0.8428 (m-40) REVERT: D 88 ASP cc_start: 0.8435 (t70) cc_final: 0.8166 (t70) REVERT: D 103 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8251 (mtpm) REVERT: D 121 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7684 (ptp-110) REVERT: D 122 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8247 (ttmm) REVERT: D 126 SER cc_start: 0.7904 (t) cc_final: 0.7635 (p) REVERT: D 128 ASP cc_start: 0.8740 (t0) cc_final: 0.8238 (t0) REVERT: D 201 CYS cc_start: 0.8883 (m) cc_final: 0.8543 (m) REVERT: D 203 ASP cc_start: 0.8241 (t0) cc_final: 0.7551 (t70) REVERT: D 213 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8162 (ttm-80) REVERT: D 216 LYS cc_start: 0.8919 (mmtm) cc_final: 0.8582 (mmmm) REVERT: D 252 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8225 (ttpt) REVERT: D 304 ASP cc_start: 0.7714 (t70) cc_final: 0.6793 (t0) REVERT: D 306 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7705 (mtm180) REVERT: D 309 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7695 (mtp85) REVERT: D 324 LYS cc_start: 0.8679 (tptm) cc_final: 0.8442 (tppt) REVERT: D 325 GLU cc_start: 0.8470 (tp30) cc_final: 0.7823 (tp30) REVERT: D 332 ASN cc_start: 0.8244 (t0) cc_final: 0.7942 (m-40) REVERT: D 391 ARG cc_start: 0.8589 (mmm160) cc_final: 0.7060 (mtm110) REVERT: D 404 ASP cc_start: 0.8031 (m-30) cc_final: 0.7475 (t70) REVERT: D 407 GLU cc_start: 0.7698 (mp0) cc_final: 0.7045 (mp0) REVERT: D 410 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7139 (mm-30) REVERT: D 414 ASN cc_start: 0.7925 (t0) cc_final: 0.7470 (m-40) REVERT: D 425 TYR cc_start: 0.7510 (m-10) cc_final: 0.7212 (m-10) REVERT: E 15 ASP cc_start: 0.8500 (t0) cc_final: 0.7990 (t0) REVERT: E 53 GLU cc_start: 0.6464 (tm-30) cc_final: 0.6060 (tm-30) REVERT: E 61 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: E 67 PHE cc_start: 0.8246 (m-10) cc_final: 0.7091 (m-10) REVERT: E 68 GLU cc_start: 0.8000 (tt0) cc_final: 0.7697 (tm-30) REVERT: E 72 ARG cc_start: 0.7754 (ptt-90) cc_final: 0.7228 (ptt-90) REVERT: E 94 ASN cc_start: 0.8231 (t0) cc_final: 0.7338 (t0) REVERT: E 113 LEU cc_start: 0.8090 (mm) cc_final: 0.7799 (mm) REVERT: E 120 GLU cc_start: 0.7252 (tt0) cc_final: 0.6902 (tt0) REVERT: E 129 GLU cc_start: 0.8229 (pm20) cc_final: 0.7982 (pm20) REVERT: E 156 CYS cc_start: 0.8677 (t) cc_final: 0.8305 (t) REVERT: E 169 ASN cc_start: 0.7261 (m-40) cc_final: 0.7049 (m-40) REVERT: E 206 ASP cc_start: 0.8613 (p0) cc_final: 0.8086 (p0) REVERT: E 213 CYS cc_start: 0.7322 (m) cc_final: 0.6584 (m) REVERT: E 244 ILE cc_start: 0.8097 (mp) cc_final: 0.7706 (tt) REVERT: E 246 PHE cc_start: 0.8304 (t80) cc_final: 0.8027 (t80) REVERT: E 307 ARG cc_start: 0.7777 (mmm160) cc_final: 0.6927 (mmm160) REVERT: E 314 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6355 (mp10) REVERT: E 327 TYR cc_start: 0.8137 (t80) cc_final: 0.7538 (t80) REVERT: E 451 ASP cc_start: 0.6997 (t0) cc_final: 0.6445 (t0) REVERT: E 483 ASN cc_start: 0.7271 (t0) cc_final: 0.6546 (t0) REVERT: E 550 TYR cc_start: 0.8348 (m-10) cc_final: 0.8045 (m-10) REVERT: E 556 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7050 (mm-30) REVERT: E 584 SER cc_start: 0.7183 (m) cc_final: 0.6633 (t) outliers start: 54 outliers final: 25 residues processed: 489 average time/residue: 1.4971 time to fit residues: 805.2868 Evaluate side-chains 479 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 442 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 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 35 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN B 190 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 416 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17849 Z= 0.240 Angle : 0.592 11.148 24276 Z= 0.300 Chirality : 0.044 0.159 2651 Planarity : 0.004 0.058 3170 Dihedral : 11.108 175.239 2517 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 3.21 % Allowed : 18.89 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.49 (0.18), residues: 2205 helix: 1.31 (0.17), residues: 910 sheet: 0.31 (0.29), residues: 339 loop : -0.58 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.006 0.001 HIS C 197 PHE 0.020 0.001 PHE E 152 TYR 0.017 0.001 TYR E 52 ARG 0.011 0.001 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 449 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8145 (t0) cc_final: 0.7462 (t0) REVERT: A 71 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: A 76 ASP cc_start: 0.8265 (m-30) cc_final: 0.7448 (m-30) REVERT: A 113 GLU cc_start: 0.7506 (mp0) cc_final: 0.6961 (mp0) REVERT: A 123 ARG cc_start: 0.7553 (tpp-160) cc_final: 0.7315 (tpp80) REVERT: A 124 LYS cc_start: 0.8172 (mttt) cc_final: 0.7811 (ttmm) REVERT: A 203 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: A 254 GLU cc_start: 0.8080 (tt0) cc_final: 0.7375 (mm-30) REVERT: A 255 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7973 (p90) REVERT: A 256 GLN cc_start: 0.8264 (mt0) cc_final: 0.7964 (mt0) REVERT: A 280 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8180 (ptpp) REVERT: A 284 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6814 (mm-30) REVERT: A 322 ASP cc_start: 0.7947 (t0) cc_final: 0.7342 (t70) REVERT: A 358 GLN cc_start: 0.8890 (tp40) cc_final: 0.8609 (mm-40) REVERT: A 399 TYR cc_start: 0.8718 (t80) cc_final: 0.8231 (t80) REVERT: A 414 GLU cc_start: 0.8308 (mp0) cc_final: 0.7262 (mp0) REVERT: A 415 GLU cc_start: 0.8068 (tt0) cc_final: 0.7552 (tm-30) REVERT: A 417 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6886 (mp0) REVERT: A 420 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7477 (mt-10) REVERT: A 423 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 433 GLU cc_start: 0.8340 (tp30) cc_final: 0.7859 (tp30) REVERT: B 45 GLU cc_start: 0.8189 (pt0) cc_final: 0.7786 (pt0) REVERT: B 48 ASN cc_start: 0.8465 (p0) cc_final: 0.8076 (p0) REVERT: B 53 GLU cc_start: 0.8222 (tt0) cc_final: 0.7600 (mm-30) REVERT: B 57 ASN cc_start: 0.8127 (m-40) cc_final: 0.7900 (m-40) REVERT: B 58 LYS cc_start: 0.7654 (tttt) cc_final: 0.7140 (pttt) REVERT: B 84 ILE cc_start: 0.8601 (tt) cc_final: 0.8342 (pt) REVERT: B 88 ASP cc_start: 0.8661 (t0) cc_final: 0.8344 (t0) REVERT: B 122 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7827 (ttpt) REVERT: B 157 GLU cc_start: 0.8383 (tp30) cc_final: 0.7851 (tm-30) REVERT: B 197 ASP cc_start: 0.8402 (m-30) cc_final: 0.8153 (m-30) REVERT: B 205 GLU cc_start: 0.7853 (tt0) cc_final: 0.7301 (mt-10) REVERT: B 267 MET cc_start: 0.8576 (mtp) cc_final: 0.8321 (mtm) REVERT: B 282 ARG cc_start: 0.7293 (ptm-80) cc_final: 0.6594 (ptm-80) REVERT: B 295 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8017 (t0) REVERT: B 327 ASP cc_start: 0.7596 (m-30) cc_final: 0.7387 (m-30) REVERT: B 332 ASN cc_start: 0.7457 (t0) cc_final: 0.7237 (t0) REVERT: B 340 TYR cc_start: 0.7959 (m-10) cc_final: 0.7570 (m-80) REVERT: B 350 LYS cc_start: 0.8629 (tptt) cc_final: 0.8290 (tptm) REVERT: B 363 MET cc_start: 0.8653 (mtm) cc_final: 0.8270 (mtp) REVERT: B 383 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7795 (tt0) REVERT: B 391 ARG cc_start: 0.8293 (mmm160) cc_final: 0.6235 (ptm-80) REVERT: B 404 ASP cc_start: 0.7905 (m-30) cc_final: 0.7178 (m-30) REVERT: B 407 GLU cc_start: 0.7495 (mp0) cc_final: 0.6737 (mp0) REVERT: B 410 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7150 (mm-30) REVERT: B 414 ASN cc_start: 0.8003 (t0) cc_final: 0.7696 (m110) REVERT: B 421 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: C 2 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7786 (mtm180) REVERT: C 36 MET cc_start: 0.8646 (ttp) cc_final: 0.8367 (ttp) REVERT: C 47 ASP cc_start: 0.8010 (p0) cc_final: 0.7255 (t0) REVERT: C 50 ASN cc_start: 0.8393 (t0) cc_final: 0.7394 (t0) REVERT: C 71 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: C 76 ASP cc_start: 0.8153 (m-30) cc_final: 0.7668 (m-30) REVERT: C 77 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8101 (mt-10) REVERT: C 84 ARG cc_start: 0.8630 (ptp90) cc_final: 0.8415 (ptp90) REVERT: C 90 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7521 (tm-30) REVERT: C 120 ASP cc_start: 0.7761 (m-30) cc_final: 0.7313 (m-30) REVERT: C 123 ARG cc_start: 0.7622 (tpp80) cc_final: 0.7250 (ttp80) REVERT: C 124 LYS cc_start: 0.8424 (ttmm) cc_final: 0.7599 (ttmm) REVERT: C 158 SER cc_start: 0.8684 (t) cc_final: 0.8365 (t) REVERT: C 196 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: C 203 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8172 (mmm) REVERT: C 207 GLU cc_start: 0.7254 (tt0) cc_final: 0.6927 (mt-10) REVERT: C 218 ASP cc_start: 0.8236 (m-30) cc_final: 0.7634 (t0) REVERT: C 221 ARG cc_start: 0.8199 (pmm-80) cc_final: 0.7816 (pmm-80) REVERT: C 254 GLU cc_start: 0.8034 (tt0) cc_final: 0.7723 (tp30) REVERT: C 265 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7839 (mp) REVERT: C 269 LEU cc_start: 0.8383 (mp) cc_final: 0.8103 (mp) REVERT: C 280 LYS cc_start: 0.8668 (mttp) cc_final: 0.7276 (mmtt) REVERT: C 284 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7488 (mm-30) REVERT: C 285 GLN cc_start: 0.8622 (mt0) cc_final: 0.8250 (mm110) REVERT: C 290 GLU cc_start: 0.7748 (mp0) cc_final: 0.7157 (mp0) REVERT: C 308 ARG cc_start: 0.8218 (mtm180) cc_final: 0.7019 (tmt-80) REVERT: C 322 ASP cc_start: 0.8371 (t0) cc_final: 0.8019 (t0) REVERT: C 377 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7759 (tmm) REVERT: C 386 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7989 (mt-10) REVERT: C 392 ASP cc_start: 0.7737 (m-30) cc_final: 0.7362 (m-30) REVERT: C 415 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8105 (mm-30) REVERT: C 417 GLU cc_start: 0.7449 (mp0) cc_final: 0.6851 (mp0) REVERT: C 420 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7241 (mm-30) REVERT: D 1 MET cc_start: 0.7493 (tpp) cc_final: 0.7232 (mmm) REVERT: D 19 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7727 (mmmt) REVERT: D 45 GLU cc_start: 0.8430 (tt0) cc_final: 0.7795 (tm-30) REVERT: D 57 ASN cc_start: 0.8624 (m-40) cc_final: 0.8418 (m-40) REVERT: D 88 ASP cc_start: 0.8425 (t70) cc_final: 0.8146 (t70) REVERT: D 103 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8080 (mtpm) REVERT: D 121 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7690 (ptp-110) REVERT: D 122 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8272 (ttmm) REVERT: D 126 SER cc_start: 0.7972 (t) cc_final: 0.7715 (p) REVERT: D 128 ASP cc_start: 0.8706 (t0) cc_final: 0.8363 (t0) REVERT: D 157 GLU cc_start: 0.8400 (tt0) cc_final: 0.7896 (tm-30) REVERT: D 201 CYS cc_start: 0.8879 (m) cc_final: 0.8528 (m) REVERT: D 203 ASP cc_start: 0.8255 (t0) cc_final: 0.7552 (t70) REVERT: D 213 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8166 (ttm-80) REVERT: D 216 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8562 (mmmm) REVERT: D 304 ASP cc_start: 0.7817 (t70) cc_final: 0.6810 (t0) REVERT: D 306 ARG cc_start: 0.8228 (mtm180) cc_final: 0.7679 (mtm180) REVERT: D 309 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7831 (mtp85) REVERT: D 324 LYS cc_start: 0.8651 (tptm) cc_final: 0.8398 (tppt) REVERT: D 325 GLU cc_start: 0.8446 (tp30) cc_final: 0.7844 (tp30) REVERT: D 332 ASN cc_start: 0.8251 (t0) cc_final: 0.7957 (m-40) REVERT: D 391 ARG cc_start: 0.8643 (mmm160) cc_final: 0.7191 (mtm180) REVERT: D 401 GLU cc_start: 0.7973 (mp0) cc_final: 0.7553 (mm-30) REVERT: D 404 ASP cc_start: 0.8029 (m-30) cc_final: 0.7521 (t0) REVERT: D 407 GLU cc_start: 0.7711 (mp0) cc_final: 0.7018 (mp0) REVERT: D 410 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7145 (mm-30) REVERT: D 414 ASN cc_start: 0.7957 (t0) cc_final: 0.7489 (m-40) REVERT: D 424 GLN cc_start: 0.8284 (pt0) cc_final: 0.7969 (pp30) REVERT: D 425 TYR cc_start: 0.7542 (m-80) cc_final: 0.7216 (m-10) REVERT: E 15 ASP cc_start: 0.8492 (t0) cc_final: 0.7992 (t0) REVERT: E 53 GLU cc_start: 0.6513 (tm-30) cc_final: 0.6127 (tm-30) REVERT: E 61 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: E 67 PHE cc_start: 0.8251 (m-10) cc_final: 0.7148 (m-10) REVERT: E 72 ARG cc_start: 0.7741 (ptt-90) cc_final: 0.7235 (ptt-90) REVERT: E 94 ASN cc_start: 0.8204 (t0) cc_final: 0.7395 (t0) REVERT: E 113 LEU cc_start: 0.8156 (mm) cc_final: 0.7897 (mm) REVERT: E 120 GLU cc_start: 0.7273 (tt0) cc_final: 0.6897 (tt0) REVERT: E 156 CYS cc_start: 0.8684 (t) cc_final: 0.8300 (t) REVERT: E 206 ASP cc_start: 0.8604 (p0) cc_final: 0.8064 (p0) REVERT: E 213 CYS cc_start: 0.7281 (m) cc_final: 0.6675 (m) REVERT: E 244 ILE cc_start: 0.8143 (mp) cc_final: 0.7727 (tt) REVERT: E 246 PHE cc_start: 0.8272 (t80) cc_final: 0.8016 (t80) REVERT: E 307 ARG cc_start: 0.7792 (mmm160) cc_final: 0.7041 (mmm160) REVERT: E 313 ARG cc_start: 0.7367 (mmt90) cc_final: 0.7143 (mmt-90) REVERT: E 314 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6423 (mp10) REVERT: E 327 TYR cc_start: 0.8198 (t80) cc_final: 0.7598 (t80) REVERT: E 459 MET cc_start: 0.8116 (mtp) cc_final: 0.7869 (mtp) REVERT: E 483 ASN cc_start: 0.7314 (t0) cc_final: 0.6580 (t0) REVERT: E 496 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7159 (tm-30) REVERT: E 550 TYR cc_start: 0.8390 (m-10) cc_final: 0.8031 (m-10) REVERT: E 556 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7058 (mm-30) REVERT: E 581 SER cc_start: 0.8330 (t) cc_final: 0.7979 (p) REVERT: E 584 SER cc_start: 0.7222 (m) cc_final: 0.6649 (t) outliers start: 59 outliers final: 33 residues processed: 477 average time/residue: 1.4953 time to fit residues: 784.4137 Evaluate side-chains 479 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 433 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 176 GLN B 190 HIS B 416 ASN C 101 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17849 Z= 0.225 Angle : 0.606 11.565 24276 Z= 0.306 Chirality : 0.045 0.250 2651 Planarity : 0.004 0.056 3170 Dihedral : 11.032 175.580 2517 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 2.99 % Allowed : 19.54 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2205 helix: 1.34 (0.17), residues: 910 sheet: 0.32 (0.29), residues: 339 loop : -0.57 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 21 HIS 0.021 0.001 HIS B 307 PHE 0.018 0.001 PHE A 255 TYR 0.019 0.001 TYR E 429 ARG 0.011 0.001 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 440 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8155 (t0) cc_final: 0.7450 (t0) REVERT: A 62 VAL cc_start: 0.8947 (t) cc_final: 0.8725 (m) REVERT: A 71 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: A 76 ASP cc_start: 0.8266 (m-30) cc_final: 0.7444 (m-30) REVERT: A 113 GLU cc_start: 0.7384 (mp0) cc_final: 0.6914 (mp0) REVERT: A 123 ARG cc_start: 0.7524 (tpp-160) cc_final: 0.7302 (tpp80) REVERT: A 124 LYS cc_start: 0.8161 (mttt) cc_final: 0.7802 (ttmm) REVERT: A 203 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8229 (mmm) REVERT: A 254 GLU cc_start: 0.8085 (tt0) cc_final: 0.7373 (mm-30) REVERT: A 255 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7963 (p90) REVERT: A 256 GLN cc_start: 0.8254 (mt0) cc_final: 0.7943 (mt0) REVERT: A 280 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8152 (ptpp) REVERT: A 284 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 306 ASP cc_start: 0.8000 (t0) cc_final: 0.7408 (t0) REVERT: A 322 ASP cc_start: 0.7946 (t0) cc_final: 0.7577 (t0) REVERT: A 399 TYR cc_start: 0.8715 (t80) cc_final: 0.8234 (t80) REVERT: A 414 GLU cc_start: 0.8326 (mp0) cc_final: 0.7246 (mp0) REVERT: A 415 GLU cc_start: 0.8059 (tt0) cc_final: 0.7583 (tm-30) REVERT: A 417 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6896 (mp0) REVERT: A 420 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7504 (mt-10) REVERT: A 423 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7935 (mm-30) REVERT: A 433 GLU cc_start: 0.8332 (tp30) cc_final: 0.7861 (tp30) REVERT: B 41 ASP cc_start: 0.8136 (m-30) cc_final: 0.7861 (m-30) REVERT: B 45 GLU cc_start: 0.8163 (pt0) cc_final: 0.7771 (pt0) REVERT: B 48 ASN cc_start: 0.8462 (p0) cc_final: 0.8066 (p0) REVERT: B 53 GLU cc_start: 0.8225 (tt0) cc_final: 0.7645 (mm-30) REVERT: B 58 LYS cc_start: 0.7649 (tttt) cc_final: 0.7137 (pttt) REVERT: B 84 ILE cc_start: 0.8572 (tt) cc_final: 0.8336 (pt) REVERT: B 88 ASP cc_start: 0.8660 (t0) cc_final: 0.8322 (t0) REVERT: B 122 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7841 (ttpt) REVERT: B 157 GLU cc_start: 0.8389 (tp30) cc_final: 0.7846 (tm-30) REVERT: B 158 GLU cc_start: 0.8364 (tp30) cc_final: 0.8121 (mt-10) REVERT: B 203 ASP cc_start: 0.8022 (t0) cc_final: 0.7583 (t0) REVERT: B 205 GLU cc_start: 0.7860 (tt0) cc_final: 0.7183 (mt-10) REVERT: B 267 MET cc_start: 0.8558 (mtp) cc_final: 0.8316 (mtm) REVERT: B 282 ARG cc_start: 0.7324 (ptm-80) cc_final: 0.6738 (ptm-80) REVERT: B 304 ASP cc_start: 0.7999 (t70) cc_final: 0.7775 (t0) REVERT: B 306 ARG cc_start: 0.8560 (mpt-90) cc_final: 0.7926 (mtm-85) REVERT: B 327 ASP cc_start: 0.7590 (m-30) cc_final: 0.7385 (m-30) REVERT: B 332 ASN cc_start: 0.7434 (t0) cc_final: 0.7223 (t0) REVERT: B 340 TYR cc_start: 0.7967 (m-10) cc_final: 0.7546 (m-80) REVERT: B 350 LYS cc_start: 0.8631 (tptt) cc_final: 0.8304 (tptm) REVERT: B 363 MET cc_start: 0.8653 (mtm) cc_final: 0.8278 (mtp) REVERT: B 383 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7791 (tt0) REVERT: B 391 ARG cc_start: 0.8308 (mmm160) cc_final: 0.6200 (ptp-170) REVERT: B 404 ASP cc_start: 0.7902 (m-30) cc_final: 0.6848 (m-30) REVERT: B 407 GLU cc_start: 0.7495 (mp0) cc_final: 0.6495 (mp0) REVERT: B 410 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7155 (mm-30) REVERT: B 414 ASN cc_start: 0.8015 (t0) cc_final: 0.7677 (m110) REVERT: B 421 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: C 2 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7795 (mtm180) REVERT: C 47 ASP cc_start: 0.8010 (p0) cc_final: 0.7262 (t0) REVERT: C 50 ASN cc_start: 0.8385 (t0) cc_final: 0.7370 (t0) REVERT: C 71 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: C 76 ASP cc_start: 0.8167 (m-30) cc_final: 0.7653 (m-30) REVERT: C 77 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7982 (mt-10) REVERT: C 90 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7469 (tm-30) REVERT: C 120 ASP cc_start: 0.7762 (m-30) cc_final: 0.7319 (m-30) REVERT: C 123 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7141 (ttp80) REVERT: C 158 SER cc_start: 0.8725 (t) cc_final: 0.8425 (t) REVERT: C 196 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: C 203 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8241 (mmm) REVERT: C 207 GLU cc_start: 0.7247 (tt0) cc_final: 0.6925 (mt-10) REVERT: C 218 ASP cc_start: 0.8228 (m-30) cc_final: 0.7631 (t0) REVERT: C 221 ARG cc_start: 0.8178 (pmm-80) cc_final: 0.7788 (pmm-80) REVERT: C 254 GLU cc_start: 0.8021 (tt0) cc_final: 0.7635 (tp30) REVERT: C 265 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7783 (mp) REVERT: C 269 LEU cc_start: 0.8380 (mp) cc_final: 0.8099 (mp) REVERT: C 280 LYS cc_start: 0.8664 (mttp) cc_final: 0.7318 (mmtt) REVERT: C 284 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7471 (mm-30) REVERT: C 285 GLN cc_start: 0.8622 (mt0) cc_final: 0.8240 (mm110) REVERT: C 290 GLU cc_start: 0.7808 (mp0) cc_final: 0.7207 (mp0) REVERT: C 297 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7783 (tp30) REVERT: C 308 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7009 (tmt-80) REVERT: C 322 ASP cc_start: 0.8369 (t0) cc_final: 0.8022 (t0) REVERT: C 377 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7776 (tmm) REVERT: C 386 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7887 (mt-10) REVERT: C 392 ASP cc_start: 0.7700 (m-30) cc_final: 0.7363 (m-30) REVERT: C 415 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8092 (mm-30) REVERT: C 417 GLU cc_start: 0.7468 (mp0) cc_final: 0.6846 (mp0) REVERT: C 420 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7195 (mm-30) REVERT: D 19 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7725 (mmmt) REVERT: D 45 GLU cc_start: 0.8417 (tt0) cc_final: 0.7781 (tm-30) REVERT: D 57 ASN cc_start: 0.8598 (m-40) cc_final: 0.8397 (m-40) REVERT: D 88 ASP cc_start: 0.8420 (t70) cc_final: 0.8136 (t70) REVERT: D 103 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8297 (mtpm) REVERT: D 121 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7689 (ptp-110) REVERT: D 122 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8283 (ttmm) REVERT: D 126 SER cc_start: 0.8020 (t) cc_final: 0.7768 (p) REVERT: D 128 ASP cc_start: 0.8691 (t0) cc_final: 0.8217 (t0) REVERT: D 157 GLU cc_start: 0.8381 (tt0) cc_final: 0.7896 (tm-30) REVERT: D 201 CYS cc_start: 0.8879 (m) cc_final: 0.8551 (m) REVERT: D 203 ASP cc_start: 0.8272 (t0) cc_final: 0.7575 (t70) REVERT: D 213 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8216 (ttp-110) REVERT: D 216 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8478 (mmmm) REVERT: D 245 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: D 304 ASP cc_start: 0.7873 (t70) cc_final: 0.6850 (t0) REVERT: D 306 ARG cc_start: 0.8227 (mtm180) cc_final: 0.7680 (mtm180) REVERT: D 309 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7837 (mtp85) REVERT: D 325 GLU cc_start: 0.8440 (tp30) cc_final: 0.7808 (tp30) REVERT: D 332 ASN cc_start: 0.8330 (t0) cc_final: 0.8052 (m-40) REVERT: D 391 ARG cc_start: 0.8649 (mmm160) cc_final: 0.7170 (mtm180) REVERT: D 404 ASP cc_start: 0.8046 (m-30) cc_final: 0.7524 (t0) REVERT: D 407 GLU cc_start: 0.7717 (mp0) cc_final: 0.7002 (mp0) REVERT: D 410 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7254 (mm-30) REVERT: D 414 ASN cc_start: 0.7961 (t0) cc_final: 0.7541 (m110) REVERT: D 424 GLN cc_start: 0.8274 (pt0) cc_final: 0.7926 (pp30) REVERT: D 425 TYR cc_start: 0.7540 (m-80) cc_final: 0.7204 (m-10) REVERT: E 15 ASP cc_start: 0.8491 (t0) cc_final: 0.7987 (t0) REVERT: E 53 GLU cc_start: 0.6470 (tm-30) cc_final: 0.6193 (tm-30) REVERT: E 61 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: E 67 PHE cc_start: 0.8247 (m-10) cc_final: 0.8040 (m-10) REVERT: E 72 ARG cc_start: 0.7750 (ptt-90) cc_final: 0.7254 (ptt-90) REVERT: E 94 ASN cc_start: 0.8175 (t0) cc_final: 0.7384 (t0) REVERT: E 113 LEU cc_start: 0.8247 (mm) cc_final: 0.8008 (mm) REVERT: E 120 GLU cc_start: 0.7274 (tt0) cc_final: 0.6881 (tt0) REVERT: E 129 GLU cc_start: 0.8004 (pm20) cc_final: 0.7722 (pm20) REVERT: E 136 VAL cc_start: 0.8219 (t) cc_final: 0.7913 (p) REVERT: E 152 PHE cc_start: 0.6767 (m-10) cc_final: 0.6532 (m-10) REVERT: E 156 CYS cc_start: 0.8642 (t) cc_final: 0.8233 (t) REVERT: E 191 TYR cc_start: 0.8315 (t80) cc_final: 0.7867 (OUTLIER) REVERT: E 206 ASP cc_start: 0.8552 (p0) cc_final: 0.7987 (p0) REVERT: E 213 CYS cc_start: 0.7296 (m) cc_final: 0.6565 (m) REVERT: E 244 ILE cc_start: 0.8147 (mp) cc_final: 0.7729 (tt) REVERT: E 246 PHE cc_start: 0.8259 (t80) cc_final: 0.7984 (t80) REVERT: E 313 ARG cc_start: 0.7361 (mmt90) cc_final: 0.7126 (mmt-90) REVERT: E 314 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6386 (mp10) REVERT: E 327 TYR cc_start: 0.8200 (t80) cc_final: 0.7548 (t80) REVERT: E 341 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.6928 (mtm110) REVERT: E 451 ASP cc_start: 0.6962 (t0) cc_final: 0.6482 (t0) REVERT: E 483 ASN cc_start: 0.7367 (t0) cc_final: 0.6673 (t0) REVERT: E 496 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7232 (tm-30) REVERT: E 550 TYR cc_start: 0.8346 (m-10) cc_final: 0.8061 (m-10) REVERT: E 556 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7063 (mm-30) REVERT: E 584 SER cc_start: 0.7228 (m) cc_final: 0.6658 (t) outliers start: 55 outliers final: 33 residues processed: 467 average time/residue: 1.4612 time to fit residues: 749.9211 Evaluate side-chains 489 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 444 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.0570 chunk 185 optimal weight: 2.9990 chunk 197 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 0.0000 chunk 178 optimal weight: 0.9980 chunk 186 optimal weight: 0.4980 chunk 196 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS B 307 HIS B 335 ASN B 416 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17849 Z= 0.183 Angle : 0.589 11.724 24276 Z= 0.298 Chirality : 0.043 0.310 2651 Planarity : 0.005 0.058 3170 Dihedral : 10.895 178.753 2517 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.55 % Rotamer: Outliers : 2.61 % Allowed : 20.09 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2205 helix: 1.42 (0.17), residues: 912 sheet: 0.31 (0.29), residues: 339 loop : -0.54 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.006 0.001 HIS D 190 PHE 0.018 0.001 PHE A 255 TYR 0.017 0.001 TYR E 52 ARG 0.014 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 450 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8159 (t0) cc_final: 0.7474 (t0) REVERT: A 62 VAL cc_start: 0.8962 (t) cc_final: 0.8756 (m) REVERT: A 76 ASP cc_start: 0.8262 (m-30) cc_final: 0.7427 (m-30) REVERT: A 113 GLU cc_start: 0.7397 (mp0) cc_final: 0.6930 (mp0) REVERT: A 123 ARG cc_start: 0.7508 (tpp-160) cc_final: 0.7306 (tpp80) REVERT: A 124 LYS cc_start: 0.8187 (mttt) cc_final: 0.7796 (ttmm) REVERT: A 254 GLU cc_start: 0.8088 (tt0) cc_final: 0.7367 (mm-30) REVERT: A 255 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7949 (p90) REVERT: A 280 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8250 (ptpp) REVERT: A 284 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6827 (mm-30) REVERT: A 302 MET cc_start: 0.8136 (mtp) cc_final: 0.7882 (mtm) REVERT: A 306 ASP cc_start: 0.7943 (t0) cc_final: 0.7388 (t0) REVERT: A 322 ASP cc_start: 0.7947 (t0) cc_final: 0.7579 (t0) REVERT: A 358 GLN cc_start: 0.8896 (tp40) cc_final: 0.8611 (mm-40) REVERT: A 399 TYR cc_start: 0.8704 (t80) cc_final: 0.8187 (t80) REVERT: A 414 GLU cc_start: 0.8302 (mp0) cc_final: 0.7700 (mp0) REVERT: A 415 GLU cc_start: 0.8057 (tt0) cc_final: 0.7519 (tm-30) REVERT: A 420 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7494 (mt-10) REVERT: A 423 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 433 GLU cc_start: 0.8311 (tp30) cc_final: 0.7850 (tp30) REVERT: B 45 GLU cc_start: 0.8121 (pt0) cc_final: 0.7747 (pt0) REVERT: B 48 ASN cc_start: 0.8418 (p0) cc_final: 0.8051 (p0) REVERT: B 53 GLU cc_start: 0.8195 (tt0) cc_final: 0.7673 (tp30) REVERT: B 57 ASN cc_start: 0.8105 (m-40) cc_final: 0.7856 (m-40) REVERT: B 58 LYS cc_start: 0.7635 (tttt) cc_final: 0.7084 (pttt) REVERT: B 88 ASP cc_start: 0.8658 (t0) cc_final: 0.8329 (t0) REVERT: B 122 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7802 (ttpt) REVERT: B 157 GLU cc_start: 0.8399 (tp30) cc_final: 0.7849 (tm-30) REVERT: B 179 VAL cc_start: 0.8496 (m) cc_final: 0.8274 (t) REVERT: B 197 ASP cc_start: 0.8498 (m-30) cc_final: 0.8241 (m-30) REVERT: B 201 CYS cc_start: 0.8676 (m) cc_final: 0.8380 (m) REVERT: B 205 GLU cc_start: 0.7895 (tt0) cc_final: 0.7320 (mt-10) REVERT: B 267 MET cc_start: 0.8562 (mtp) cc_final: 0.8299 (mtm) REVERT: B 327 ASP cc_start: 0.7574 (m-30) cc_final: 0.7369 (m-30) REVERT: B 332 ASN cc_start: 0.7351 (t0) cc_final: 0.7151 (t0) REVERT: B 340 TYR cc_start: 0.7974 (m-10) cc_final: 0.7641 (m-80) REVERT: B 350 LYS cc_start: 0.8635 (tptt) cc_final: 0.8259 (tptm) REVERT: B 363 MET cc_start: 0.8596 (mtm) cc_final: 0.8305 (mtp) REVERT: B 383 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7848 (tt0) REVERT: B 391 ARG cc_start: 0.8294 (mmm160) cc_final: 0.6445 (mtm180) REVERT: B 404 ASP cc_start: 0.7888 (m-30) cc_final: 0.6801 (m-30) REVERT: B 407 GLU cc_start: 0.7498 (mp0) cc_final: 0.6488 (mp0) REVERT: B 410 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7103 (mm-30) REVERT: B 414 ASN cc_start: 0.8045 (t0) cc_final: 0.7748 (m110) REVERT: B 421 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: C 2 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7630 (mtm180) REVERT: C 47 ASP cc_start: 0.8010 (p0) cc_final: 0.7264 (t0) REVERT: C 50 ASN cc_start: 0.8399 (t0) cc_final: 0.7442 (t0) REVERT: C 77 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 90 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7581 (tm-30) REVERT: C 120 ASP cc_start: 0.7758 (m-30) cc_final: 0.7556 (m-30) REVERT: C 121 ARG cc_start: 0.6770 (tpp80) cc_final: 0.5659 (tpp80) REVERT: C 123 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7307 (tpp80) REVERT: C 158 SER cc_start: 0.8749 (t) cc_final: 0.8476 (t) REVERT: C 196 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8219 (mt-10) REVERT: C 203 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8250 (mmm) REVERT: C 207 GLU cc_start: 0.7245 (tt0) cc_final: 0.6791 (mt-10) REVERT: C 218 ASP cc_start: 0.8191 (m-30) cc_final: 0.7593 (t0) REVERT: C 221 ARG cc_start: 0.8204 (pmm-80) cc_final: 0.7822 (pmm-80) REVERT: C 254 GLU cc_start: 0.7995 (tt0) cc_final: 0.7691 (tp30) REVERT: C 265 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7803 (mp) REVERT: C 280 LYS cc_start: 0.8687 (mttp) cc_final: 0.7333 (mmtt) REVERT: C 284 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7443 (mm-30) REVERT: C 285 GLN cc_start: 0.8610 (mt0) cc_final: 0.8234 (mm110) REVERT: C 290 GLU cc_start: 0.7817 (mp0) cc_final: 0.7330 (mp0) REVERT: C 308 ARG cc_start: 0.8237 (mtm180) cc_final: 0.6955 (tmt-80) REVERT: C 322 ASP cc_start: 0.8366 (t0) cc_final: 0.7946 (t0) REVERT: C 377 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7741 (tmm) REVERT: C 392 ASP cc_start: 0.7589 (m-30) cc_final: 0.7253 (m-30) REVERT: C 415 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8103 (mm-30) REVERT: C 417 GLU cc_start: 0.7459 (mp0) cc_final: 0.6839 (mp0) REVERT: C 420 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7190 (mm-30) REVERT: C 434 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7688 (pp20) REVERT: D 1 MET cc_start: 0.7478 (tpp) cc_final: 0.7251 (mmm) REVERT: D 19 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7697 (mmmt) REVERT: D 22 GLU cc_start: 0.8197 (tp30) cc_final: 0.7815 (mm-30) REVERT: D 45 GLU cc_start: 0.8394 (tt0) cc_final: 0.7768 (tm-30) REVERT: D 57 ASN cc_start: 0.8558 (m-40) cc_final: 0.8316 (m-40) REVERT: D 88 ASP cc_start: 0.8407 (t70) cc_final: 0.8119 (t70) REVERT: D 103 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8170 (mtpm) REVERT: D 118 ASP cc_start: 0.7784 (m-30) cc_final: 0.7537 (p0) REVERT: D 121 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7684 (ptp-110) REVERT: D 122 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8285 (ttmm) REVERT: D 126 SER cc_start: 0.8026 (t) cc_final: 0.7782 (p) REVERT: D 128 ASP cc_start: 0.8633 (t0) cc_final: 0.8313 (t0) REVERT: D 157 GLU cc_start: 0.8289 (tt0) cc_final: 0.7744 (tm-30) REVERT: D 201 CYS cc_start: 0.8878 (m) cc_final: 0.8560 (m) REVERT: D 203 ASP cc_start: 0.8321 (t0) cc_final: 0.7636 (t70) REVERT: D 213 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.8233 (ttp-110) REVERT: D 216 LYS cc_start: 0.8890 (mmtm) cc_final: 0.8388 (mmmm) REVERT: D 300 MET cc_start: 0.8809 (mtm) cc_final: 0.8493 (mtm) REVERT: D 304 ASP cc_start: 0.7886 (t70) cc_final: 0.6909 (t0) REVERT: D 306 ARG cc_start: 0.8218 (mtm180) cc_final: 0.7662 (mtm180) REVERT: D 309 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7895 (mtp85) REVERT: D 325 GLU cc_start: 0.8413 (tp30) cc_final: 0.7733 (tp30) REVERT: D 332 ASN cc_start: 0.8285 (t0) cc_final: 0.8041 (m-40) REVERT: D 391 ARG cc_start: 0.8569 (mmm160) cc_final: 0.7040 (mtm180) REVERT: D 401 GLU cc_start: 0.7912 (mp0) cc_final: 0.7417 (mm-30) REVERT: D 404 ASP cc_start: 0.8035 (m-30) cc_final: 0.7511 (t70) REVERT: D 407 GLU cc_start: 0.7761 (mp0) cc_final: 0.7076 (mp0) REVERT: D 410 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7145 (mm-30) REVERT: D 414 ASN cc_start: 0.7971 (t0) cc_final: 0.7484 (m-40) REVERT: D 424 GLN cc_start: 0.8282 (pt0) cc_final: 0.7937 (pp30) REVERT: D 425 TYR cc_start: 0.7509 (m-80) cc_final: 0.7182 (m-80) REVERT: E 15 ASP cc_start: 0.8497 (t0) cc_final: 0.7977 (t0) REVERT: E 61 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: E 67 PHE cc_start: 0.8097 (m-10) cc_final: 0.7428 (m-10) REVERT: E 72 ARG cc_start: 0.7779 (ptt-90) cc_final: 0.7461 (ptt180) REVERT: E 94 ASN cc_start: 0.8015 (t0) cc_final: 0.7320 (t0) REVERT: E 120 GLU cc_start: 0.7255 (tt0) cc_final: 0.6861 (tt0) REVERT: E 129 GLU cc_start: 0.8018 (pm20) cc_final: 0.7720 (pm20) REVERT: E 136 VAL cc_start: 0.8266 (t) cc_final: 0.7945 (p) REVERT: E 156 CYS cc_start: 0.8623 (t) cc_final: 0.8199 (t) REVERT: E 206 ASP cc_start: 0.8534 (p0) cc_final: 0.7984 (p0) REVERT: E 213 CYS cc_start: 0.7101 (m) cc_final: 0.6458 (m) REVERT: E 244 ILE cc_start: 0.8111 (mp) cc_final: 0.7689 (tt) REVERT: E 246 PHE cc_start: 0.8238 (t80) cc_final: 0.7902 (t80) REVERT: E 305 ASP cc_start: 0.7462 (t70) cc_final: 0.7044 (t0) REVERT: E 307 ARG cc_start: 0.7807 (mmm160) cc_final: 0.6610 (mmm160) REVERT: E 314 GLN cc_start: 0.6872 (mp10) cc_final: 0.6183 (mp10) REVERT: E 327 TYR cc_start: 0.8196 (t80) cc_final: 0.7524 (t80) REVERT: E 341 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.6975 (mtm110) REVERT: E 483 ASN cc_start: 0.7390 (t0) cc_final: 0.6636 (t0) REVERT: E 550 TYR cc_start: 0.8286 (m-10) cc_final: 0.7985 (m-10) REVERT: E 556 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7006 (mm-30) REVERT: E 584 SER cc_start: 0.7164 (m) cc_final: 0.6646 (t) outliers start: 48 outliers final: 22 residues processed: 471 average time/residue: 1.4740 time to fit residues: 763.6240 Evaluate side-chains 466 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 436 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 190 HIS B 307 HIS B 335 ASN B 416 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN D 334 GLN E 98 GLN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17849 Z= 0.233 Angle : 0.620 11.652 24276 Z= 0.312 Chirality : 0.045 0.300 2651 Planarity : 0.005 0.056 3170 Dihedral : 10.901 179.638 2517 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 2.34 % Allowed : 20.85 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2205 helix: 1.37 (0.17), residues: 912 sheet: 0.26 (0.29), residues: 339 loop : -0.55 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.020 0.001 HIS B 307 PHE 0.023 0.001 PHE A 49 TYR 0.020 0.001 TYR E 335 ARG 0.013 0.001 ARG E 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 431 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8152 (t0) cc_final: 0.7473 (t0) REVERT: A 55 GLU cc_start: 0.7804 (tt0) cc_final: 0.7427 (tp30) REVERT: A 62 VAL cc_start: 0.8959 (t) cc_final: 0.8748 (m) REVERT: A 76 ASP cc_start: 0.8276 (m-30) cc_final: 0.7449 (m-30) REVERT: A 113 GLU cc_start: 0.7391 (mp0) cc_final: 0.6909 (mp0) REVERT: A 123 ARG cc_start: 0.7500 (tpp-160) cc_final: 0.7291 (tpp80) REVERT: A 124 LYS cc_start: 0.8164 (mttt) cc_final: 0.7804 (ttmm) REVERT: A 212 ILE cc_start: 0.7306 (tt) cc_final: 0.7058 (pt) REVERT: A 254 GLU cc_start: 0.8106 (tt0) cc_final: 0.7387 (mm-30) REVERT: A 255 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8000 (p90) REVERT: A 280 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8149 (ptpp) REVERT: A 284 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 302 MET cc_start: 0.8129 (mtp) cc_final: 0.7862 (mtm) REVERT: A 306 ASP cc_start: 0.7946 (t0) cc_final: 0.7371 (t0) REVERT: A 322 ASP cc_start: 0.7945 (t0) cc_final: 0.7567 (t0) REVERT: A 399 TYR cc_start: 0.8719 (t80) cc_final: 0.8235 (t80) REVERT: A 414 GLU cc_start: 0.8313 (mp0) cc_final: 0.7197 (mp0) REVERT: A 415 GLU cc_start: 0.8063 (tt0) cc_final: 0.7566 (tm-30) REVERT: A 417 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6932 (mp0) REVERT: A 420 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7486 (mt-10) REVERT: A 423 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 433 GLU cc_start: 0.8289 (tp30) cc_final: 0.7811 (tp30) REVERT: B 22 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7988 (mm-30) REVERT: B 41 ASP cc_start: 0.8137 (m-30) cc_final: 0.7866 (m-30) REVERT: B 45 GLU cc_start: 0.8132 (pt0) cc_final: 0.7751 (pt0) REVERT: B 48 ASN cc_start: 0.8466 (p0) cc_final: 0.8092 (p0) REVERT: B 53 GLU cc_start: 0.8220 (tt0) cc_final: 0.7844 (tp30) REVERT: B 57 ASN cc_start: 0.8128 (m-40) cc_final: 0.7835 (m-40) REVERT: B 58 LYS cc_start: 0.7600 (tttt) cc_final: 0.7179 (pttt) REVERT: B 88 ASP cc_start: 0.8659 (t0) cc_final: 0.8393 (t70) REVERT: B 157 GLU cc_start: 0.8401 (tp30) cc_final: 0.7850 (tm-30) REVERT: B 205 GLU cc_start: 0.7901 (tt0) cc_final: 0.7325 (mt-10) REVERT: B 267 MET cc_start: 0.8561 (mtp) cc_final: 0.8304 (mtm) REVERT: B 306 ARG cc_start: 0.8597 (mpt-90) cc_final: 0.7934 (mtm-85) REVERT: B 340 TYR cc_start: 0.7960 (m-10) cc_final: 0.7535 (m-80) REVERT: B 350 LYS cc_start: 0.8625 (tptt) cc_final: 0.8278 (tptm) REVERT: B 363 MET cc_start: 0.8620 (mtm) cc_final: 0.8245 (mtp) REVERT: B 383 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7838 (tt0) REVERT: B 391 ARG cc_start: 0.8347 (mmm160) cc_final: 0.6178 (ptp-170) REVERT: B 404 ASP cc_start: 0.7913 (m-30) cc_final: 0.6847 (m-30) REVERT: B 407 GLU cc_start: 0.7495 (mp0) cc_final: 0.6464 (mp0) REVERT: B 410 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7134 (mm-30) REVERT: B 414 ASN cc_start: 0.8075 (t0) cc_final: 0.7757 (m110) REVERT: B 421 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: C 2 ARG cc_start: 0.8273 (mtm180) cc_final: 0.7998 (mtm180) REVERT: C 47 ASP cc_start: 0.8019 (p0) cc_final: 0.7298 (t0) REVERT: C 50 ASN cc_start: 0.8399 (t0) cc_final: 0.7438 (t0) REVERT: C 77 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7982 (mt-10) REVERT: C 90 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7573 (tm-30) REVERT: C 121 ARG cc_start: 0.6774 (tpp80) cc_final: 0.5695 (tpp80) REVERT: C 123 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7294 (tpp80) REVERT: C 158 SER cc_start: 0.8744 (t) cc_final: 0.8466 (t) REVERT: C 207 GLU cc_start: 0.7266 (tt0) cc_final: 0.6916 (mt-10) REVERT: C 218 ASP cc_start: 0.8204 (m-30) cc_final: 0.7574 (t0) REVERT: C 221 ARG cc_start: 0.8200 (pmm-80) cc_final: 0.7806 (pmm-80) REVERT: C 254 GLU cc_start: 0.8006 (tt0) cc_final: 0.7693 (tp30) REVERT: C 265 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7751 (mp) REVERT: C 280 LYS cc_start: 0.8671 (mttp) cc_final: 0.7333 (mmtt) REVERT: C 284 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7453 (mm-30) REVERT: C 285 GLN cc_start: 0.8623 (mt0) cc_final: 0.8254 (mm110) REVERT: C 290 GLU cc_start: 0.7831 (mp0) cc_final: 0.7619 (mp0) REVERT: C 308 ARG cc_start: 0.8252 (mtm180) cc_final: 0.6924 (tmt-80) REVERT: C 322 ASP cc_start: 0.8377 (t0) cc_final: 0.8052 (t0) REVERT: C 377 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7767 (tmm) REVERT: C 392 ASP cc_start: 0.7587 (m-30) cc_final: 0.7245 (m-30) REVERT: C 415 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8136 (mm-30) REVERT: C 417 GLU cc_start: 0.7504 (mp0) cc_final: 0.6898 (mp0) REVERT: C 420 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7197 (mm-30) REVERT: D 19 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7716 (mmmt) REVERT: D 22 GLU cc_start: 0.8231 (tp30) cc_final: 0.7826 (mm-30) REVERT: D 45 GLU cc_start: 0.8407 (tt0) cc_final: 0.7770 (tm-30) REVERT: D 53 GLU cc_start: 0.7699 (tp30) cc_final: 0.7443 (tm-30) REVERT: D 57 ASN cc_start: 0.8575 (m-40) cc_final: 0.8350 (m-40) REVERT: D 88 ASP cc_start: 0.8419 (t70) cc_final: 0.8134 (t70) REVERT: D 103 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8296 (mtpm) REVERT: D 118 ASP cc_start: 0.7785 (m-30) cc_final: 0.7549 (p0) REVERT: D 121 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7740 (ptp-110) REVERT: D 122 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8295 (ttmm) REVERT: D 126 SER cc_start: 0.8034 (t) cc_final: 0.7796 (p) REVERT: D 128 ASP cc_start: 0.8643 (t0) cc_final: 0.8175 (t0) REVERT: D 157 GLU cc_start: 0.8317 (tt0) cc_final: 0.7894 (tm-30) REVERT: D 201 CYS cc_start: 0.8877 (m) cc_final: 0.8544 (m) REVERT: D 203 ASP cc_start: 0.8348 (t0) cc_final: 0.7654 (t70) REVERT: D 213 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.8192 (ttp-110) REVERT: D 216 LYS cc_start: 0.8885 (mmtm) cc_final: 0.8566 (mmmm) REVERT: D 300 MET cc_start: 0.8802 (mtm) cc_final: 0.8474 (mtm) REVERT: D 304 ASP cc_start: 0.7908 (t70) cc_final: 0.6922 (t0) REVERT: D 306 ARG cc_start: 0.8230 (mtm180) cc_final: 0.7684 (mtm180) REVERT: D 309 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7858 (mtp85) REVERT: D 325 GLU cc_start: 0.8345 (tp30) cc_final: 0.7777 (tp30) REVERT: D 332 ASN cc_start: 0.8295 (t0) cc_final: 0.8056 (m-40) REVERT: D 404 ASP cc_start: 0.8051 (m-30) cc_final: 0.7648 (p0) REVERT: D 407 GLU cc_start: 0.7769 (mp0) cc_final: 0.6924 (mm-30) REVERT: D 410 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7172 (mm-30) REVERT: D 414 ASN cc_start: 0.7952 (t0) cc_final: 0.7508 (m-40) REVERT: D 424 GLN cc_start: 0.8272 (pt0) cc_final: 0.8016 (pp30) REVERT: D 425 TYR cc_start: 0.7533 (m-80) cc_final: 0.7235 (m-80) REVERT: E 15 ASP cc_start: 0.8486 (t0) cc_final: 0.7952 (t0) REVERT: E 61 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: E 72 ARG cc_start: 0.7815 (ptt-90) cc_final: 0.7042 (ptt-90) REVERT: E 94 ASN cc_start: 0.7973 (t0) cc_final: 0.7448 (t0) REVERT: E 120 GLU cc_start: 0.7284 (tt0) cc_final: 0.6856 (tt0) REVERT: E 129 GLU cc_start: 0.8011 (pm20) cc_final: 0.7712 (pm20) REVERT: E 136 VAL cc_start: 0.8215 (t) cc_final: 0.7891 (p) REVERT: E 156 CYS cc_start: 0.8638 (t) cc_final: 0.8237 (t) REVERT: E 206 ASP cc_start: 0.8528 (p0) cc_final: 0.8031 (p0) REVERT: E 213 CYS cc_start: 0.7183 (m) cc_final: 0.6476 (m) REVERT: E 244 ILE cc_start: 0.8119 (mp) cc_final: 0.7674 (tt) REVERT: E 246 PHE cc_start: 0.8234 (t80) cc_final: 0.7939 (t80) REVERT: E 307 ARG cc_start: 0.7804 (mmm160) cc_final: 0.7584 (tpp80) REVERT: E 314 GLN cc_start: 0.6952 (mp10) cc_final: 0.6271 (mp10) REVERT: E 475 GLN cc_start: 0.8117 (mp10) cc_final: 0.7876 (mp10) REVERT: E 483 ASN cc_start: 0.7486 (t0) cc_final: 0.6752 (t0) REVERT: E 550 TYR cc_start: 0.8345 (m-10) cc_final: 0.8028 (m-10) REVERT: E 556 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7064 (mm-30) REVERT: E 584 SER cc_start: 0.7191 (m) cc_final: 0.6674 (t) outliers start: 43 outliers final: 25 residues processed: 451 average time/residue: 1.5006 time to fit residues: 743.8752 Evaluate side-chains 473 residues out of total 1911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 442 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS B 307 HIS B 335 ASN B 416 ASN B 423 GLN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN E 165 GLN E 339 HIS ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.095842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.086963 restraints weight = 29913.391| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.98 r_work: 0.3158 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17849 Z= 0.220 Angle : 0.617 11.748 24276 Z= 0.312 Chirality : 0.044 0.292 2651 Planarity : 0.005 0.057 3170 Dihedral : 10.763 176.969 2517 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 2.12 % Allowed : 21.23 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.56 (0.18), residues: 2205 helix: 1.42 (0.17), residues: 906 sheet: 0.27 (0.29), residues: 339 loop : -0.56 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 21 HIS 0.011 0.001 HIS B 307 PHE 0.023 0.001 PHE A 49 TYR 0.024 0.001 TYR A 161 ARG 0.012 0.001 ARG E 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10722.47 seconds wall clock time: 186 minutes 8.68 seconds (11168.68 seconds total)