Starting phenix.real_space_refine on Thu Jan 18 07:24:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t11_25587/01_2024/7t11_25587_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t11_25587/01_2024/7t11_25587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t11_25587/01_2024/7t11_25587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t11_25587/01_2024/7t11_25587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t11_25587/01_2024/7t11_25587_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t11_25587/01_2024/7t11_25587_neut_updated.pdb" } resolution = 2.7 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= -0.000 sd= 0.097 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5245 2.51 5 N 1383 2.21 5 O 1465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8151 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1563 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 15, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2490 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 362 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "S" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1642 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 71 Unusual residues: {'THO': 1} Classifications: {'peptide': 7, 'undetermined': 1} Modifications used: {'PEPT-D': 2} Link IDs: {'TRANS': 7} Chain: "R" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2023 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 11, 'TRANS': 273} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 5.08, per 1000 atoms: 0.62 Number of scatterers: 8151 At special positions: 0 Unit cell: (99.6957, 121.85, 113.329, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1465 8.00 N 1383 7.00 C 5245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 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: 3.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN P 1 " pdb=" CB DTR P 4 " Number of C-beta restraints generated: 2116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 33.9% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.513A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.054A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.886A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.922A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.809A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.593A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 42 removed outlier: 4.161A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing helix chain 'R' and resid 44 through 70 removed outlier: 3.600A pdb=" N ILE R 49 " --> pdb=" O VAL R 45 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE R 51 " --> pdb=" O THR R 47 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS R 54 " --> pdb=" O TYR R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 104 removed outlier: 4.002A pdb=" N GLY R 95 " --> pdb=" O LEU R 91 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU R 96 " --> pdb=" O PHE R 92 " (cutoff:3.500A) Proline residue: R 97 - end of helix removed outlier: 3.537A pdb=" N MET R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 145 removed outlier: 3.541A pdb=" N THR R 120 " --> pdb=" O ARG R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 153 No H-bonds generated for 'chain 'R' and resid 151 through 153' Processing helix chain 'R' and resid 156 through 173 removed outlier: 3.553A pdb=" N MET R 164 " --> pdb=" O LYS R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 179 Processing helix chain 'R' and resid 202 through 214 Processing helix chain 'R' and resid 218 through 237 removed outlier: 3.903A pdb=" N SER R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 280 removed outlier: 4.014A pdb=" N LYS R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL R 254 " --> pdb=" O ASN R 250 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE R 266 " --> pdb=" O VAL R 262 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 288 through 303 removed outlier: 3.939A pdb=" N VAL R 299 " --> pdb=" O ASP R 295 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU R 300 " --> pdb=" O PHE R 296 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 312 Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.755A pdb=" N GLN R 324 " --> pdb=" O LYS R 320 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN R 325 " --> pdb=" O LYS R 321 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL R 326 " --> pdb=" O SER R 322 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.922A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.053A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.046A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.723A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.992A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.627A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.553A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.628A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.541A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.538A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER S 194 " --> pdb=" O THR S 201 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.714A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 182 through 185 369 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 3.33 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: 1297 1.31 - 1.44: 2328 1.44 - 1.56: 4621 1.56 - 1.69: 0 1.69 - 1.82: 81 Bond restraints: 8327 Sorted by residual: bond pdb=" C THO P 8 " pdb=" O THO P 8 " ideal model delta sigma weight residual 1.231 1.410 -0.179 2.00e-02 2.50e+03 8.00e+01 bond pdb=" C ILE S 177 " pdb=" O ILE S 177 " ideal model delta sigma weight residual 1.236 1.195 0.041 9.90e-03 1.02e+04 1.74e+01 bond pdb=" CA ASN S 182 " pdb=" C ASN S 182 " ideal model delta sigma weight residual 1.525 1.464 0.061 2.10e-02 2.27e+03 8.45e+00 bond pdb=" C TYR S 178 " pdb=" O TYR S 178 " ideal model delta sigma weight residual 1.234 1.199 0.035 1.26e-02 6.30e+03 7.88e+00 bond pdb=" C LEU S 183 " pdb=" O LEU S 183 " ideal model delta sigma weight residual 1.234 1.201 0.033 1.22e-02 6.72e+03 7.48e+00 ... (remaining 8322 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 195 107.15 - 113.87: 4668 113.87 - 120.59: 3243 120.59 - 127.31: 3188 127.31 - 134.02: 82 Bond angle restraints: 11376 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.70 131.65 -9.95 1.80e+00 3.09e-01 3.05e+01 angle pdb=" CA THO P 8 " pdb=" C THO P 8 " pdb=" O THO P 8 " ideal model delta sigma weight residual 120.80 112.17 8.63 1.70e+00 3.46e-01 2.58e+01 angle pdb=" CA ILE S 177 " pdb=" C ILE S 177 " pdb=" N TYR S 178 " ideal model delta sigma weight residual 116.18 120.44 -4.26 1.24e+00 6.50e-01 1.18e+01 angle pdb=" N GLN R 187 " pdb=" CA GLN R 187 " pdb=" C GLN R 187 " ideal model delta sigma weight residual 110.35 105.62 4.73 1.38e+00 5.25e-01 1.17e+01 angle pdb=" N ARG R 190 " pdb=" CA ARG R 190 " pdb=" C ARG R 190 " ideal model delta sigma weight residual 108.38 112.70 -4.32 1.35e+00 5.49e-01 1.02e+01 ... (remaining 11371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4580 17.38 - 34.75: 188 34.75 - 52.13: 36 52.13 - 69.51: 4 69.51 - 86.89: 4 Dihedral angle restraints: 4812 sinusoidal: 1531 harmonic: 3281 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" N MET S 180 " pdb=" C MET S 180 " pdb=" CA MET S 180 " pdb=" CB MET S 180 " ideal model delta harmonic sigma weight residual 122.80 131.98 -9.18 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1254 0.082 - 0.164: 96 0.164 - 0.245: 1 0.245 - 0.327: 1 0.327 - 0.409: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA MET S 180 " pdb=" N MET S 180 " pdb=" C MET S 180 " pdb=" CB MET S 180 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ARG S 179 " pdb=" N ARG S 179 " pdb=" C ARG S 179 " pdb=" CB ARG S 179 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1350 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO S 75 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 175 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO R 176 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 176 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 176 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 236 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 75 2.67 - 3.22: 7166 3.22 - 3.78: 11460 3.78 - 4.34: 15460 4.34 - 4.90: 27151 Nonbonded interactions: 61312 Sorted by model distance: nonbonded pdb=" O LEU S 176 " pdb=" CD1 ILE S 177 " model vdw 2.107 3.460 nonbonded pdb=" ND2 ASN R 186 " pdb=" O ARG R 190 " model vdw 2.199 2.520 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.288 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.346 2.440 nonbonded pdb=" O ARG S 38 " pdb=" N GLU S 46 " model vdw 2.361 2.520 ... (remaining 61307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.370 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.760 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 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 : 0.004 0.179 8327 Z= 0.235 Angle : 0.610 9.947 11376 Z= 0.364 Chirality : 0.043 0.409 1353 Planarity : 0.004 0.082 1438 Dihedral : 10.763 86.887 2687 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.27 % Allowed : 0.13 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.96 (0.25), residues: 1107 helix: 2.20 (0.28), residues: 378 sheet: 0.87 (0.30), residues: 286 loop : -0.92 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 188 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE B 234 TYR 0.013 0.001 TYR S 178 ARG 0.002 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.842 Fit side-chains REVERT: B 101 MET cc_start: 0.7918 (mtt) cc_final: 0.7706 (mtt) REVERT: S 128 MET cc_start: 0.5487 (mmt) cc_final: 0.5152 (mmp) REVERT: R 135 VAL cc_start: 0.7954 (p) cc_final: 0.7685 (m) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 1.0448 time to fit residues: 128.9424 Evaluate side-chains 84 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8327 Z= 0.231 Angle : 0.592 7.317 11376 Z= 0.320 Chirality : 0.043 0.159 1353 Planarity : 0.005 0.065 1438 Dihedral : 4.474 37.237 1204 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.54 % Allowed : 8.41 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.03 (0.25), residues: 1107 helix: 2.48 (0.27), residues: 381 sheet: 0.79 (0.32), residues: 268 loop : -0.98 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 36 HIS 0.007 0.002 HIS S 35 PHE 0.018 0.002 PHE B 151 TYR 0.021 0.002 TYR B 59 ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.952 Fit side-chains REVERT: A 268 LEU cc_start: 0.7437 (mt) cc_final: 0.7187 (mt) REVERT: A 307 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.5517 (t80) REVERT: B 43 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.5389 (mm) REVERT: B 101 MET cc_start: 0.7891 (mtt) cc_final: 0.7617 (mtt) REVERT: B 195 ASP cc_start: 0.5514 (OUTLIER) cc_final: 0.4935 (p0) REVERT: R 63 LEU cc_start: 0.6050 (tt) cc_final: 0.5716 (tp) REVERT: R 278 SER cc_start: 0.7727 (p) cc_final: 0.7460 (p) outliers start: 19 outliers final: 5 residues processed: 93 average time/residue: 1.0530 time to fit residues: 105.4902 Evaluate side-chains 88 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 214 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 107 optimal weight: 0.0670 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN R 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8327 Z= 0.117 Angle : 0.450 6.420 11376 Z= 0.244 Chirality : 0.039 0.144 1353 Planarity : 0.004 0.053 1438 Dihedral : 3.949 36.140 1204 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.27 % Allowed : 9.75 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.45 (0.25), residues: 1107 helix: 2.84 (0.27), residues: 380 sheet: 1.09 (0.32), residues: 272 loop : -0.80 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 151 TYR 0.008 0.001 TYR B 59 ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.862 Fit side-chains REVERT: A 307 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.5569 (t80) REVERT: B 101 MET cc_start: 0.7727 (mtt) cc_final: 0.7486 (mtt) REVERT: B 195 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.4949 (p0) REVERT: R 63 LEU cc_start: 0.6190 (tt) cc_final: 0.5926 (tp) REVERT: R 278 SER cc_start: 0.7491 (p) cc_final: 0.7288 (p) outliers start: 17 outliers final: 7 residues processed: 94 average time/residue: 1.0454 time to fit residues: 105.8811 Evaluate side-chains 93 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN R 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8327 Z= 0.206 Angle : 0.553 6.915 11376 Z= 0.299 Chirality : 0.042 0.153 1353 Planarity : 0.004 0.052 1438 Dihedral : 4.347 36.175 1204 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.67 % Allowed : 11.48 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.25 (0.25), residues: 1107 helix: 2.75 (0.27), residues: 379 sheet: 1.17 (0.32), residues: 247 loop : -1.01 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 63 HIS 0.005 0.002 HIS B 183 PHE 0.016 0.002 PHE A 196 TYR 0.016 0.002 TYR B 59 ARG 0.002 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.976 Fit side-chains REVERT: A 307 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.5829 (t80) REVERT: A 308 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7757 (mt-10) REVERT: B 43 ILE cc_start: 0.5903 (OUTLIER) cc_final: 0.5617 (mm) REVERT: B 101 MET cc_start: 0.7873 (mtt) cc_final: 0.7589 (mtt) REVERT: B 134 ARG cc_start: 0.7721 (ptp90) cc_final: 0.7354 (ppt170) REVERT: B 195 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5033 (p0) REVERT: R 55 ILE cc_start: 0.6166 (pt) cc_final: 0.5943 (pp) REVERT: R 63 LEU cc_start: 0.6183 (tt) cc_final: 0.5933 (tp) REVERT: R 278 SER cc_start: 0.7573 (p) cc_final: 0.7342 (p) outliers start: 20 outliers final: 9 residues processed: 93 average time/residue: 1.0285 time to fit residues: 102.9540 Evaluate side-chains 92 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8327 Z= 0.180 Angle : 0.519 6.475 11376 Z= 0.280 Chirality : 0.041 0.149 1353 Planarity : 0.004 0.052 1438 Dihedral : 4.252 35.998 1204 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.40 % Allowed : 12.95 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.19 (0.25), residues: 1107 helix: 2.72 (0.27), residues: 380 sheet: 0.97 (0.31), residues: 264 loop : -1.04 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 36 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.002 PHE B 151 TYR 0.013 0.001 TYR B 59 ARG 0.004 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.928 Fit side-chains REVERT: A 307 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.5920 (t80) REVERT: A 308 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7614 (mt-10) REVERT: B 101 MET cc_start: 0.7818 (mtt) cc_final: 0.7546 (mtt) REVERT: B 134 ARG cc_start: 0.7724 (ptp90) cc_final: 0.7363 (ppt170) REVERT: B 195 ASP cc_start: 0.5626 (OUTLIER) cc_final: 0.5061 (p0) REVERT: S 46 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: R 63 LEU cc_start: 0.6147 (tt) cc_final: 0.5931 (tp) REVERT: R 278 SER cc_start: 0.7346 (p) cc_final: 0.6990 (p) outliers start: 18 outliers final: 7 residues processed: 89 average time/residue: 1.1374 time to fit residues: 109.4535 Evaluate side-chains 90 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 192 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.0060 chunk 105 optimal weight: 0.0980 chunk 87 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN R 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8327 Z= 0.108 Angle : 0.434 6.155 11376 Z= 0.235 Chirality : 0.039 0.140 1353 Planarity : 0.003 0.049 1438 Dihedral : 3.782 32.860 1204 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.14 % Allowed : 13.75 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.48 (0.25), residues: 1107 helix: 2.95 (0.27), residues: 379 sheet: 1.09 (0.31), residues: 278 loop : -0.88 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE R 98 TYR 0.007 0.001 TYR B 59 ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.931 Fit side-chains REVERT: A 307 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.5778 (t80) REVERT: A 308 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: B 101 MET cc_start: 0.7768 (mtt) cc_final: 0.7503 (mtt) REVERT: B 134 ARG cc_start: 0.7670 (ptp90) cc_final: 0.7326 (ppt170) REVERT: B 195 ASP cc_start: 0.5560 (OUTLIER) cc_final: 0.4955 (p0) REVERT: R 55 ILE cc_start: 0.6534 (pp) cc_final: 0.6088 (mm) REVERT: R 84 ASN cc_start: 0.7702 (m-40) cc_final: 0.7475 (m-40) REVERT: R 278 SER cc_start: 0.7070 (p) cc_final: 0.6766 (p) outliers start: 16 outliers final: 6 residues processed: 92 average time/residue: 0.9981 time to fit residues: 99.2279 Evaluate side-chains 92 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 0.0070 chunk 77 optimal weight: 0.2980 chunk 59 optimal weight: 0.3980 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 0.0770 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS R 102 GLN R 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8327 Z= 0.101 Angle : 0.415 5.970 11376 Z= 0.224 Chirality : 0.039 0.137 1353 Planarity : 0.003 0.047 1438 Dihedral : 3.529 29.987 1204 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.47 % Allowed : 14.69 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.67 (0.25), residues: 1107 helix: 3.07 (0.27), residues: 379 sheet: 1.14 (0.31), residues: 277 loop : -0.69 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE B 199 TYR 0.006 0.001 TYR R 180 ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.944 Fit side-chains REVERT: A 307 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.5739 (t80) REVERT: A 308 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: B 101 MET cc_start: 0.7775 (mtt) cc_final: 0.7501 (mtt) REVERT: B 134 ARG cc_start: 0.7654 (ptp90) cc_final: 0.7293 (ppt170) REVERT: B 195 ASP cc_start: 0.5565 (OUTLIER) cc_final: 0.4931 (p0) REVERT: R 55 ILE cc_start: 0.6516 (pp) cc_final: 0.6097 (mm) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 1.1030 time to fit residues: 106.6589 Evaluate side-chains 92 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN R 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8327 Z= 0.178 Angle : 0.504 6.347 11376 Z= 0.272 Chirality : 0.041 0.148 1353 Planarity : 0.004 0.051 1438 Dihedral : 3.991 31.442 1204 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.87 % Allowed : 14.15 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.46 (0.25), residues: 1107 helix: 2.96 (0.27), residues: 379 sheet: 1.05 (0.31), residues: 263 loop : -0.84 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE R 296 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.938 Fit side-chains REVERT: A 307 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.5961 (t80) REVERT: A 308 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: B 43 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5763 (mm) REVERT: B 101 MET cc_start: 0.7808 (mtt) cc_final: 0.7528 (mtt) REVERT: B 134 ARG cc_start: 0.7739 (ptp90) cc_final: 0.7370 (ppt170) REVERT: B 195 ASP cc_start: 0.5599 (OUTLIER) cc_final: 0.5018 (p0) REVERT: R 55 ILE cc_start: 0.6376 (pp) cc_final: 0.5985 (mm) outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 1.0566 time to fit residues: 98.8927 Evaluate side-chains 92 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 76 optimal weight: 0.0870 chunk 30 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 0.2980 chunk 64 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8327 Z= 0.097 Angle : 0.411 5.739 11376 Z= 0.222 Chirality : 0.039 0.133 1353 Planarity : 0.003 0.047 1438 Dihedral : 3.552 29.604 1204 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.47 % Allowed : 14.69 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.70 (0.25), residues: 1107 helix: 3.11 (0.27), residues: 379 sheet: 1.16 (0.31), residues: 278 loop : -0.70 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.003 0.000 HIS S 35 PHE 0.017 0.001 PHE R 296 TYR 0.007 0.001 TYR S 102 ARG 0.006 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.898 Fit side-chains REVERT: A 307 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.5791 (t80) REVERT: A 308 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: B 101 MET cc_start: 0.7730 (mtt) cc_final: 0.7469 (mtt) REVERT: B 134 ARG cc_start: 0.7659 (ptp90) cc_final: 0.7297 (ppt170) REVERT: B 195 ASP cc_start: 0.5549 (OUTLIER) cc_final: 0.4924 (p0) REVERT: R 55 ILE cc_start: 0.6322 (pp) cc_final: 0.5923 (mm) outliers start: 11 outliers final: 5 residues processed: 86 average time/residue: 1.0284 time to fit residues: 95.2029 Evaluate side-chains 92 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0050 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8327 Z= 0.123 Angle : 0.441 6.026 11376 Z= 0.238 Chirality : 0.039 0.141 1353 Planarity : 0.003 0.048 1438 Dihedral : 3.649 29.297 1204 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.34 % Allowed : 15.09 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.69 (0.25), residues: 1107 helix: 3.12 (0.27), residues: 379 sheet: 1.16 (0.31), residues: 274 loop : -0.71 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 269 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE R 296 TYR 0.007 0.001 TYR B 59 ARG 0.006 0.000 ARG A 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.902 Fit side-chains REVERT: A 307 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.5913 (t80) REVERT: A 308 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: B 101 MET cc_start: 0.7773 (mtt) cc_final: 0.7510 (mtt) REVERT: B 134 ARG cc_start: 0.7691 (ptp90) cc_final: 0.7327 (ppt170) REVERT: B 195 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.4967 (p0) REVERT: R 55 ILE cc_start: 0.6343 (pp) cc_final: 0.5939 (mm) outliers start: 10 outliers final: 5 residues processed: 88 average time/residue: 1.0676 time to fit residues: 100.9762 Evaluate side-chains 92 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 10 optimal weight: 0.0030 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN R 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.210762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.175470 restraints weight = 8736.925| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.17 r_work: 0.3722 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8327 Z= 0.214 Angle : 0.545 6.698 11376 Z= 0.295 Chirality : 0.042 0.152 1353 Planarity : 0.004 0.051 1438 Dihedral : 4.227 31.558 1204 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.20 % Allowed : 15.22 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.38 (0.25), residues: 1107 helix: 2.96 (0.27), residues: 378 sheet: 0.98 (0.31), residues: 268 loop : -0.94 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 269 HIS 0.006 0.002 HIS B 183 PHE 0.021 0.002 PHE R 296 TYR 0.013 0.002 TYR B 59 ARG 0.006 0.000 ARG A 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.14 seconds wall clock time: 54 minutes 17.28 seconds (3257.28 seconds total)