Starting phenix.real_space_refine on Fri Feb 14 18:53:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6met_9109/02_2025/6met_9109.cif Found real_map, /net/cci-nas-00/data/ceres_data/6met_9109/02_2025/6met_9109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6met_9109/02_2025/6met_9109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6met_9109/02_2025/6met_9109.map" model { file = "/net/cci-nas-00/data/ceres_data/6met_9109/02_2025/6met_9109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6met_9109/02_2025/6met_9109.cif" } resolution = 4.5 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1602 atoms to isotropic. 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 53 5.16 5 C 5697 2.51 5 N 1448 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8911 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3103 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2816 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 347} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2562 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.53, per 1000 atoms: 0.62 Number of scatterers: 8911 At special positions: 0 Unit cell: (148.26, 173.676, 111.195, 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 53 16.00 O 1713 8.00 N 1448 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 73 " distance=2.03 Simple disulfide: pdb=" SG CYS G 118 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 125 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 330 " distance=2.03 Simple disulfide: pdb=" SG CYS G 376 " - pdb=" SG CYS G 440 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 413 " distance=2.03 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 178 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG C 1 " - " ASN G 234 " " NAG D 1 " - " ASN G 241 " " NAG E 1 " - " ASN G 262 " " NAG F 1 " - " ASN G 276 " " NAG G 601 " - " ASN G 87 " " NAG G 619 " - " ASN G 338 " " NAG G 620 " - " ASN G 354 " " NAG G 626 " - " ASN G 395 " " NAG G 627 " - " ASN G 459 " " NAG G 628 " - " ASN G 197 " " NAG G 631 " - " ASN G 390 " " NAG H 1 " - " ASN G 295 " " NAG I 1 " - " ASN G 331 " " NAG J 1 " - " ASN G 301 " " NAG K 1 " - " ASN G 384 " " NAG L 1 " - " ASN G 443 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 30.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.713A pdb=" N GLU G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE G 108 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU G 115 " --> pdb=" O TRP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 353 removed outlier: 4.686A pdb=" N ASP G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 340 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 371 removed outlier: 3.623A pdb=" N PHE G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 389 removed outlier: 3.841A pdb=" N PHE G 389 " --> pdb=" O THR G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 477 removed outlier: 3.737A pdb=" N SER G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 removed outlier: 4.208A pdb=" N ASP A 63 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.777A pdb=" N SER A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 32 through 58 removed outlier: 3.599A pdb=" N LEU B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 81 Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.903A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 131 removed outlier: 3.836A pdb=" N GLY B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 removed outlier: 3.621A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.580A pdb=" N ASN B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.509A pdb=" N GLY B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 260 removed outlier: 3.553A pdb=" N HIS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.677A pdb=" N THR B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 288 removed outlier: 3.771A pdb=" N GLN B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.897A pdb=" N ILE B 295 " --> pdb=" O CYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 removed outlier: 3.585A pdb=" N VAL B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.527A pdb=" N LYS G 45 " --> pdb=" O ARG G 486 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS G 483 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 55 Processing sheet with id=AA3, first strand: chain 'G' and resid 196 through 202 removed outlier: 3.609A pdb=" N VAL G 119 " --> pdb=" O MET G 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 271 through 273 Processing sheet with id=AA5, first strand: chain 'G' and resid 408 through 414 removed outlier: 3.580A pdb=" N LEU G 332 " --> pdb=" O ILE G 409 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 413 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA G 328 " --> pdb=" O CYS G 413 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN G 295 " --> pdb=" O ASN G 331 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 294 " --> pdb=" O SER G 442 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 357 through 359 Processing sheet with id=AA7, first strand: chain 'G' and resid 372 through 376 Processing sheet with id=AA8, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.531A pdb=" N VAL A 12 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 71 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.961A pdb=" N TRP A 28 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AB3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.842A pdb=" N LEU A 108 " --> pdb=" O LEU A 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB5, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AB6, first strand: chain 'A' and resid 183 through 189 removed outlier: 6.532A pdb=" N SER A 184 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL A 290 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 186 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N MET A 292 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS A 188 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALA A 294 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 281 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 276 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 275 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 237 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 183 through 189 removed outlier: 6.532A pdb=" N SER A 184 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL A 290 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 186 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N MET A 292 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS A 188 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALA A 294 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.820A pdb=" N PHE A 198 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 255 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.810A pdb=" N VAL A 326 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 317 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 314 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 348 " --> pdb=" O MET A 314 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY A 341 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS A 360 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP A 343 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A 358 " --> pdb=" O TRP A 343 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS A 345 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 356 " --> pdb=" O CYS A 345 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 347 " --> pdb=" O LEU A 354 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 828 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: 2.47 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2482 1.34 - 1.46: 1882 1.46 - 1.58: 4664 1.58 - 1.70: 2 1.70 - 1.82: 70 Bond restraints: 9100 Sorted by residual: bond pdb=" O3 TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.458 1.634 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" O2 TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.461 1.635 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" OH TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" OH TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.679 1.542 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" N GLN A 243 " pdb=" CA GLN A 243 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.40e+01 ... (remaining 9095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 11878 2.40 - 4.80: 380 4.80 - 7.21: 79 7.21 - 9.61: 21 9.61 - 12.01: 6 Bond angle restraints: 12364 Sorted by residual: angle pdb=" C ALA A 278 " pdb=" N LYS A 279 " pdb=" CA LYS A 279 " ideal model delta sigma weight residual 121.33 133.34 -12.01 1.40e+00 5.10e-01 7.36e+01 angle pdb=" N ASP A 244 " pdb=" CA ASP A 244 " pdb=" C ASP A 244 " ideal model delta sigma weight residual 113.45 122.68 -9.23 1.39e+00 5.18e-01 4.41e+01 angle pdb=" C ASN G 279 " pdb=" N ASN G 280 " pdb=" CA ASN G 280 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" N ALA A 201 " pdb=" CA ALA A 201 " pdb=" C ALA A 201 " ideal model delta sigma weight residual 108.49 117.08 -8.59 1.65e+00 3.67e-01 2.71e+01 angle pdb=" N LYS A 234 " pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 109.59 101.98 7.61 1.47e+00 4.63e-01 2.68e+01 ... (remaining 12359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.31: 5644 23.31 - 46.62: 165 46.62 - 69.93: 22 69.93 - 93.24: 28 93.24 - 116.55: 13 Dihedral angle restraints: 5872 sinusoidal: 2749 harmonic: 3123 Sorted by residual: dihedral pdb=" CB CYS G 118 " pdb=" SG CYS G 118 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -172.00 86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS G 376 " pdb=" SG CYS G 376 " pdb=" SG CYS G 440 " pdb=" CB CYS G 440 " ideal model delta sinusoidal sigma weight residual 93.00 162.04 -69.04 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CA ALA G 317 " pdb=" C ALA G 317 " pdb=" N THR G 318 " pdb=" CA THR G 318 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 5869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 1503 0.236 - 0.471: 14 0.471 - 0.707: 1 0.707 - 0.943: 0 0.943 - 1.179: 1 Chirality restraints: 1519 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN G 384 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.58 1.18 2.00e-01 2.50e+01 3.47e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.59e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN G 301 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 1516 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 384 " 0.197 2.00e-02 2.50e+03 1.77e-01 3.92e+02 pdb=" CG ASN G 384 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN G 384 " -0.134 2.00e-02 2.50e+03 pdb=" ND2 ASN G 384 " -0.224 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.163 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C7 NAG K 2 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.217 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 A2G B 401 " 0.158 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" C7 A2G B 401 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A2G B 401 " 0.116 2.00e-02 2.50e+03 pdb=" N2 A2G B 401 " -0.213 2.00e-02 2.50e+03 pdb=" O7 A2G B 401 " -0.019 2.00e-02 2.50e+03 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 62 2.57 - 3.15: 6657 3.15 - 3.73: 12402 3.73 - 4.32: 17103 4.32 - 4.90: 28074 Nonbonded interactions: 64298 Sorted by model distance: nonbonded pdb=" CG2 THR G 209 " pdb=" O4 MAN E 4 " model vdw 1.985 3.460 nonbonded pdb=" ND2 ASN A 233 " pdb=" N LYS A 234 " model vdw 2.049 3.200 nonbonded pdb=" O LYS A 234 " pdb=" CG GLU A 235 " model vdw 2.104 3.440 nonbonded pdb=" O GLU G 268 " pdb=" OD1 ASP G 269 " model vdw 2.159 3.040 nonbonded pdb=" NE2 HIS A 107 " pdb=" O GLU A 277 " model vdw 2.180 3.120 ... (remaining 64293 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 'C' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'J' } 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 group one per residue 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.500 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 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 : 0.007 0.176 9100 Z= 0.455 Angle : 1.080 12.012 12364 Z= 0.575 Chirality : 0.072 1.179 1519 Planarity : 0.009 0.135 1505 Dihedral : 13.542 116.551 3810 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.03 % Favored : 91.49 % Rotamer: Outliers : 1.37 % Allowed : 2.85 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.19 (0.21), residues: 1058 helix: -1.99 (0.25), residues: 281 sheet: -2.20 (0.32), residues: 221 loop : -3.57 (0.19), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 86 HIS 0.004 0.001 HIS G 372 PHE 0.029 0.002 PHE G 380 TYR 0.015 0.002 TYR B 3 ARG 0.004 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 273 time to evaluate : 1.012 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: symmetry clash revert: symmetry clash REVERT: G 251 ILE cc_start: 0.8613 (mt) cc_final: 0.8402 (mm) REVERT: G 480 TYR cc_start: 0.7245 (p90) cc_final: 0.6931 (p90) REVERT: G 487 ILE cc_start: 0.3812 (OUTLIER) cc_final: 0.2320 (pt) REVERT: A 156 THR cc_start: 0.8504 (p) cc_final: 0.7840 (p) REVERT: B 33 LEU cc_start: 0.6200 (mt) cc_final: 0.3942 (mm) REVERT: B 68 TYR cc_start: 0.5832 (m-10) cc_final: 0.5609 (m-10) REVERT: B 117 PHE cc_start: 0.7372 (m-10) cc_final: 0.6900 (m-80) REVERT: B 285 LEU cc_start: 0.7303 (tp) cc_final: 0.7039 (tp) outliers start: 13 outliers final: 2 residues processed: 283 average time/residue: 0.2448 time to fit residues: 91.2508 Evaluate side-chains 152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS G 102 GLN G 249 HIS G 417 GLN G 420 ASN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN A 163 GLN A 358 ASN B 93 GLN B 231 HIS B 252 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.066191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047611 restraints weight = 56262.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049121 restraints weight = 33672.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050082 restraints weight = 23777.068| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9100 Z= 0.308 Angle : 0.825 8.087 12364 Z= 0.417 Chirality : 0.051 0.404 1519 Planarity : 0.006 0.109 1505 Dihedral : 11.902 111.832 1793 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.07 (0.23), residues: 1058 helix: -0.14 (0.29), residues: 295 sheet: -1.91 (0.31), residues: 228 loop : -3.31 (0.21), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 95 HIS 0.010 0.002 HIS G 104 PHE 0.015 0.002 PHE A 198 TYR 0.025 0.002 TYR B 37 ARG 0.006 0.001 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.9413 (mp) cc_final: 0.9112 (mp) REVERT: G 210 PHE cc_start: 0.7958 (t80) cc_final: 0.7073 (t80) REVERT: G 290 ASP cc_start: 0.8968 (t70) cc_final: 0.8584 (t0) REVERT: G 480 TYR cc_start: 0.8516 (p90) cc_final: 0.8295 (p90) REVERT: A 37 LEU cc_start: 0.9613 (tp) cc_final: 0.9236 (tp) REVERT: A 53 ASP cc_start: 0.8504 (m-30) cc_final: 0.8053 (p0) REVERT: A 97 VAL cc_start: 0.8507 (t) cc_final: 0.8247 (t) REVERT: A 279 LYS cc_start: 0.8750 (tptm) cc_final: 0.8535 (ttpp) REVERT: B 2 ASP cc_start: 0.8133 (t0) cc_final: 0.7910 (t0) REVERT: B 33 LEU cc_start: 0.9393 (mt) cc_final: 0.9056 (mm) REVERT: B 40 VAL cc_start: 0.9779 (t) cc_final: 0.9497 (t) REVERT: B 86 TRP cc_start: 0.9229 (m100) cc_final: 0.9015 (m100) REVERT: B 112 PHE cc_start: 0.8976 (t80) cc_final: 0.8689 (t80) REVERT: B 251 TYR cc_start: 0.9328 (t80) cc_final: 0.9069 (t80) REVERT: B 287 MET cc_start: 0.9227 (mmp) cc_final: 0.8815 (mmm) REVERT: B 291 CYS cc_start: 0.9687 (p) cc_final: 0.9481 (p) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2009 time to fit residues: 45.3997 Evaluate side-chains 112 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.066012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.046984 restraints weight = 57584.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048586 restraints weight = 33706.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049634 restraints weight = 23542.337| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9100 Z= 0.187 Angle : 0.685 7.674 12364 Z= 0.340 Chirality : 0.048 0.395 1519 Planarity : 0.005 0.071 1505 Dihedral : 10.201 108.240 1793 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.68 (0.24), residues: 1058 helix: 0.26 (0.31), residues: 294 sheet: -1.70 (0.31), residues: 237 loop : -3.13 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 94 HIS 0.006 0.001 HIS G 65 PHE 0.012 0.001 PHE G 315 TYR 0.023 0.002 TYR B 37 ARG 0.005 0.001 ARG G 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.961 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: G 115 LEU cc_start: 0.9422 (mp) cc_final: 0.8749 (mp) REVERT: G 259 LEU cc_start: 0.9450 (mt) cc_final: 0.9178 (tt) REVERT: G 290 ASP cc_start: 0.8937 (t70) cc_final: 0.8528 (t0) REVERT: G 379 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8509 (mm-30) REVERT: G 421 MET cc_start: 0.8388 (ptp) cc_final: 0.8012 (ptp) REVERT: G 480 TYR cc_start: 0.8564 (p90) cc_final: 0.8328 (p90) REVERT: A 37 LEU cc_start: 0.9657 (tp) cc_final: 0.9262 (tp) REVERT: A 53 ASP cc_start: 0.8547 (m-30) cc_final: 0.8262 (p0) REVERT: A 97 VAL cc_start: 0.8709 (t) cc_final: 0.8508 (t) REVERT: A 279 LYS cc_start: 0.8820 (tptm) cc_final: 0.8459 (mtmm) REVERT: B 2 ASP cc_start: 0.8236 (t0) cc_final: 0.7966 (t0) REVERT: B 33 LEU cc_start: 0.9585 (mt) cc_final: 0.9147 (mm) REVERT: B 37 TYR cc_start: 0.9293 (m-80) cc_final: 0.8932 (m-80) REVERT: B 251 TYR cc_start: 0.9402 (t80) cc_final: 0.9172 (t80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2215 time to fit residues: 49.6019 Evaluate side-chains 112 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 0.0170 chunk 16 optimal weight: 0.2980 chunk 66 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 ASN G 279 ASN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN A 284 HIS B 93 GLN B 231 HIS B 267 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.063606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045068 restraints weight = 57145.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046474 restraints weight = 35054.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.047458 restraints weight = 25224.615| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9100 Z= 0.219 Angle : 0.677 8.609 12364 Z= 0.341 Chirality : 0.048 0.373 1519 Planarity : 0.004 0.049 1505 Dihedral : 8.879 108.588 1793 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.43 (0.24), residues: 1058 helix: 0.34 (0.31), residues: 294 sheet: -1.54 (0.32), residues: 253 loop : -2.92 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 94 HIS 0.016 0.001 HIS G 71 PHE 0.014 0.001 PHE A 198 TYR 0.036 0.002 TYR G 217 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.9376 (mp) cc_final: 0.8786 (mp) REVERT: G 290 ASP cc_start: 0.8997 (t70) cc_final: 0.8645 (t0) REVERT: G 379 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8581 (mm-30) REVERT: G 480 TYR cc_start: 0.8799 (p90) cc_final: 0.8481 (p90) REVERT: A 276 LEU cc_start: 0.9017 (tp) cc_final: 0.8797 (tp) REVERT: A 279 LYS cc_start: 0.8742 (tptm) cc_final: 0.8422 (ttpp) REVERT: B 2 ASP cc_start: 0.8299 (t0) cc_final: 0.7992 (t0) REVERT: B 33 LEU cc_start: 0.9586 (mt) cc_final: 0.9159 (mm) REVERT: B 37 TYR cc_start: 0.9261 (m-80) cc_final: 0.8501 (m-80) REVERT: B 43 PHE cc_start: 0.9310 (m-10) cc_final: 0.9083 (m-80) REVERT: B 279 MET cc_start: 0.9003 (ptp) cc_final: 0.8715 (ptt) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1819 time to fit residues: 36.2435 Evaluate side-chains 102 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 72 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 ASN G 279 ASN G 308 HIS ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 231 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.058454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.040969 restraints weight = 64411.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.042318 restraints weight = 37875.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.043165 restraints weight = 26741.870| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 9100 Z= 0.438 Angle : 0.902 12.590 12364 Z= 0.446 Chirality : 0.053 0.404 1519 Planarity : 0.006 0.056 1505 Dihedral : 9.142 116.564 1793 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.83 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.45 (0.24), residues: 1058 helix: 0.15 (0.30), residues: 294 sheet: -1.51 (0.32), residues: 273 loop : -2.86 (0.23), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP G 475 HIS 0.009 0.002 HIS G 71 PHE 0.018 0.003 PHE G 464 TYR 0.034 0.003 TYR G 217 ARG 0.007 0.001 ARG G 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7945 (p90) cc_final: 0.7744 (p90) REVERT: G 421 MET cc_start: 0.8360 (ptp) cc_final: 0.8052 (ptp) REVERT: G 480 TYR cc_start: 0.9017 (p90) cc_final: 0.8687 (p90) REVERT: A 173 ASP cc_start: 0.9213 (p0) cc_final: 0.8971 (t0) REVERT: A 276 LEU cc_start: 0.9067 (tp) cc_final: 0.8772 (tp) REVERT: B 2 ASP cc_start: 0.8465 (t0) cc_final: 0.8061 (t0) REVERT: B 33 LEU cc_start: 0.9505 (mt) cc_final: 0.9161 (mm) REVERT: B 43 PHE cc_start: 0.9240 (m-10) cc_final: 0.8921 (m-80) REVERT: B 161 LEU cc_start: 0.9170 (tt) cc_final: 0.8915 (mt) REVERT: B 261 GLN cc_start: 0.8919 (mm110) cc_final: 0.8445 (tm-30) REVERT: B 279 MET cc_start: 0.8961 (ptp) cc_final: 0.8721 (ptp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1973 time to fit residues: 31.2178 Evaluate side-chains 82 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 279 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.060817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.042747 restraints weight = 61995.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044161 restraints weight = 36050.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.045056 restraints weight = 25301.351| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9100 Z= 0.196 Angle : 0.700 8.860 12364 Z= 0.343 Chirality : 0.048 0.377 1519 Planarity : 0.004 0.037 1505 Dihedral : 8.322 110.239 1793 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.81 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.11 (0.25), residues: 1058 helix: 0.59 (0.31), residues: 294 sheet: -1.43 (0.32), residues: 270 loop : -2.68 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 475 HIS 0.004 0.001 HIS G 104 PHE 0.015 0.001 PHE A 198 TYR 0.048 0.002 TYR G 217 ARG 0.008 0.001 ARG G 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.9351 (mm) cc_final: 0.9086 (mp) REVERT: G 260 LEU cc_start: 0.9608 (mm) cc_final: 0.9388 (mm) REVERT: G 421 MET cc_start: 0.8295 (ptp) cc_final: 0.7985 (ptp) REVERT: G 476 ARG cc_start: 0.8893 (mtt90) cc_final: 0.8473 (mtm-85) REVERT: G 480 TYR cc_start: 0.8827 (p90) cc_final: 0.8480 (p90) REVERT: A 323 GLU cc_start: 0.7617 (tm-30) cc_final: 0.6101 (pm20) REVERT: B 2 ASP cc_start: 0.8429 (t0) cc_final: 0.8102 (t0) REVERT: B 43 PHE cc_start: 0.9231 (m-10) cc_final: 0.8882 (m-80) REVERT: B 74 ILE cc_start: 0.9452 (mt) cc_final: 0.9194 (tt) REVERT: B 161 LEU cc_start: 0.9156 (tt) cc_final: 0.8889 (mt) REVERT: B 261 GLN cc_start: 0.8869 (mm110) cc_final: 0.8371 (tm-30) REVERT: B 279 MET cc_start: 0.8901 (ptp) cc_final: 0.8701 (ptp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1828 time to fit residues: 30.6773 Evaluate side-chains 89 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 ASN G 279 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.058506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.041057 restraints weight = 64288.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.042409 restraints weight = 37566.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.043278 restraints weight = 26400.833| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9100 Z= 0.325 Angle : 0.770 9.510 12364 Z= 0.379 Chirality : 0.049 0.381 1519 Planarity : 0.005 0.041 1505 Dihedral : 8.113 108.302 1793 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.36 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.12 (0.25), residues: 1058 helix: 0.50 (0.30), residues: 293 sheet: -1.40 (0.30), residues: 289 loop : -2.67 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 475 HIS 0.005 0.001 HIS G 65 PHE 0.018 0.002 PHE A 43 TYR 0.034 0.002 TYR G 217 ARG 0.012 0.001 ARG G 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 382 TYR cc_start: 0.8917 (m-10) cc_final: 0.8587 (m-10) REVERT: G 421 MET cc_start: 0.8228 (ptp) cc_final: 0.7901 (ptp) REVERT: G 476 ARG cc_start: 0.8993 (mtt90) cc_final: 0.8633 (mtm-85) REVERT: G 480 TYR cc_start: 0.8941 (p90) cc_final: 0.8600 (p90) REVERT: A 276 LEU cc_start: 0.9147 (tp) cc_final: 0.8940 (tp) REVERT: A 323 GLU cc_start: 0.7671 (tm-30) cc_final: 0.6120 (pm20) REVERT: B 2 ASP cc_start: 0.8618 (t0) cc_final: 0.8245 (t0) REVERT: B 43 PHE cc_start: 0.9231 (m-10) cc_final: 0.8910 (m-80) REVERT: B 74 ILE cc_start: 0.9455 (mt) cc_final: 0.9232 (tt) REVERT: B 161 LEU cc_start: 0.9223 (tt) cc_final: 0.8941 (mt) REVERT: B 261 GLN cc_start: 0.8878 (mm110) cc_final: 0.8515 (tm-30) REVERT: B 287 MET cc_start: 0.9411 (mtm) cc_final: 0.9002 (mtm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1840 time to fit residues: 27.9427 Evaluate side-chains 83 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.0020 chunk 80 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.059409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.041839 restraints weight = 63199.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043198 restraints weight = 36894.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044106 restraints weight = 25927.284| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9100 Z= 0.198 Angle : 0.706 12.645 12364 Z= 0.341 Chirality : 0.048 0.358 1519 Planarity : 0.004 0.058 1505 Dihedral : 7.209 94.038 1793 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.25), residues: 1058 helix: 0.75 (0.31), residues: 294 sheet: -1.56 (0.32), residues: 254 loop : -2.51 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 475 HIS 0.003 0.001 HIS A 256 PHE 0.009 0.001 PHE A 196 TYR 0.016 0.002 TYR B 37 ARG 0.009 0.000 ARG G 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.8693 (t80) cc_final: 0.8458 (t80) REVERT: G 421 MET cc_start: 0.8265 (ptp) cc_final: 0.7939 (ptp) REVERT: G 476 ARG cc_start: 0.8971 (mtt90) cc_final: 0.8678 (mtm-85) REVERT: G 480 TYR cc_start: 0.8901 (p90) cc_final: 0.8520 (p90) REVERT: A 235 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9128 (tm-30) REVERT: A 276 LEU cc_start: 0.9168 (tp) cc_final: 0.8953 (tp) REVERT: A 323 GLU cc_start: 0.7675 (tm-30) cc_final: 0.6116 (pm20) REVERT: B 2 ASP cc_start: 0.8592 (t0) cc_final: 0.8246 (t0) REVERT: B 43 PHE cc_start: 0.9218 (m-10) cc_final: 0.8898 (m-80) REVERT: B 74 ILE cc_start: 0.9444 (mt) cc_final: 0.9226 (tt) REVERT: B 161 LEU cc_start: 0.9222 (tt) cc_final: 0.8940 (mt) REVERT: B 261 GLN cc_start: 0.8868 (mm110) cc_final: 0.8482 (tm-30) REVERT: B 287 MET cc_start: 0.9314 (mtm) cc_final: 0.8934 (mtm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2134 time to fit residues: 33.6922 Evaluate side-chains 84 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS B 175 HIS B 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.059596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.042108 restraints weight = 62352.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.043495 restraints weight = 36542.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.044385 restraints weight = 25672.157| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.7783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9100 Z= 0.183 Angle : 0.688 10.461 12364 Z= 0.332 Chirality : 0.047 0.348 1519 Planarity : 0.004 0.055 1505 Dihedral : 6.703 81.852 1793 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.84 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.25), residues: 1058 helix: 0.84 (0.31), residues: 294 sheet: -1.41 (0.32), residues: 255 loop : -2.52 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 475 HIS 0.005 0.001 HIS A 256 PHE 0.016 0.001 PHE A 198 TYR 0.015 0.002 TYR G 217 ARG 0.008 0.000 ARG G 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: G 210 PHE cc_start: 0.8645 (t80) cc_final: 0.8417 (t80) REVERT: G 260 LEU cc_start: 0.9597 (mm) cc_final: 0.9339 (mm) REVERT: G 421 MET cc_start: 0.8302 (ptp) cc_final: 0.8018 (ptp) REVERT: G 476 ARG cc_start: 0.8927 (mtt90) cc_final: 0.8720 (mtm-85) REVERT: G 480 TYR cc_start: 0.8812 (p90) cc_final: 0.8439 (p90) REVERT: A 235 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9149 (tm-30) REVERT: A 276 LEU cc_start: 0.9128 (tp) cc_final: 0.8900 (tp) REVERT: A 323 GLU cc_start: 0.7630 (tm-30) cc_final: 0.6070 (pm20) REVERT: B 2 ASP cc_start: 0.8532 (t0) cc_final: 0.8145 (t0) REVERT: B 33 LEU cc_start: 0.9526 (mm) cc_final: 0.9067 (mm) REVERT: B 37 TYR cc_start: 0.9296 (m-80) cc_final: 0.9086 (m-80) REVERT: B 43 PHE cc_start: 0.9211 (m-10) cc_final: 0.8889 (m-80) REVERT: B 161 LEU cc_start: 0.9214 (tt) cc_final: 0.8930 (mt) REVERT: B 261 GLN cc_start: 0.8848 (mm110) cc_final: 0.8470 (tm-30) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1916 time to fit residues: 29.4962 Evaluate side-chains 82 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 0.0010 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 279 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.059450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.041947 restraints weight = 62546.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.043332 restraints weight = 36040.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.044232 restraints weight = 25100.359| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.7959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9100 Z= 0.192 Angle : 0.705 10.039 12364 Z= 0.339 Chirality : 0.048 0.348 1519 Planarity : 0.004 0.054 1505 Dihedral : 6.201 58.990 1793 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.63 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.88 (0.25), residues: 1058 helix: 0.79 (0.30), residues: 296 sheet: -1.37 (0.32), residues: 255 loop : -2.49 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 475 HIS 0.003 0.001 HIS A 256 PHE 0.013 0.001 PHE A 198 TYR 0.023 0.002 TYR G 217 ARG 0.007 0.000 ARG G 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: G 99 MET cc_start: 0.9253 (ptp) cc_final: 0.8926 (ptt) REVERT: G 210 PHE cc_start: 0.8753 (t80) cc_final: 0.8495 (t80) REVERT: G 217 TYR cc_start: 0.9151 (m-80) cc_final: 0.8422 (m-10) REVERT: G 260 LEU cc_start: 0.9604 (mm) cc_final: 0.9337 (mm) REVERT: G 421 MET cc_start: 0.8392 (ptp) cc_final: 0.8041 (ptp) REVERT: G 476 ARG cc_start: 0.9002 (mtt90) cc_final: 0.8761 (mtm-85) REVERT: G 480 TYR cc_start: 0.8892 (p90) cc_final: 0.8507 (p90) REVERT: A 235 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9146 (tm-30) REVERT: A 276 LEU cc_start: 0.9149 (tp) cc_final: 0.8923 (tp) REVERT: A 323 GLU cc_start: 0.7561 (tm-30) cc_final: 0.6008 (pm20) REVERT: B 2 ASP cc_start: 0.8454 (t0) cc_final: 0.8061 (t0) REVERT: B 33 LEU cc_start: 0.9494 (mm) cc_final: 0.9051 (mm) REVERT: B 43 PHE cc_start: 0.9216 (m-10) cc_final: 0.8893 (m-80) REVERT: B 161 LEU cc_start: 0.9234 (tt) cc_final: 0.8989 (mt) REVERT: B 251 TYR cc_start: 0.9422 (t80) cc_final: 0.9189 (t80) REVERT: B 261 GLN cc_start: 0.8911 (mm110) cc_final: 0.8530 (tm-30) REVERT: B 279 MET cc_start: 0.8823 (ptp) cc_final: 0.8609 (ptp) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1787 time to fit residues: 27.1566 Evaluate side-chains 81 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 102 GLN G 279 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.060115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.042583 restraints weight = 60238.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.043913 restraints weight = 35526.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.044806 restraints weight = 25075.448| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.8083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9100 Z= 0.164 Angle : 0.698 14.580 12364 Z= 0.335 Chirality : 0.048 0.337 1519 Planarity : 0.004 0.052 1505 Dihedral : 5.542 46.717 1793 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.25), residues: 1058 helix: 0.72 (0.31), residues: 296 sheet: -1.29 (0.31), residues: 257 loop : -2.47 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 306 HIS 0.003 0.001 HIS A 256 PHE 0.013 0.001 PHE A 198 TYR 0.030 0.002 TYR B 37 ARG 0.007 0.000 ARG G 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.04 seconds wall clock time: 53 minutes 56.75 seconds (3236.75 seconds total)