Starting phenix.real_space_refine on Mon Jul 28 16:53:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6met_9109/07_2025/6met_9109.cif Found real_map, /net/cci-nas-00/data/ceres_data/6met_9109/07_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_9109/07_2025/6met_9109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6met_9109/07_2025/6met_9109.map" model { file = "/net/cci-nas-00/data/ceres_data/6met_9109/07_2025/6met_9109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6met_9109/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.75, per 1000 atoms: 0.65 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: 2.54 Conformation dependent library (CDL) restraints added in 950.0 milliseconds 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: 0.94 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: 2.44 Time building geometry restraints manager: 2.93 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.740 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- 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 : 0.010 0.479 9145 Z= 0.757 Angle : 1.160 26.492 12481 Z= 0.591 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 Details of bonding type rmsd link_NAG-ASN : bond 0.12010 ( 16) link_NAG-ASN : angle 6.66349 ( 48) link_ALPHA1-6 : bond 0.00458 ( 1) link_ALPHA1-6 : angle 1.11768 ( 3) link_BETA1-4 : bond 0.00604 ( 12) link_BETA1-4 : angle 2.17695 ( 36) link_ALPHA1-2 : bond 0.00372 ( 1) link_ALPHA1-2 : angle 2.76447 ( 3) link_ALPHA1-3 : bond 0.00682 ( 1) link_ALPHA1-3 : angle 1.10851 ( 3) hydrogen bonds : bond 0.28718 ( 304) hydrogen bonds : angle 10.30008 ( 828) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.46525 ( 24) covalent geometry : bond 0.00679 ( 9100) covalent geometry : angle 1.07971 (12364) Misc. bond : bond 0.41293 ( 2) *********************** 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 : 0.908 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: 0.2456 time to fit residues: 91.6311 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 : 1.082 ------------------------------------------------------------------------------- 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 = 0.066195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047596 restraints weight = 56262.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049076 restraints weight = 33657.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050104 restraints weight = 24011.783| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9145 Z= 0.226 Angle : 0.857 9.422 12481 Z= 0.423 Chirality : 0.051 0.404 1519 Planarity : 0.006 0.110 1505 Dihedral : 11.904 111.829 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 16) link_NAG-ASN : angle 3.28762 ( 48) link_ALPHA1-6 : bond 0.01192 ( 1) link_ALPHA1-6 : angle 2.93492 ( 3) link_BETA1-4 : bond 0.00459 ( 12) link_BETA1-4 : angle 1.96868 ( 36) link_ALPHA1-2 : bond 0.00680 ( 1) link_ALPHA1-2 : angle 2.96033 ( 3) link_ALPHA1-3 : bond 0.01019 ( 1) link_ALPHA1-3 : angle 2.19380 ( 3) hydrogen bonds : bond 0.05399 ( 304) hydrogen bonds : angle 6.83918 ( 828) SS BOND : bond 0.00418 ( 12) SS BOND : angle 0.97964 ( 24) covalent geometry : bond 0.00477 ( 9100) covalent geometry : angle 0.82511 (12364) Misc. bond : bond 0.00409 ( 2) *********************** 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 : 1.059 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: 0.9399 (mp) cc_final: 0.9102 (mp) REVERT: G 210 PHE cc_start: 0.7911 (t80) cc_final: 0.7023 (t80) REVERT: G 290 ASP cc_start: 0.8959 (t70) cc_final: 0.8580 (t0) REVERT: G 480 TYR cc_start: 0.8478 (p90) cc_final: 0.8256 (p90) REVERT: A 37 LEU cc_start: 0.9587 (tp) cc_final: 0.9207 (tp) REVERT: A 53 ASP cc_start: 0.8477 (m-30) cc_final: 0.8035 (p0) REVERT: A 97 VAL cc_start: 0.8478 (t) cc_final: 0.8223 (t) REVERT: A 279 LYS cc_start: 0.8747 (tptm) cc_final: 0.8535 (ttpp) REVERT: B 2 ASP cc_start: 0.8096 (t0) cc_final: 0.7877 (t0) REVERT: B 33 LEU cc_start: 0.9387 (mt) cc_final: 0.9041 (mm) REVERT: B 40 VAL cc_start: 0.9781 (t) cc_final: 0.9496 (t) REVERT: B 86 TRP cc_start: 0.9238 (m100) cc_final: 0.9024 (m100) REVERT: B 112 PHE cc_start: 0.8978 (t80) cc_final: 0.8692 (t80) REVERT: B 251 TYR cc_start: 0.9316 (t80) cc_final: 0.9060 (t80) REVERT: B 287 MET cc_start: 0.9215 (mmp) cc_final: 0.8806 (mmm) REVERT: B 291 CYS cc_start: 0.9683 (p) cc_final: 0.9479 (p) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1980 time to fit residues: 44.9252 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 : 1.020 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 308 HIS ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS B 231 HIS B 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.063587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.044720 restraints weight = 59031.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.046249 restraints weight = 34761.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047242 restraints weight = 24440.228| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9145 Z= 0.220 Angle : 0.777 9.022 12481 Z= 0.381 Chirality : 0.048 0.395 1519 Planarity : 0.005 0.073 1505 Dihedral : 10.131 111.446 1793 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.56 % Favored : 92.34 % 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: 0.23 (0.30), residues: 296 sheet: -1.60 (0.32), residues: 236 loop : -3.18 (0.21), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 393 HIS 0.007 0.001 HIS G 65 PHE 0.017 0.002 PHE G 315 TYR 0.020 0.002 TYR B 37 ARG 0.008 0.001 ARG B 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 16) link_NAG-ASN : angle 3.07521 ( 48) link_ALPHA1-6 : bond 0.00843 ( 1) link_ALPHA1-6 : angle 2.66334 ( 3) link_BETA1-4 : bond 0.00413 ( 12) link_BETA1-4 : angle 1.82264 ( 36) link_ALPHA1-2 : bond 0.00401 ( 1) link_ALPHA1-2 : angle 2.24917 ( 3) link_ALPHA1-3 : bond 0.00794 ( 1) link_ALPHA1-3 : angle 1.92278 ( 3) hydrogen bonds : bond 0.04683 ( 304) hydrogen bonds : angle 6.25853 ( 828) SS BOND : bond 0.00730 ( 12) SS BOND : angle 1.34031 ( 24) covalent geometry : bond 0.00475 ( 9100) covalent geometry : angle 0.74594 (12364) Misc. bond : bond 0.00114 ( 2) *********************** 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 132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.933 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: 0.9426 (mp) cc_final: 0.9120 (mp) REVERT: G 290 ASP cc_start: 0.9028 (t70) cc_final: 0.8699 (t0) REVERT: G 379 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8534 (mm-30) REVERT: G 421 MET cc_start: 0.8328 (ptp) cc_final: 0.7892 (ptp) REVERT: G 475 TRP cc_start: 0.8700 (m-10) cc_final: 0.8477 (m-10) REVERT: G 480 TYR cc_start: 0.8797 (p90) cc_final: 0.8558 (p90) REVERT: A 53 ASP cc_start: 0.8597 (m-30) cc_final: 0.8367 (p0) REVERT: A 279 LYS cc_start: 0.8768 (tptm) cc_final: 0.8322 (ttpp) REVERT: A 323 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7383 (pm20) REVERT: B 2 ASP cc_start: 0.8353 (t0) cc_final: 0.8088 (t0) REVERT: B 33 LEU cc_start: 0.9570 (mt) cc_final: 0.9222 (mm) REVERT: B 37 TYR cc_start: 0.9287 (m-80) cc_final: 0.8979 (m-80) REVERT: B 176 TYR cc_start: 0.8761 (m-10) cc_final: 0.8511 (m-80) REVERT: B 251 TYR cc_start: 0.9432 (t80) cc_final: 0.9182 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2123 time to fit residues: 40.0999 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 : 1.038 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 0.4980 chunk 66 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 ASN G 229 ASN ** G 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 71 ASN B 93 GLN B 231 HIS ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.062254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043890 restraints weight = 59794.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045344 restraints weight = 35415.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046292 restraints weight = 25015.820| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9145 Z= 0.186 Angle : 0.734 9.317 12481 Z= 0.358 Chirality : 0.048 0.378 1519 Planarity : 0.005 0.050 1505 Dihedral : 8.904 110.100 1793 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.13 % Favored : 91.78 % 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: -2.35 (0.24), residues: 1058 helix: 0.54 (0.31), residues: 294 sheet: -1.54 (0.32), residues: 262 loop : -2.95 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 94 HIS 0.010 0.001 HIS B 175 PHE 0.019 0.002 PHE B 43 TYR 0.040 0.002 TYR G 217 ARG 0.002 0.000 ARG B 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 16) link_NAG-ASN : angle 2.86911 ( 48) link_ALPHA1-6 : bond 0.01216 ( 1) link_ALPHA1-6 : angle 2.92539 ( 3) link_BETA1-4 : bond 0.00389 ( 12) link_BETA1-4 : angle 1.60056 ( 36) link_ALPHA1-2 : bond 0.00468 ( 1) link_ALPHA1-2 : angle 2.02145 ( 3) link_ALPHA1-3 : bond 0.00936 ( 1) link_ALPHA1-3 : angle 1.85233 ( 3) hydrogen bonds : bond 0.04034 ( 304) hydrogen bonds : angle 5.89044 ( 828) SS BOND : bond 0.00503 ( 12) SS BOND : angle 1.44130 ( 24) covalent geometry : bond 0.00397 ( 9100) covalent geometry : angle 0.70460 (12364) Misc. bond : bond 0.00077 ( 2) *********************** 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 123 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 99 MET cc_start: 0.9080 (ptp) cc_final: 0.8868 (ptt) REVERT: G 103 MET cc_start: 0.8131 (mmp) cc_final: 0.7266 (mmp) REVERT: G 115 LEU cc_start: 0.9424 (mp) cc_final: 0.9154 (mp) REVERT: G 210 PHE cc_start: 0.8336 (t80) cc_final: 0.7611 (t80) REVERT: G 217 TYR cc_start: 0.8511 (m-10) cc_final: 0.7909 (m-10) REVERT: G 379 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8513 (mm-30) REVERT: G 382 TYR cc_start: 0.8887 (m-10) cc_final: 0.8531 (m-10) REVERT: G 480 TYR cc_start: 0.8874 (p90) cc_final: 0.8569 (p90) REVERT: A 276 LEU cc_start: 0.9057 (tp) cc_final: 0.8836 (tp) REVERT: A 323 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7396 (pm20) REVERT: B 2 ASP cc_start: 0.8347 (t0) cc_final: 0.7984 (t0) REVERT: B 33 LEU cc_start: 0.9569 (mt) cc_final: 0.9209 (mm) REVERT: B 37 TYR cc_start: 0.9270 (m-80) cc_final: 0.8986 (m-80) REVERT: B 43 PHE cc_start: 0.9288 (m-80) cc_final: 0.8791 (m-80) REVERT: B 161 LEU cc_start: 0.9231 (tt) cc_final: 0.8990 (mt) REVERT: B 251 TYR cc_start: 0.9453 (t80) cc_final: 0.9235 (t80) REVERT: B 279 MET cc_start: 0.8997 (ptp) cc_final: 0.8773 (ptt) REVERT: B 291 CYS cc_start: 0.9532 (p) cc_final: 0.9327 (p) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2453 time to fit residues: 43.7903 Evaluate side-chains 93 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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: 6.9990 chunk 104 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 164 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** 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 = 0.3384 r_free = 0.3384 target = 0.056845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039480 restraints weight = 63354.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.040750 restraints weight = 37826.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041583 restraints weight = 26933.468| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.7246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 9145 Z= 0.357 Angle : 0.981 11.859 12481 Z= 0.473 Chirality : 0.055 0.403 1519 Planarity : 0.006 0.053 1505 Dihedral : 9.421 119.442 1793 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.49 % Favored : 89.41 % Rotamer: Outliers : 0.11 % Allowed : 3.59 % 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: -2.62 (0.24), residues: 1058 helix: 0.08 (0.29), residues: 294 sheet: -1.62 (0.30), residues: 286 loop : -3.03 (0.24), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 157 HIS 0.005 0.002 HIS G 216 PHE 0.027 0.003 PHE A 43 TYR 0.029 0.003 TYR G 217 ARG 0.005 0.001 ARG G 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 16) link_NAG-ASN : angle 3.81334 ( 48) link_ALPHA1-6 : bond 0.02087 ( 1) link_ALPHA1-6 : angle 4.20021 ( 3) link_BETA1-4 : bond 0.00690 ( 12) link_BETA1-4 : angle 2.30808 ( 36) link_ALPHA1-2 : bond 0.00430 ( 1) link_ALPHA1-2 : angle 1.98484 ( 3) link_ALPHA1-3 : bond 0.00659 ( 1) link_ALPHA1-3 : angle 2.46958 ( 3) hydrogen bonds : bond 0.04646 ( 304) hydrogen bonds : angle 6.52162 ( 828) SS BOND : bond 0.00648 ( 12) SS BOND : angle 1.88322 ( 24) covalent geometry : bond 0.00756 ( 9100) covalent geometry : angle 0.94133 (12364) Misc. bond : bond 0.00147 ( 2) *********************** 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 102 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.8013 (p90) cc_final: 0.7799 (p90) REVERT: G 382 TYR cc_start: 0.9127 (m-10) cc_final: 0.8824 (m-10) REVERT: G 421 MET cc_start: 0.8312 (ptp) cc_final: 0.7987 (ptp) REVERT: G 471 MET cc_start: 0.9505 (mmp) cc_final: 0.9299 (mmm) REVERT: G 480 TYR cc_start: 0.9106 (p90) cc_final: 0.8695 (p90) REVERT: A 173 ASP cc_start: 0.9260 (p0) cc_final: 0.9011 (t0) REVERT: A 198 PHE cc_start: 0.8037 (m-10) cc_final: 0.7833 (m-80) REVERT: B 2 ASP cc_start: 0.8719 (t0) cc_final: 0.8335 (t0) REVERT: B 33 LEU cc_start: 0.9578 (mt) cc_final: 0.9191 (mm) REVERT: B 37 TYR cc_start: 0.9237 (m-80) cc_final: 0.8956 (m-80) REVERT: B 43 PHE cc_start: 0.9287 (m-80) cc_final: 0.8804 (m-80) REVERT: B 85 PHE cc_start: 0.9281 (m-80) cc_final: 0.9021 (m-80) REVERT: B 161 LEU cc_start: 0.9186 (tt) cc_final: 0.8928 (mt) REVERT: B 251 TYR cc_start: 0.9572 (t80) cc_final: 0.9371 (t80) REVERT: B 261 GLN cc_start: 0.8972 (mm110) cc_final: 0.8678 (tm-30) REVERT: B 287 MET cc_start: 0.9280 (mmp) cc_final: 0.9029 (mmm) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.2991 time to fit residues: 44.4670 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 : 2.004 ------------------------------------------------------------------------------- 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: 2.9990 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.059424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.041777 restraints weight = 62505.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.043145 restraints weight = 36797.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.044052 restraints weight = 26078.734| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.7196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9145 Z= 0.145 Angle : 0.738 10.411 12481 Z= 0.353 Chirality : 0.049 0.368 1519 Planarity : 0.004 0.045 1505 Dihedral : 8.439 110.607 1793 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -2.20 (0.25), residues: 1058 helix: 0.75 (0.31), residues: 293 sheet: -1.66 (0.30), residues: 275 loop : -2.79 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 475 HIS 0.004 0.001 HIS A 256 PHE 0.014 0.002 PHE G 92 TYR 0.028 0.002 TYR G 217 ARG 0.014 0.001 ARG G 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 16) link_NAG-ASN : angle 3.01902 ( 48) link_ALPHA1-6 : bond 0.01419 ( 1) link_ALPHA1-6 : angle 2.80288 ( 3) link_BETA1-4 : bond 0.00361 ( 12) link_BETA1-4 : angle 1.50496 ( 36) link_ALPHA1-2 : bond 0.00210 ( 1) link_ALPHA1-2 : angle 1.91061 ( 3) link_ALPHA1-3 : bond 0.01045 ( 1) link_ALPHA1-3 : angle 1.75577 ( 3) hydrogen bonds : bond 0.03878 ( 304) hydrogen bonds : angle 5.84378 ( 828) SS BOND : bond 0.00363 ( 12) SS BOND : angle 2.11002 ( 24) covalent geometry : bond 0.00309 ( 9100) covalent geometry : angle 0.70442 (12364) Misc. bond : bond 0.00073 ( 2) *********************** 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 110 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.8040 (p90) cc_final: 0.7812 (p90) REVERT: G 382 TYR cc_start: 0.9108 (m-10) cc_final: 0.8861 (m-10) REVERT: G 421 MET cc_start: 0.8371 (ptp) cc_final: 0.8117 (ptp) REVERT: G 480 TYR cc_start: 0.8918 (p90) cc_final: 0.8554 (p90) REVERT: A 235 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9133 (tm-30) REVERT: B 2 ASP cc_start: 0.8717 (t0) cc_final: 0.8430 (t0) REVERT: B 33 LEU cc_start: 0.9563 (mt) cc_final: 0.9159 (mm) REVERT: B 37 TYR cc_start: 0.9223 (m-80) cc_final: 0.8995 (m-80) REVERT: B 43 PHE cc_start: 0.9279 (m-80) cc_final: 0.8770 (m-80) REVERT: B 74 ILE cc_start: 0.9458 (mt) cc_final: 0.9199 (tt) REVERT: B 161 LEU cc_start: 0.9202 (tt) cc_final: 0.8936 (mt) REVERT: B 261 GLN cc_start: 0.8867 (mm110) cc_final: 0.8500 (tm-30) REVERT: B 287 MET cc_start: 0.9082 (mmp) cc_final: 0.8878 (mmm) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1970 time to fit residues: 31.1424 Evaluate side-chains 87 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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: 2.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.059549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.041819 restraints weight = 62612.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.043200 restraints weight = 36694.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.044126 restraints weight = 25882.294| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.7311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9145 Z= 0.136 Angle : 0.728 9.082 12481 Z= 0.347 Chirality : 0.048 0.355 1519 Planarity : 0.004 0.051 1505 Dihedral : 7.928 105.290 1793 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.75 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -2.06 (0.25), residues: 1058 helix: 0.85 (0.31), residues: 294 sheet: -1.53 (0.30), residues: 275 loop : -2.73 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 475 HIS 0.003 0.001 HIS G 104 PHE 0.009 0.001 PHE A 196 TYR 0.022 0.002 TYR G 217 ARG 0.008 0.000 ARG G 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 16) link_NAG-ASN : angle 2.81132 ( 48) link_ALPHA1-6 : bond 0.01088 ( 1) link_ALPHA1-6 : angle 2.51459 ( 3) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.47425 ( 36) link_ALPHA1-2 : bond 0.00285 ( 1) link_ALPHA1-2 : angle 1.79497 ( 3) link_ALPHA1-3 : bond 0.01079 ( 1) link_ALPHA1-3 : angle 1.50315 ( 3) hydrogen bonds : bond 0.03832 ( 304) hydrogen bonds : angle 5.64021 ( 828) SS BOND : bond 0.00241 ( 12) SS BOND : angle 1.57981 ( 24) covalent geometry : bond 0.00292 ( 9100) covalent geometry : angle 0.69982 (12364) Misc. bond : bond 0.00064 ( 2) *********************** 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 109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.8123 (p90) cc_final: 0.7900 (p90) REVERT: G 101 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8152 (tp30) REVERT: G 103 MET cc_start: 0.8056 (mmp) cc_final: 0.7366 (mmp) REVERT: G 105 GLU cc_start: 0.8606 (pm20) cc_final: 0.7912 (pm20) REVERT: G 217 TYR cc_start: 0.8978 (m-80) cc_final: 0.8485 (m-10) REVERT: G 382 TYR cc_start: 0.9008 (m-10) cc_final: 0.8626 (m-10) REVERT: G 421 MET cc_start: 0.8337 (ptp) cc_final: 0.8083 (ptp) REVERT: G 476 ARG cc_start: 0.8955 (mtt90) cc_final: 0.8697 (mtt90) REVERT: G 480 TYR cc_start: 0.8877 (p90) cc_final: 0.8497 (p90) REVERT: A 235 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9146 (tm-30) REVERT: A 276 LEU cc_start: 0.9153 (tp) cc_final: 0.8930 (tp) REVERT: A 306 TRP cc_start: 0.7975 (m100) cc_final: 0.7684 (t-100) REVERT: B 2 ASP cc_start: 0.8411 (t0) cc_final: 0.8084 (t0) REVERT: B 33 LEU cc_start: 0.9561 (mt) cc_final: 0.9140 (mm) REVERT: B 37 TYR cc_start: 0.9199 (m-80) cc_final: 0.8970 (m-80) REVERT: B 43 PHE cc_start: 0.9283 (m-80) cc_final: 0.8755 (m-80) REVERT: B 74 ILE cc_start: 0.9462 (mt) cc_final: 0.9232 (tt) REVERT: B 161 LEU cc_start: 0.9211 (tt) cc_final: 0.8943 (mt) REVERT: B 176 TYR cc_start: 0.8701 (m-80) cc_final: 0.8425 (m-80) REVERT: B 261 GLN cc_start: 0.8880 (mm110) cc_final: 0.8536 (tm-30) REVERT: B 279 MET cc_start: 0.9056 (ptp) cc_final: 0.8760 (ptp) REVERT: B 287 MET cc_start: 0.9039 (mmp) cc_final: 0.8838 (mmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1953 time to fit residues: 31.3463 Evaluate side-chains 90 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 30 optimal weight: 0.0570 chunk 75 optimal weight: 0.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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** ** A 39 ASN ** 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 = 0.3428 r_free = 0.3428 target = 0.058856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.041262 restraints weight = 63422.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.042633 restraints weight = 36964.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.043508 restraints weight = 25991.323| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.7603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9145 Z= 0.154 Angle : 0.717 9.132 12481 Z= 0.343 Chirality : 0.047 0.351 1519 Planarity : 0.004 0.048 1505 Dihedral : 7.039 90.421 1793 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 1.02 (0.31), residues: 292 sheet: -1.41 (0.31), residues: 275 loop : -2.63 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 475 HIS 0.003 0.001 HIS B 289 PHE 0.017 0.002 PHE A 198 TYR 0.021 0.001 TYR G 217 ARG 0.008 0.001 ARG G 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 16) link_NAG-ASN : angle 2.76722 ( 48) link_ALPHA1-6 : bond 0.01057 ( 1) link_ALPHA1-6 : angle 2.74782 ( 3) link_BETA1-4 : bond 0.00322 ( 12) link_BETA1-4 : angle 1.53362 ( 36) link_ALPHA1-2 : bond 0.00248 ( 1) link_ALPHA1-2 : angle 2.08146 ( 3) link_ALPHA1-3 : bond 0.00667 ( 1) link_ALPHA1-3 : angle 1.45196 ( 3) hydrogen bonds : bond 0.03684 ( 304) hydrogen bonds : angle 5.49509 ( 828) SS BOND : bond 0.00276 ( 12) SS BOND : angle 1.35251 ( 24) covalent geometry : bond 0.00330 ( 9100) covalent geometry : angle 0.68973 (12364) Misc. bond : bond 0.00066 ( 2) *********************** 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 110 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 105 GLU cc_start: 0.8665 (pm20) cc_final: 0.8445 (pm20) REVERT: G 382 TYR cc_start: 0.9043 (m-10) cc_final: 0.8672 (m-10) REVERT: G 421 MET cc_start: 0.8303 (ptp) cc_final: 0.7981 (ptp) REVERT: G 480 TYR cc_start: 0.8945 (p90) cc_final: 0.8545 (p90) REVERT: A 235 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9123 (tm-30) REVERT: A 276 LEU cc_start: 0.9195 (tp) cc_final: 0.8981 (tp) REVERT: B 2 ASP cc_start: 0.8399 (t0) cc_final: 0.8068 (t0) REVERT: B 33 LEU cc_start: 0.9562 (mt) cc_final: 0.9159 (mm) REVERT: B 43 PHE cc_start: 0.9298 (m-80) cc_final: 0.8775 (m-80) REVERT: B 74 ILE cc_start: 0.9437 (mt) cc_final: 0.9225 (tt) REVERT: B 161 LEU cc_start: 0.9219 (tt) cc_final: 0.8933 (mt) REVERT: B 261 GLN cc_start: 0.8971 (mm110) cc_final: 0.8715 (tm-30) REVERT: B 279 MET cc_start: 0.8941 (ptp) cc_final: 0.8706 (ptp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2137 time to fit residues: 34.0986 Evaluate side-chains 88 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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: 0.6980 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 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 279 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.060113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.042341 restraints weight = 61283.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.043746 restraints weight = 35845.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.044681 restraints weight = 25101.061| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.7729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9145 Z= 0.118 Angle : 0.705 9.941 12481 Z= 0.335 Chirality : 0.048 0.337 1519 Planarity : 0.004 0.043 1505 Dihedral : 6.594 78.984 1793 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.81 (0.25), residues: 1058 helix: 1.08 (0.31), residues: 292 sheet: -1.33 (0.31), residues: 275 loop : -2.61 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 306 HIS 0.012 0.001 HIS B 175 PHE 0.024 0.001 PHE A 198 TYR 0.037 0.002 TYR B 37 ARG 0.007 0.000 ARG G 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 16) link_NAG-ASN : angle 2.60536 ( 48) link_ALPHA1-6 : bond 0.01068 ( 1) link_ALPHA1-6 : angle 3.07327 ( 3) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.41244 ( 36) link_ALPHA1-2 : bond 0.00241 ( 1) link_ALPHA1-2 : angle 1.87215 ( 3) link_ALPHA1-3 : bond 0.00731 ( 1) link_ALPHA1-3 : angle 1.39885 ( 3) hydrogen bonds : bond 0.03633 ( 304) hydrogen bonds : angle 5.36164 ( 828) SS BOND : bond 0.00367 ( 12) SS BOND : angle 1.88050 ( 24) covalent geometry : bond 0.00251 ( 9100) covalent geometry : angle 0.67706 (12364) Misc. bond : bond 0.00049 ( 2) *********************** 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 114 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.8131 (p90) cc_final: 0.7923 (p90) REVERT: G 101 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8234 (tp30) REVERT: G 105 GLU cc_start: 0.8645 (pm20) cc_final: 0.7954 (pm20) REVERT: G 260 LEU cc_start: 0.9631 (mm) cc_final: 0.9342 (mm) REVERT: G 382 TYR cc_start: 0.8978 (m-10) cc_final: 0.8608 (m-10) REVERT: G 421 MET cc_start: 0.8337 (ptp) cc_final: 0.8081 (ptp) REVERT: G 476 ARG cc_start: 0.8999 (mtt90) cc_final: 0.8674 (mtt90) REVERT: G 480 TYR cc_start: 0.8873 (p90) cc_final: 0.8465 (p90) REVERT: A 235 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9125 (tm-30) REVERT: A 276 LEU cc_start: 0.9137 (tp) cc_final: 0.8907 (tp) REVERT: B 2 ASP cc_start: 0.8288 (t0) cc_final: 0.7940 (t0) REVERT: B 43 PHE cc_start: 0.9263 (m-80) cc_final: 0.8742 (m-80) REVERT: B 74 ILE cc_start: 0.9426 (mt) cc_final: 0.9216 (tt) REVERT: B 161 LEU cc_start: 0.9226 (tt) cc_final: 0.8945 (mt) REVERT: B 176 TYR cc_start: 0.8855 (m-80) cc_final: 0.8650 (m-80) REVERT: B 261 GLN cc_start: 0.8919 (mm110) cc_final: 0.8504 (tm-30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2246 time to fit residues: 37.6402 Evaluate side-chains 87 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS B 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.059103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041684 restraints weight = 62682.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.043021 restraints weight = 36630.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.043900 restraints weight = 25729.729| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.7958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9145 Z= 0.154 Angle : 0.736 13.601 12481 Z= 0.346 Chirality : 0.048 0.347 1519 Planarity : 0.004 0.044 1505 Dihedral : 6.061 48.058 1793 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.47 % Favored : 92.44 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.79 % 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: -1.83 (0.25), residues: 1058 helix: 0.99 (0.31), residues: 292 sheet: -1.31 (0.31), residues: 276 loop : -2.60 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 306 HIS 0.003 0.001 HIS B 289 PHE 0.018 0.002 PHE A 198 TYR 0.021 0.002 TYR B 68 ARG 0.012 0.001 ARG G 486 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 16) link_NAG-ASN : angle 2.66322 ( 48) link_ALPHA1-6 : bond 0.01254 ( 1) link_ALPHA1-6 : angle 2.88798 ( 3) link_BETA1-4 : bond 0.00337 ( 12) link_BETA1-4 : angle 1.51980 ( 36) link_ALPHA1-2 : bond 0.00267 ( 1) link_ALPHA1-2 : angle 1.85128 ( 3) link_ALPHA1-3 : bond 0.00496 ( 1) link_ALPHA1-3 : angle 1.63323 ( 3) hydrogen bonds : bond 0.03648 ( 304) hydrogen bonds : angle 5.39160 ( 828) SS BOND : bond 0.00220 ( 12) SS BOND : angle 1.51113 ( 24) covalent geometry : bond 0.00332 ( 9100) covalent geometry : angle 0.71031 (12364) Misc. bond : bond 0.00052 ( 2) ********************** 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 108 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 101 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8218 (tp30) REVERT: G 105 GLU cc_start: 0.8666 (pm20) cc_final: 0.8027 (pm20) REVERT: G 217 TYR cc_start: 0.9059 (m-80) cc_final: 0.8525 (m-80) REVERT: G 382 TYR cc_start: 0.8956 (m-10) cc_final: 0.8590 (m-10) REVERT: G 421 MET cc_start: 0.8416 (ptp) cc_final: 0.8159 (ptp) REVERT: G 476 ARG cc_start: 0.9070 (mtt90) cc_final: 0.8616 (mtm-85) REVERT: G 480 TYR cc_start: 0.8925 (p90) cc_final: 0.8535 (p90) REVERT: A 235 GLU cc_start: 0.9476 (mt-10) cc_final: 0.9144 (tm-30) REVERT: A 276 LEU cc_start: 0.9127 (tp) cc_final: 0.8915 (tp) REVERT: B 2 ASP cc_start: 0.8363 (t0) cc_final: 0.8018 (t0) REVERT: B 43 PHE cc_start: 0.9262 (m-80) cc_final: 0.8761 (m-80) REVERT: B 74 ILE cc_start: 0.9432 (mt) cc_final: 0.9213 (tt) REVERT: B 161 LEU cc_start: 0.9233 (tt) cc_final: 0.8990 (mt) REVERT: B 255 LEU cc_start: 0.9679 (tt) cc_final: 0.9336 (mt) REVERT: B 261 GLN cc_start: 0.8990 (mm110) cc_final: 0.8737 (tm-30) REVERT: B 287 MET cc_start: 0.9148 (mmp) cc_final: 0.8887 (mmm) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.1856 time to fit residues: 29.1784 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 : 0.945 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.059208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.041590 restraints weight = 62916.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.042962 restraints weight = 36394.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043835 restraints weight = 25435.797| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.8126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9145 Z= 0.138 Angle : 0.719 9.328 12481 Z= 0.340 Chirality : 0.047 0.340 1519 Planarity : 0.004 0.047 1505 Dihedral : 5.677 47.708 1793 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.76 (0.25), residues: 1058 helix: 1.08 (0.31), residues: 292 sheet: -1.26 (0.31), residues: 275 loop : -2.59 (0.24), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 306 HIS 0.003 0.001 HIS B 289 PHE 0.014 0.001 PHE A 198 TYR 0.017 0.002 TYR B 251 ARG 0.006 0.001 ARG G 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 16) link_NAG-ASN : angle 2.60848 ( 48) link_ALPHA1-6 : bond 0.01074 ( 1) link_ALPHA1-6 : angle 1.60625 ( 3) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 1.46280 ( 36) link_ALPHA1-2 : bond 0.00231 ( 1) link_ALPHA1-2 : angle 1.82594 ( 3) link_ALPHA1-3 : bond 0.00301 ( 1) link_ALPHA1-3 : angle 1.48396 ( 3) hydrogen bonds : bond 0.03626 ( 304) hydrogen bonds : angle 5.26435 ( 828) SS BOND : bond 0.00194 ( 12) SS BOND : angle 1.36105 ( 24) covalent geometry : bond 0.00298 ( 9100) covalent geometry : angle 0.69576 (12364) Misc. bond : bond 0.00053 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4126.11 seconds wall clock time: 78 minutes 18.67 seconds (4698.67 seconds total)