Starting phenix.real_space_refine on Wed Sep 17 18:47:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6met_9109/09_2025/6met_9109.cif Found real_map, /net/cci-nas-00/data/ceres_data/6met_9109/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2025/6met_9109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2025/6met_9109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2025/6met_9109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2025/6met_9109.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG: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: 2.59, per 1000 atoms: 0.29 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: 1.22 Conformation dependent library (CDL) restraints added in 345.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.24 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: 1.17 Time building geometry restraints manager: 1.51 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 140 TYR 0.015 0.002 TYR B 3 PHE 0.029 0.002 PHE G 380 TRP 0.034 0.002 TRP B 86 HIS 0.004 0.001 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00679 ( 9100) covalent geometry : angle 1.07971 (12364) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.46525 ( 24) hydrogen bonds : bond 0.28718 ( 304) hydrogen bonds : angle 10.30008 ( 828) Misc. bond : bond 0.41293 ( 2) 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) 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_NAG-ASN : bond 0.12010 ( 16) link_NAG-ASN : angle 6.66349 ( 48) *********************** 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 : 0.333 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: 0.1034 time to fit residues: 39.0526 Evaluate side-chains 152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 2.5504 ------------------------------------------------------------------------------- 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 231 HIS B 252 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.066293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.047670 restraints weight = 56953.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.049197 restraints weight = 33881.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.050226 restraints weight = 23921.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050858 restraints weight = 18808.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051325 restraints weight = 16061.774| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9145 Z= 0.217 Angle : 0.847 9.190 12481 Z= 0.416 Chirality : 0.050 0.394 1519 Planarity : 0.006 0.100 1505 Dihedral : 11.659 110.884 1793 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.23), residues: 1058 helix: -0.17 (0.29), residues: 295 sheet: -2.00 (0.31), residues: 231 loop : -3.28 (0.22), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 60 TYR 0.030 0.002 TYR B 37 PHE 0.016 0.002 PHE A 198 TRP 0.017 0.002 TRP G 95 HIS 0.009 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9100) covalent geometry : angle 0.81517 (12364) SS BOND : bond 0.00311 ( 12) SS BOND : angle 0.98869 ( 24) hydrogen bonds : bond 0.05198 ( 304) hydrogen bonds : angle 6.75218 ( 828) Misc. bond : bond 0.00127 ( 2) link_ALPHA1-2 : bond 0.00782 ( 1) link_ALPHA1-2 : angle 3.04396 ( 3) link_ALPHA1-3 : bond 0.00945 ( 1) link_ALPHA1-3 : angle 2.24201 ( 3) link_ALPHA1-6 : bond 0.00379 ( 1) link_ALPHA1-6 : angle 2.69483 ( 3) link_BETA1-4 : bond 0.00469 ( 12) link_BETA1-4 : angle 2.03436 ( 36) link_NAG-ASN : bond 0.00538 ( 16) link_NAG-ASN : angle 3.23932 ( 48) *********************** 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 : 0.304 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: 0.9371 (mp) cc_final: 0.9073 (mp) REVERT: G 210 PHE cc_start: 0.7871 (t80) cc_final: 0.6970 (t80) REVERT: G 290 ASP cc_start: 0.8954 (t70) cc_final: 0.8574 (t0) REVERT: G 480 TYR cc_start: 0.8464 (p90) cc_final: 0.8254 (p90) REVERT: A 37 LEU cc_start: 0.9609 (tp) cc_final: 0.9240 (tp) REVERT: A 53 ASP cc_start: 0.8429 (m-30) cc_final: 0.8010 (p0) REVERT: A 97 VAL cc_start: 0.8472 (t) cc_final: 0.8214 (t) REVERT: A 279 LYS cc_start: 0.8727 (tptm) cc_final: 0.8512 (ttpp) REVERT: B 2 ASP cc_start: 0.8046 (t0) cc_final: 0.7842 (t0) REVERT: B 33 LEU cc_start: 0.9348 (mt) cc_final: 0.8969 (mm) REVERT: B 40 VAL cc_start: 0.9772 (t) cc_final: 0.9462 (t) REVERT: B 86 TRP cc_start: 0.9264 (m100) cc_final: 0.9047 (m100) REVERT: B 108 TYR cc_start: 0.9098 (t80) cc_final: 0.8783 (t80) REVERT: B 112 PHE cc_start: 0.8941 (t80) cc_final: 0.8689 (t80) REVERT: B 287 MET cc_start: 0.9207 (mmp) cc_final: 0.8828 (mmm) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0860 time to fit residues: 19.6122 Evaluate side-chains 108 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.066217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047317 restraints weight = 57206.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048860 restraints weight = 34111.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.049842 restraints weight = 24172.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050550 restraints weight = 19181.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.050971 restraints weight = 16372.530| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4670 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= 0.138 Angle : 0.725 9.930 12481 Z= 0.350 Chirality : 0.048 0.394 1519 Planarity : 0.005 0.066 1505 Dihedral : 10.134 108.506 1793 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.24), residues: 1058 helix: 0.29 (0.31), residues: 294 sheet: -1.70 (0.31), residues: 245 loop : -3.10 (0.22), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 313 TYR 0.023 0.002 TYR B 37 PHE 0.013 0.001 PHE G 315 TRP 0.012 0.001 TRP B 94 HIS 0.006 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9100) covalent geometry : angle 0.69323 (12364) SS BOND : bond 0.00234 ( 12) SS BOND : angle 1.48230 ( 24) hydrogen bonds : bond 0.04585 ( 304) hydrogen bonds : angle 6.13790 ( 828) Misc. bond : bond 0.00071 ( 2) link_ALPHA1-2 : bond 0.00580 ( 1) link_ALPHA1-2 : angle 2.45306 ( 3) link_ALPHA1-3 : bond 0.01175 ( 1) link_ALPHA1-3 : angle 1.89925 ( 3) link_ALPHA1-6 : bond 0.01234 ( 1) link_ALPHA1-6 : angle 2.97582 ( 3) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 1.72254 ( 36) link_NAG-ASN : bond 0.00414 ( 16) link_NAG-ASN : angle 2.86987 ( 48) *********************** 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 154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.9335 (mp) cc_final: 0.8707 (mp) REVERT: G 259 LEU cc_start: 0.9393 (mt) cc_final: 0.9158 (tt) REVERT: G 290 ASP cc_start: 0.8895 (t70) cc_final: 0.8515 (t0) REVERT: G 379 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8373 (mm-30) REVERT: G 421 MET cc_start: 0.8430 (ptp) cc_final: 0.8032 (ptp) REVERT: G 480 TYR cc_start: 0.8501 (p90) cc_final: 0.8246 (p90) REVERT: A 37 LEU cc_start: 0.9600 (tp) cc_final: 0.9225 (tp) REVERT: A 53 ASP cc_start: 0.8385 (m-30) cc_final: 0.8161 (p0) REVERT: A 97 VAL cc_start: 0.8620 (t) cc_final: 0.8415 (t) REVERT: A 279 LYS cc_start: 0.8806 (tptm) cc_final: 0.8471 (mtmm) REVERT: B 2 ASP cc_start: 0.8053 (t0) cc_final: 0.7811 (t0) REVERT: B 33 LEU cc_start: 0.9561 (mt) cc_final: 0.9059 (mm) REVERT: B 37 TYR cc_start: 0.9153 (m-80) cc_final: 0.8857 (m-80) REVERT: B 251 TYR cc_start: 0.9057 (t80) cc_final: 0.8697 (t80) REVERT: B 279 MET cc_start: 0.8871 (ptp) cc_final: 0.8438 (ptt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0904 time to fit residues: 19.8234 Evaluate side-chains 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 0.3980 chunk 79 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 ASN G 279 ASN ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN A 284 HIS B 231 HIS B 267 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.062610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.044221 restraints weight = 60884.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.045658 restraints weight = 36333.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.046608 restraints weight = 25799.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047242 restraints weight = 20542.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047622 restraints weight = 17618.842| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9145 Z= 0.195 Angle : 0.747 7.943 12481 Z= 0.366 Chirality : 0.049 0.378 1519 Planarity : 0.005 0.050 1505 Dihedral : 8.985 110.784 1793 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.75 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.24), residues: 1058 helix: 0.37 (0.30), residues: 293 sheet: -1.59 (0.32), residues: 253 loop : -2.94 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 486 TYR 0.037 0.002 TYR G 217 PHE 0.013 0.002 PHE B 109 TRP 0.016 0.002 TRP G 34 HIS 0.012 0.002 HIS G 71 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9100) covalent geometry : angle 0.71743 (12364) SS BOND : bond 0.00415 ( 12) SS BOND : angle 1.49724 ( 24) hydrogen bonds : bond 0.04219 ( 304) hydrogen bonds : angle 5.91199 ( 828) Misc. bond : bond 0.00088 ( 2) link_ALPHA1-2 : bond 0.00847 ( 1) link_ALPHA1-2 : angle 1.95286 ( 3) link_ALPHA1-3 : bond 0.00947 ( 1) link_ALPHA1-3 : angle 1.82871 ( 3) link_ALPHA1-6 : bond 0.01544 ( 1) link_ALPHA1-6 : angle 3.28074 ( 3) link_BETA1-4 : bond 0.00426 ( 12) link_BETA1-4 : angle 1.69096 ( 36) link_NAG-ASN : bond 0.00431 ( 16) link_NAG-ASN : angle 2.86417 ( 48) *********************** 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 129 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7846 (p90) cc_final: 0.7644 (p90) REVERT: G 99 MET cc_start: 0.9061 (ptp) cc_final: 0.8735 (ptt) REVERT: G 103 MET cc_start: 0.7979 (mmp) cc_final: 0.6962 (mmp) REVERT: G 115 LEU cc_start: 0.9286 (mp) cc_final: 0.9065 (mp) REVERT: G 217 TYR cc_start: 0.8190 (m-10) cc_final: 0.7842 (m-10) REVERT: G 375 ASN cc_start: 0.8444 (t0) cc_final: 0.7892 (t0) REVERT: G 379 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8495 (mm-30) REVERT: G 480 TYR cc_start: 0.8786 (p90) cc_final: 0.8452 (p90) REVERT: A 279 LYS cc_start: 0.8723 (tptm) cc_final: 0.8449 (mtpt) REVERT: A 323 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7427 (pm20) REVERT: B 2 ASP cc_start: 0.8187 (t0) cc_final: 0.7869 (t0) REVERT: B 33 LEU cc_start: 0.9563 (mt) cc_final: 0.9183 (mm) REVERT: B 37 TYR cc_start: 0.9146 (m-80) cc_final: 0.8885 (m-80) REVERT: B 43 PHE cc_start: 0.9268 (m-10) cc_final: 0.9056 (m-80) REVERT: B 261 GLN cc_start: 0.8792 (mm110) cc_final: 0.8336 (tm-30) REVERT: B 287 MET cc_start: 0.9088 (mmp) cc_final: 0.8809 (mmm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0822 time to fit residues: 15.7052 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 30.0000 chunk 89 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 ASN G 279 ASN ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 231 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.060409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.042304 restraints weight = 60465.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.043696 restraints weight = 36164.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.044624 restraints weight = 25713.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045240 restraints weight = 20401.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.045582 restraints weight = 17456.733| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9145 Z= 0.226 Angle : 0.789 10.841 12481 Z= 0.382 Chirality : 0.050 0.391 1519 Planarity : 0.005 0.048 1505 Dihedral : 8.661 112.501 1793 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.56 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.25), residues: 1058 helix: 0.55 (0.30), residues: 291 sheet: -1.54 (0.31), residues: 275 loop : -2.84 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 131 TYR 0.024 0.002 TYR B 176 PHE 0.014 0.002 PHE G 92 TRP 0.026 0.002 TRP G 475 HIS 0.018 0.002 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 9100) covalent geometry : angle 0.75518 (12364) SS BOND : bond 0.00455 ( 12) SS BOND : angle 1.36380 ( 24) hydrogen bonds : bond 0.04018 ( 304) hydrogen bonds : angle 5.86322 ( 828) Misc. bond : bond 0.00095 ( 2) link_ALPHA1-2 : bond 0.00152 ( 1) link_ALPHA1-2 : angle 1.92053 ( 3) link_ALPHA1-3 : bond 0.00874 ( 1) link_ALPHA1-3 : angle 1.97198 ( 3) link_ALPHA1-6 : bond 0.01363 ( 1) link_ALPHA1-6 : angle 3.07914 ( 3) link_BETA1-4 : bond 0.00363 ( 12) link_BETA1-4 : angle 1.59973 ( 36) link_NAG-ASN : bond 0.00474 ( 16) link_NAG-ASN : angle 3.30894 ( 48) *********************** 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 117 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7880 (p90) cc_final: 0.7666 (p90) REVERT: G 115 LEU cc_start: 0.9340 (mp) cc_final: 0.8984 (mp) REVERT: G 379 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8575 (mm-30) REVERT: G 421 MET cc_start: 0.8527 (ptp) cc_final: 0.8141 (ptp) REVERT: G 480 TYR cc_start: 0.8964 (p90) cc_final: 0.8612 (p90) REVERT: B 2 ASP cc_start: 0.8371 (t0) cc_final: 0.8002 (t0) REVERT: B 33 LEU cc_start: 0.9570 (mt) cc_final: 0.9117 (mm) REVERT: B 37 TYR cc_start: 0.9156 (m-80) cc_final: 0.8944 (m-80) REVERT: B 43 PHE cc_start: 0.9233 (m-10) cc_final: 0.8939 (m-80) REVERT: B 161 LEU cc_start: 0.9186 (tt) cc_final: 0.8930 (mt) REVERT: B 251 TYR cc_start: 0.9125 (t80) cc_final: 0.8860 (t80) REVERT: B 261 GLN cc_start: 0.8893 (mm110) cc_final: 0.8479 (tm-30) REVERT: B 279 MET cc_start: 0.8981 (ptp) cc_final: 0.8459 (ptp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0730 time to fit residues: 13.1055 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 : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 54 optimal weight: 0.0070 chunk 89 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 48 optimal weight: 8.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 ASN G 279 ASN ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.062455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.044219 restraints weight = 58617.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.045626 restraints weight = 35442.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.046559 restraints weight = 25284.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047167 restraints weight = 20131.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047547 restraints weight = 17280.239| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9145 Z= 0.124 Angle : 0.711 12.934 12481 Z= 0.341 Chirality : 0.048 0.365 1519 Planarity : 0.004 0.040 1505 Dihedral : 8.038 107.113 1793 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 0.11 % Allowed : 2.00 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.25), residues: 1058 helix: 0.78 (0.31), residues: 292 sheet: -1.40 (0.32), residues: 268 loop : -2.75 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 304 TYR 0.042 0.002 TYR G 217 PHE 0.012 0.001 PHE B 245 TRP 0.011 0.001 TRP G 475 HIS 0.004 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9100) covalent geometry : angle 0.68354 (12364) SS BOND : bond 0.00280 ( 12) SS BOND : angle 1.61277 ( 24) hydrogen bonds : bond 0.03760 ( 304) hydrogen bonds : angle 5.54002 ( 828) Misc. bond : bond 0.00052 ( 2) link_ALPHA1-2 : bond 0.00016 ( 1) link_ALPHA1-2 : angle 1.72893 ( 3) link_ALPHA1-3 : bond 0.00794 ( 1) link_ALPHA1-3 : angle 1.16768 ( 3) link_ALPHA1-6 : bond 0.01723 ( 1) link_ALPHA1-6 : angle 2.93063 ( 3) link_BETA1-4 : bond 0.00402 ( 12) link_BETA1-4 : angle 1.36335 ( 36) link_NAG-ASN : bond 0.00431 ( 16) link_NAG-ASN : angle 2.74455 ( 48) *********************** 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 125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7918 (p90) cc_final: 0.7704 (p90) REVERT: G 115 LEU cc_start: 0.9161 (mp) cc_final: 0.8825 (mp) REVERT: G 379 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8597 (mm-30) REVERT: G 421 MET cc_start: 0.8407 (ptp) cc_final: 0.8194 (ptp) REVERT: G 449 LEU cc_start: 0.9574 (mm) cc_final: 0.8919 (tp) REVERT: G 480 TYR cc_start: 0.8800 (p90) cc_final: 0.8459 (p90) REVERT: A 74 LEU cc_start: 0.9314 (mt) cc_final: 0.9049 (mt) REVERT: A 276 LEU cc_start: 0.8839 (tp) cc_final: 0.8568 (tp) REVERT: A 323 GLU cc_start: 0.7457 (tm-30) cc_final: 0.5928 (pm20) REVERT: B 2 ASP cc_start: 0.8256 (t0) cc_final: 0.7957 (t0) REVERT: B 33 LEU cc_start: 0.9560 (mt) cc_final: 0.9117 (mm) REVERT: B 43 PHE cc_start: 0.9212 (m-10) cc_final: 0.8879 (m-80) REVERT: B 74 ILE cc_start: 0.9447 (mt) cc_final: 0.9183 (tt) REVERT: B 161 LEU cc_start: 0.9196 (tt) cc_final: 0.8958 (mt) REVERT: B 176 TYR cc_start: 0.8612 (m-10) cc_final: 0.8356 (m-80) REVERT: B 190 TRP cc_start: 0.8721 (m-10) cc_final: 0.8369 (m-10) REVERT: B 261 GLN cc_start: 0.8827 (mm110) cc_final: 0.8309 (tm-30) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.0751 time to fit residues: 14.2100 Evaluate side-chains 99 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 279 ASN ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3473 r_free = 0.3473 target = 0.061010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.043013 restraints weight = 59369.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.044391 restraints weight = 35300.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045304 restraints weight = 24918.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.045941 restraints weight = 19703.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.046296 restraints weight = 16810.563| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.6885 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 : 0.709 11.025 12481 Z= 0.340 Chirality : 0.048 0.364 1519 Planarity : 0.004 0.059 1505 Dihedral : 7.497 102.691 1793 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.25), residues: 1058 helix: 0.83 (0.30), residues: 291 sheet: -1.29 (0.32), residues: 274 loop : -2.70 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 304 TYR 0.045 0.002 TYR B 37 PHE 0.015 0.001 PHE A 198 TRP 0.014 0.001 TRP G 475 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9100) covalent geometry : angle 0.68241 (12364) SS BOND : bond 0.00327 ( 12) SS BOND : angle 1.49958 ( 24) hydrogen bonds : bond 0.03720 ( 304) hydrogen bonds : angle 5.46694 ( 828) Misc. bond : bond 0.00058 ( 2) link_ALPHA1-2 : bond 0.00130 ( 1) link_ALPHA1-2 : angle 1.78926 ( 3) link_ALPHA1-3 : bond 0.00858 ( 1) link_ALPHA1-3 : angle 1.54034 ( 3) link_ALPHA1-6 : bond 0.01055 ( 1) link_ALPHA1-6 : angle 2.33575 ( 3) link_BETA1-4 : bond 0.00340 ( 12) link_BETA1-4 : angle 1.48288 ( 36) link_NAG-ASN : bond 0.00375 ( 16) link_NAG-ASN : angle 2.72038 ( 48) *********************** 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 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7941 (p90) cc_final: 0.7729 (p90) REVERT: G 210 PHE cc_start: 0.8268 (t80) cc_final: 0.8015 (t80) REVERT: G 375 ASN cc_start: 0.8467 (t0) cc_final: 0.8054 (t0) REVERT: G 382 TYR cc_start: 0.8748 (m-10) cc_final: 0.8416 (m-10) REVERT: G 447 LEU cc_start: 0.9123 (mt) cc_final: 0.8908 (mt) REVERT: G 449 LEU cc_start: 0.9623 (mm) cc_final: 0.8943 (tp) REVERT: G 480 TYR cc_start: 0.8906 (p90) cc_final: 0.8518 (p90) REVERT: A 114 LEU cc_start: 0.8852 (tp) cc_final: 0.8522 (mt) REVERT: A 276 LEU cc_start: 0.8873 (tp) cc_final: 0.8610 (tp) REVERT: A 323 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6018 (pm20) REVERT: B 2 ASP cc_start: 0.8482 (t0) cc_final: 0.8168 (t0) REVERT: B 43 PHE cc_start: 0.9190 (m-10) cc_final: 0.8835 (m-80) REVERT: B 74 ILE cc_start: 0.9450 (mt) cc_final: 0.9230 (tt) REVERT: B 161 LEU cc_start: 0.9197 (tt) cc_final: 0.8934 (mt) REVERT: B 176 TYR cc_start: 0.8741 (m-10) cc_final: 0.8438 (m-80) REVERT: B 251 TYR cc_start: 0.9126 (t80) cc_final: 0.8872 (t80) REVERT: B 261 GLN cc_start: 0.8876 (mm110) cc_final: 0.8307 (tm-30) REVERT: B 279 MET cc_start: 0.8853 (ptp) cc_final: 0.8497 (ptp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0783 time to fit residues: 13.3970 Evaluate side-chains 89 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 279 ASN ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3461 r_free = 0.3461 target = 0.060397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.042402 restraints weight = 62436.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.043826 restraints weight = 36390.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.044745 restraints weight = 25486.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045368 restraints weight = 20185.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.045718 restraints weight = 17259.381| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9145 Z= 0.160 Angle : 0.714 10.380 12481 Z= 0.340 Chirality : 0.048 0.362 1519 Planarity : 0.004 0.058 1505 Dihedral : 6.678 82.376 1793 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.37 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.25), residues: 1058 helix: 0.85 (0.30), residues: 293 sheet: -1.33 (0.31), residues: 269 loop : -2.59 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 304 TYR 0.021 0.002 TYR G 217 PHE 0.017 0.001 PHE A 198 TRP 0.020 0.001 TRP G 475 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9100) covalent geometry : angle 0.68687 (12364) SS BOND : bond 0.00313 ( 12) SS BOND : angle 1.64091 ( 24) hydrogen bonds : bond 0.03651 ( 304) hydrogen bonds : angle 5.36559 ( 828) Misc. bond : bond 0.00062 ( 2) link_ALPHA1-2 : bond 0.00212 ( 1) link_ALPHA1-2 : angle 1.77113 ( 3) link_ALPHA1-3 : bond 0.00783 ( 1) link_ALPHA1-3 : angle 1.39357 ( 3) link_ALPHA1-6 : bond 0.01291 ( 1) link_ALPHA1-6 : angle 3.13243 ( 3) link_BETA1-4 : bond 0.00338 ( 12) link_BETA1-4 : angle 1.47518 ( 36) link_NAG-ASN : bond 0.00368 ( 16) link_NAG-ASN : angle 2.68181 ( 48) *********************** 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 : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7946 (p90) cc_final: 0.7737 (p90) REVERT: G 115 LEU cc_start: 0.9161 (mp) cc_final: 0.8810 (mp) REVERT: G 382 TYR cc_start: 0.8788 (m-10) cc_final: 0.8502 (m-10) REVERT: G 421 MET cc_start: 0.8715 (ptp) cc_final: 0.8298 (pmm) REVERT: G 447 LEU cc_start: 0.9273 (mt) cc_final: 0.9043 (mt) REVERT: G 480 TYR cc_start: 0.8941 (p90) cc_final: 0.8552 (p90) REVERT: A 276 LEU cc_start: 0.8983 (tp) cc_final: 0.8727 (tp) REVERT: A 323 GLU cc_start: 0.7449 (tm-30) cc_final: 0.5964 (pm20) REVERT: B 2 ASP cc_start: 0.8528 (t0) cc_final: 0.8209 (t0) REVERT: B 33 LEU cc_start: 0.9499 (mm) cc_final: 0.9014 (mm) REVERT: B 43 PHE cc_start: 0.9197 (m-10) cc_final: 0.8854 (m-80) REVERT: B 74 ILE cc_start: 0.9425 (mt) cc_final: 0.9221 (tt) REVERT: B 161 LEU cc_start: 0.9167 (tt) cc_final: 0.8902 (mt) REVERT: B 176 TYR cc_start: 0.8715 (m-10) cc_final: 0.8394 (m-80) REVERT: B 251 TYR cc_start: 0.9261 (t80) cc_final: 0.8956 (t80) REVERT: B 261 GLN cc_start: 0.8905 (mm110) cc_final: 0.8428 (tm-30) REVERT: B 279 MET cc_start: 0.8878 (ptp) cc_final: 0.8562 (ptp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0778 time to fit residues: 12.8118 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.060901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.042899 restraints weight = 59035.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.044244 restraints weight = 35610.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045122 restraints weight = 25343.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.045743 restraints weight = 20223.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.046126 restraints weight = 17369.756| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.7416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9145 Z= 0.129 Angle : 0.719 11.232 12481 Z= 0.341 Chirality : 0.047 0.353 1519 Planarity : 0.004 0.055 1505 Dihedral : 6.190 62.291 1793 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.25), residues: 1058 helix: 0.90 (0.30), residues: 294 sheet: -1.27 (0.31), residues: 270 loop : -2.55 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 304 TYR 0.020 0.002 TYR G 217 PHE 0.017 0.001 PHE A 198 TRP 0.017 0.001 TRP A 306 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9100) covalent geometry : angle 0.69283 (12364) SS BOND : bond 0.00280 ( 12) SS BOND : angle 1.93710 ( 24) hydrogen bonds : bond 0.03588 ( 304) hydrogen bonds : angle 5.20478 ( 828) Misc. bond : bond 0.00048 ( 2) link_ALPHA1-2 : bond 0.00146 ( 1) link_ALPHA1-2 : angle 1.76997 ( 3) link_ALPHA1-3 : bond 0.00596 ( 1) link_ALPHA1-3 : angle 1.36172 ( 3) link_ALPHA1-6 : bond 0.01451 ( 1) link_ALPHA1-6 : angle 3.05191 ( 3) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.40680 ( 36) link_NAG-ASN : bond 0.00378 ( 16) link_NAG-ASN : angle 2.55905 ( 48) *********************** 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 107 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7872 (p90) cc_final: 0.7663 (p90) REVERT: G 382 TYR cc_start: 0.8732 (m-10) cc_final: 0.8421 (m-10) REVERT: G 421 MET cc_start: 0.8556 (ptp) cc_final: 0.8257 (pmm) REVERT: G 447 LEU cc_start: 0.9256 (mt) cc_final: 0.8798 (mt) REVERT: G 480 TYR cc_start: 0.8836 (p90) cc_final: 0.8466 (p90) REVERT: A 276 LEU cc_start: 0.8868 (tp) cc_final: 0.8617 (tp) REVERT: A 323 GLU cc_start: 0.7414 (tm-30) cc_final: 0.5862 (pm20) REVERT: B 2 ASP cc_start: 0.8425 (t0) cc_final: 0.8072 (t0) REVERT: B 33 LEU cc_start: 0.9461 (mm) cc_final: 0.8710 (pp) REVERT: B 43 PHE cc_start: 0.9176 (m-10) cc_final: 0.8828 (m-80) REVERT: B 74 ILE cc_start: 0.9413 (mt) cc_final: 0.9207 (tt) REVERT: B 161 LEU cc_start: 0.9142 (tt) cc_final: 0.8879 (mt) REVERT: B 176 TYR cc_start: 0.8672 (m-10) cc_final: 0.8315 (m-80) REVERT: B 251 TYR cc_start: 0.9215 (t80) cc_final: 0.8817 (t80) REVERT: B 261 GLN cc_start: 0.8846 (mm110) cc_final: 0.8321 (tm-30) REVERT: B 279 MET cc_start: 0.8824 (ptp) cc_final: 0.8444 (ptp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0774 time to fit residues: 12.7012 Evaluate side-chains 85 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 7.9990 chunk 73 optimal weight: 40.0000 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.059924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.042305 restraints weight = 60128.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.043672 restraints weight = 35564.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.044605 restraints weight = 24970.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045169 restraints weight = 19729.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.045590 restraints weight = 16939.357| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7664 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= 0.142 Angle : 0.699 9.894 12481 Z= 0.332 Chirality : 0.047 0.354 1519 Planarity : 0.004 0.053 1505 Dihedral : 5.605 48.114 1793 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.47 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.25), residues: 1058 helix: 0.85 (0.30), residues: 296 sheet: -1.15 (0.31), residues: 262 loop : -2.52 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 304 TYR 0.022 0.002 TYR G 217 PHE 0.014 0.001 PHE A 198 TRP 0.021 0.001 TRP A 306 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9100) covalent geometry : angle 0.67432 (12364) SS BOND : bond 0.00269 ( 12) SS BOND : angle 1.62393 ( 24) hydrogen bonds : bond 0.03601 ( 304) hydrogen bonds : angle 5.21654 ( 828) Misc. bond : bond 0.00049 ( 2) link_ALPHA1-2 : bond 0.00123 ( 1) link_ALPHA1-2 : angle 1.74219 ( 3) link_ALPHA1-3 : bond 0.00429 ( 1) link_ALPHA1-3 : angle 1.46543 ( 3) link_ALPHA1-6 : bond 0.00896 ( 1) link_ALPHA1-6 : angle 1.43927 ( 3) link_BETA1-4 : bond 0.00330 ( 12) link_BETA1-4 : angle 1.45776 ( 36) link_NAG-ASN : bond 0.00372 ( 16) link_NAG-ASN : angle 2.56711 ( 48) ********************** 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 106 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.8028 (p90) cc_final: 0.7825 (p90) REVERT: G 382 TYR cc_start: 0.8803 (m-10) cc_final: 0.8441 (m-10) REVERT: G 421 MET cc_start: 0.8637 (ptp) cc_final: 0.8314 (pmm) REVERT: G 447 LEU cc_start: 0.9355 (mt) cc_final: 0.8904 (mt) REVERT: G 480 TYR cc_start: 0.8935 (p90) cc_final: 0.8555 (p90) REVERT: A 276 LEU cc_start: 0.8968 (tp) cc_final: 0.8732 (tp) REVERT: A 323 GLU cc_start: 0.7415 (tm-30) cc_final: 0.5908 (pm20) REVERT: B 2 ASP cc_start: 0.8540 (t0) cc_final: 0.8243 (t0) REVERT: B 43 PHE cc_start: 0.9179 (m-10) cc_final: 0.8833 (m-80) REVERT: B 74 ILE cc_start: 0.9434 (mt) cc_final: 0.9202 (tt) REVERT: B 161 LEU cc_start: 0.9185 (tt) cc_final: 0.8918 (mt) REVERT: B 176 TYR cc_start: 0.8750 (m-10) cc_final: 0.8511 (m-80) REVERT: B 261 GLN cc_start: 0.8871 (mm110) cc_final: 0.8351 (tm-30) REVERT: B 287 MET cc_start: 0.9409 (mtm) cc_final: 0.8498 (ptp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0791 time to fit residues: 12.7308 Evaluate side-chains 80 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.059723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.042088 restraints weight = 59413.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.043445 restraints weight = 35292.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044354 restraints weight = 24920.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.044921 restraints weight = 19698.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.045331 restraints weight = 16888.683| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.7869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9145 Z= 0.142 Angle : 0.705 17.299 12481 Z= 0.333 Chirality : 0.047 0.353 1519 Planarity : 0.004 0.051 1505 Dihedral : 5.473 48.134 1793 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.25), residues: 1058 helix: 0.81 (0.30), residues: 297 sheet: -1.12 (0.31), residues: 264 loop : -2.46 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 304 TYR 0.020 0.002 TYR G 217 PHE 0.014 0.001 PHE A 198 TRP 0.023 0.001 TRP A 306 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9100) covalent geometry : angle 0.68158 (12364) SS BOND : bond 0.00242 ( 12) SS BOND : angle 1.36321 ( 24) hydrogen bonds : bond 0.03636 ( 304) hydrogen bonds : angle 5.16059 ( 828) Misc. bond : bond 0.00049 ( 2) link_ALPHA1-2 : bond 0.00128 ( 1) link_ALPHA1-2 : angle 1.74199 ( 3) link_ALPHA1-3 : bond 0.00213 ( 1) link_ALPHA1-3 : angle 1.62526 ( 3) link_ALPHA1-6 : bond 0.00754 ( 1) link_ALPHA1-6 : angle 1.39058 ( 3) link_BETA1-4 : bond 0.00317 ( 12) link_BETA1-4 : angle 1.44242 ( 36) link_NAG-ASN : bond 0.00382 ( 16) link_NAG-ASN : angle 2.55194 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.97 seconds wall clock time: 31 minutes 28.85 seconds (1888.85 seconds total)