Starting phenix.real_space_refine on Fri Sep 11 17:09:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6met_9109/09_2026/6met_9109.cif Found real_map, /net/cci-nas-00/data/ceres_data/6met_9109/09_2026/6met_9109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2026/6met_9109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2026/6met_9109.map" model { file = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2026/6met_9109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2026/6met_9109.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2026/6met_9109.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6met_9109/09_2026/6met_9109.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 1.46, per 1000 atoms: 0.16 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: 0.78 Conformation dependent library (CDL) restraints added in 283.4 milliseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 30.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 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: 1.12 Time building geometry restraints manager: 1.02 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 - 17.20: 4983 17.20 - 34.40: 174 34.40 - 51.60: 40 51.60 - 68.80: 8 68.80 - 86.00: 7 Dihedral angle restraints: 5212 sinusoidal: 2089 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 5209 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.440 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5361 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 : 9.953 75.515 3150 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 are 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/Z covalent geometry : bond 0.00679 / 0.37 ( 9100) covalent geometry : angle 1.07971 / 0.58 (12364) SS BOND : bond 0.00312 / 0.22 ( 12) SS BOND : angle 1.46525 / 0.92 ( 24) hydrogen bonds : bond 0.28718 / 18.81 ( 304) hydrogen bonds : angle 10.30008 / 7.11 ( 828) Misc. bond : bond 0.41293 / 20.83 ( 2) link_ALPHA1-2 : bond 0.00372 / 0.20 ( 1) link_ALPHA1-2 : angle 2.76447 / 2.11 ( 3) link_ALPHA1-3 : bond 0.00682 / 0.36 ( 1) link_ALPHA1-3 : angle 1.10851 / 0.96 ( 3) link_ALPHA1-6 : bond 0.00458 / 0.24 ( 1) link_ALPHA1-6 : angle 1.11768 / 0.77 ( 3) link_BETA1-4 : bond 0.00604 / 0.43 ( 12) link_BETA1-4 : angle 2.17695 / 1.22 ( 36) link_NAG-ASN : bond 0.12010 / 9.37 ( 16) link_NAG-ASN : angle 6.66349 / 5.44 ( 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 : 0.206 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: 0.8392 (mm) REVERT: G 487 ILE cc_start: 0.3812 (OUTLIER) cc_final: 0.2332 (pt) REVERT: A 156 THR cc_start: 0.8504 (p) cc_final: 0.7838 (p) REVERT: B 33 LEU cc_start: 0.6199 (mt) cc_final: 0.3941 (mm) REVERT: B 68 TYR cc_start: 0.5832 (m-10) cc_final: 0.5608 (m-10) REVERT: B 117 PHE cc_start: 0.7372 (m-10) cc_final: 0.6889 (m-80) REVERT: B 285 LEU cc_start: 0.7304 (tp) cc_final: 0.7044 (tp) outliers start: 13 outliers final: 2 residues processed: 283 average time/residue: 0.0923 time to fit residues: 35.0330 Evaluate side-chains 155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 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: 9.9990 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... ** 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 148 GLN A 163 GLN A 358 ASN B 93 GLN B 231 HIS B 252 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.066631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048080 restraints weight = 56360.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.049624 restraints weight = 33605.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.050600 restraints weight = 23678.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.051324 restraints weight = 18712.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.051731 restraints weight = 15838.848| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9145 Z= 0.220 Angle : 0.833 9.605 12481 Z= 0.415 Chirality : 0.050 0.370 1519 Planarity : 0.006 0.110 1505 Dihedral : 5.520 60.621 1133 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.23), residues: 1058 helix: -0.22 (0.29), residues: 295 sheet: -1.95 (0.31), residues: 225 loop : -3.30 (0.21), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 304 TYR 0.026 0.002 TYR B 37 PHE 0.016 0.002 PHE G 380 TRP 0.019 0.002 TRP G 95 HIS 0.009 0.001 HIS G 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 ( 9100) covalent geometry : angle 0.80411 / 0.41 (12364) SS BOND : bond 0.01201 / 0.77 ( 12) SS BOND : angle 0.85857 / 0.54 ( 24) hydrogen bonds : bond 0.05800 / 3.77 ( 304) hydrogen bonds : angle 6.88430 / 4.76 ( 828) Misc. bond : bond 0.00106 / 0.06 ( 2) link_ALPHA1-2 : bond 0.00546 / 0.29 ( 1) link_ALPHA1-2 : angle 2.81025 / 1.93 ( 3) link_ALPHA1-3 : bond 0.00931 / 0.49 ( 1) link_ALPHA1-3 : angle 1.58838 / 1.08 ( 3) link_ALPHA1-6 : bond 0.00425 / 0.22 ( 1) link_ALPHA1-6 : angle 1.39561 / 1.04 ( 3) link_BETA1-4 : bond 0.00516 / 0.33 ( 12) link_BETA1-4 : angle 1.68770 / 1.11 ( 36) link_NAG-ASN : bond 0.00470 / 0.24 ( 16) link_NAG-ASN : angle 3.25247 / 2.19 ( 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 163 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.340 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: 0.9384 (mp) cc_final: 0.9107 (mp) REVERT: G 210 PHE cc_start: 0.7925 (t80) cc_final: 0.7097 (t80) REVERT: G 259 LEU cc_start: 0.9309 (mt) cc_final: 0.9065 (tt) REVERT: G 290 ASP cc_start: 0.8930 (t70) cc_final: 0.8574 (t0) REVERT: G 480 TYR cc_start: 0.8673 (p90) cc_final: 0.8415 (p90) REVERT: A 37 LEU cc_start: 0.9608 (tp) cc_final: 0.9269 (tp) REVERT: A 53 ASP cc_start: 0.8441 (m-30) cc_final: 0.7994 (p0) REVERT: A 86 VAL cc_start: 0.8811 (m) cc_final: 0.8555 (m) REVERT: A 97 VAL cc_start: 0.8473 (t) cc_final: 0.8228 (t) REVERT: A 279 LYS cc_start: 0.8365 (tptm) cc_final: 0.8137 (ttpp) REVERT: B 33 LEU cc_start: 0.9351 (mt) cc_final: 0.8961 (mm) REVERT: B 37 TYR cc_start: 0.9033 (m-10) cc_final: 0.8786 (m-80) REVERT: B 40 VAL cc_start: 0.9775 (t) cc_final: 0.9508 (t) REVERT: B 86 TRP cc_start: 0.9235 (m100) cc_final: 0.9030 (m100) REVERT: B 112 PHE cc_start: 0.8946 (t80) cc_final: 0.8661 (t80) REVERT: B 251 TYR cc_start: 0.9327 (t80) cc_final: 0.9063 (t80) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0799 time to fit residues: 18.8601 Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.066185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.047334 restraints weight = 57475.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.048872 restraints weight = 34361.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.049933 restraints weight = 24243.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.050636 restraints weight = 19208.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.050979 restraints weight = 16359.771| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9145 Z= 0.140 Angle : 0.706 9.805 12481 Z= 0.345 Chirality : 0.046 0.345 1519 Planarity : 0.005 0.067 1505 Dihedral : 5.248 57.345 1133 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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 are not related in a simple way. whole: -2.72 (0.24), residues: 1058 helix: 0.23 (0.31), residues: 296 sheet: -1.71 (0.32), residues: 226 loop : -3.15 (0.21), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 334 TYR 0.022 0.002 TYR G 223 PHE 0.013 0.001 PHE A 198 TRP 0.012 0.001 TRP B 94 HIS 0.005 0.001 HIS G 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 9100) covalent geometry : angle 0.67819 / 0.34 (12364) SS BOND : bond 0.00356 / 0.21 ( 12) SS BOND : angle 1.29578 / 0.77 ( 24) hydrogen bonds : bond 0.04676 / 3.02 ( 304) hydrogen bonds : angle 6.16213 / 4.27 ( 828) Misc. bond : bond 0.00087 / 0.05 ( 2) link_ALPHA1-2 : bond 0.00538 / 0.28 ( 1) link_ALPHA1-2 : angle 2.29896 / 1.62 ( 3) link_ALPHA1-3 : bond 0.00701 / 0.37 ( 1) link_ALPHA1-3 : angle 1.54072 / 1.15 ( 3) link_ALPHA1-6 : bond 0.00432 / 0.23 ( 1) link_ALPHA1-6 : angle 1.26192 / 0.94 ( 3) link_BETA1-4 : bond 0.00332 / 0.21 ( 12) link_BETA1-4 : angle 1.45908 / 0.95 ( 36) link_NAG-ASN : bond 0.00391 / 0.20 ( 16) link_NAG-ASN : angle 2.83605 / 1.89 ( 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 : 0.344 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: 0.9339 (mp) cc_final: 0.8687 (mp) REVERT: G 290 ASP cc_start: 0.8913 (t70) cc_final: 0.8512 (t0) REVERT: G 379 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8398 (mm-30) REVERT: G 421 MET cc_start: 0.8508 (ptp) cc_final: 0.8100 (ptp) REVERT: A 37 LEU cc_start: 0.9614 (tp) cc_final: 0.9232 (tp) REVERT: A 53 ASP cc_start: 0.8396 (m-30) cc_final: 0.8120 (p0) REVERT: A 86 VAL cc_start: 0.8755 (m) cc_final: 0.8399 (p) REVERT: A 97 VAL cc_start: 0.8612 (t) cc_final: 0.8409 (t) REVERT: A 276 LEU cc_start: 0.8968 (tp) cc_final: 0.8657 (pt) REVERT: B 2 ASP cc_start: 0.8046 (t0) cc_final: 0.7820 (t0) REVERT: B 33 LEU cc_start: 0.9346 (mt) cc_final: 0.8940 (mm) REVERT: B 43 PHE cc_start: 0.8884 (m-80) cc_final: 0.8676 (m-80) REVERT: B 85 PHE cc_start: 0.9180 (m-80) cc_final: 0.8876 (m-80) REVERT: B 251 TYR cc_start: 0.9321 (t80) cc_final: 0.9100 (t80) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0765 time to fit residues: 17.2281 Evaluate side-chains 116 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 4.9990 chunk 79 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 62 optimal weight: 0.0470 chunk 95 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 93 GLN 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 = 0.3487 r_free = 0.3487 target = 0.061567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.043497 restraints weight = 61675.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.044891 restraints weight = 36899.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.045803 restraints weight = 26243.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046409 restraints weight = 20994.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046774 restraints weight = 18059.038| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9145 Z= 0.235 Angle : 0.791 8.600 12481 Z= 0.390 Chirality : 0.048 0.324 1519 Planarity : 0.005 0.056 1505 Dihedral : 5.449 51.850 1133 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.24), residues: 1058 helix: 0.29 (0.30), residues: 294 sheet: -1.51 (0.33), residues: 240 loop : -2.95 (0.22), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.037 0.003 TYR G 217 PHE 0.014 0.002 PHE B 85 TRP 0.031 0.002 TRP G 475 HIS 0.015 0.002 HIS G 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 ( 9100) covalent geometry : angle 0.76461 / 0.38 (12364) SS BOND : bond 0.00825 / 0.48 ( 12) SS BOND : angle 1.51413 / 0.88 ( 24) hydrogen bonds : bond 0.04344 / 2.83 ( 304) hydrogen bonds : angle 6.04581 / 4.17 ( 828) Misc. bond : bond 0.00115 / 0.06 ( 2) link_ALPHA1-2 : bond 0.00438 / 0.23 ( 1) link_ALPHA1-2 : angle 1.93563 / 1.33 ( 3) link_ALPHA1-3 : bond 0.00260 / 0.14 ( 1) link_ALPHA1-3 : angle 1.77724 / 1.35 ( 3) link_ALPHA1-6 : bond 0.00054 / 0.03 ( 1) link_ALPHA1-6 : angle 1.27563 / 0.80 ( 3) link_BETA1-4 : bond 0.00433 / 0.28 ( 12) link_BETA1-4 : angle 1.76432 / 1.18 ( 36) link_NAG-ASN : bond 0.00477 / 0.28 ( 16) link_NAG-ASN : angle 2.85021 / 1.93 ( 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 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7939 (p90) cc_final: 0.7737 (p90) REVERT: G 94 MET cc_start: 0.9007 (ppp) cc_final: 0.8702 (ppp) REVERT: G 99 MET cc_start: 0.9101 (ptp) cc_final: 0.8894 (ptt) REVERT: G 115 LEU cc_start: 0.9330 (mp) cc_final: 0.9082 (mp) REVERT: G 375 ASN cc_start: 0.8395 (t0) cc_final: 0.8078 (t0) REVERT: G 379 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8649 (mm-30) REVERT: G 421 MET cc_start: 0.8224 (ptp) cc_final: 0.7642 (ptp) REVERT: G 480 TYR cc_start: 0.8866 (p90) cc_final: 0.8543 (p90) REVERT: A 323 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7397 (pm20) REVERT: B 2 ASP cc_start: 0.8299 (t0) cc_final: 0.7949 (t0) REVERT: B 33 LEU cc_start: 0.9470 (mt) cc_final: 0.9238 (mm) REVERT: B 43 PHE cc_start: 0.8886 (m-80) cc_final: 0.8597 (m-80) REVERT: B 261 GLN cc_start: 0.8831 (mm110) cc_final: 0.8469 (tm-30) REVERT: B 279 MET cc_start: 0.8995 (ptp) cc_final: 0.8772 (ptt) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.0717 time to fit residues: 13.4509 Evaluate side-chains 95 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 0.5980 chunk 93 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN G 279 ASN G 308 HIS ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 194 GLN B 231 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.061492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.043253 restraints weight = 62602.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.044663 restraints weight = 36618.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.045600 restraints weight = 25893.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046172 restraints weight = 20592.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046593 restraints weight = 17799.915| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9145 Z= 0.182 Angle : 0.714 8.674 12481 Z= 0.350 Chirality : 0.047 0.315 1519 Planarity : 0.005 0.055 1505 Dihedral : 5.288 49.367 1133 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.25), residues: 1058 helix: 0.62 (0.31), residues: 292 sheet: -1.37 (0.32), residues: 270 loop : -2.90 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 131 TYR 0.029 0.002 TYR G 217 PHE 0.009 0.001 PHE G 315 TRP 0.018 0.002 TRP G 475 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 9100) covalent geometry : angle 0.68322 / 0.34 (12364) SS BOND : bond 0.00357 / 0.25 ( 12) SS BOND : angle 1.34738 / 0.85 ( 24) hydrogen bonds : bond 0.03949 / 2.56 ( 304) hydrogen bonds : angle 5.83296 / 4.04 ( 828) Misc. bond : bond 0.00078 / 0.04 ( 2) link_ALPHA1-2 : bond 0.00362 / 0.19 ( 1) link_ALPHA1-2 : angle 1.79838 / 1.32 ( 3) link_ALPHA1-3 : bond 0.00286 / 0.15 ( 1) link_ALPHA1-3 : angle 1.79262 / 1.46 ( 3) link_ALPHA1-6 : bond 0.00406 / 0.21 ( 1) link_ALPHA1-6 : angle 1.37664 / 1.02 ( 3) link_BETA1-4 : bond 0.00325 / 0.20 ( 12) link_BETA1-4 : angle 1.51579 / 0.99 ( 36) link_NAG-ASN : bond 0.00361 / 0.19 ( 16) link_NAG-ASN : angle 3.00807 / 1.97 ( 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 : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7893 (p90) cc_final: 0.7676 (p90) REVERT: G 94 MET cc_start: 0.8926 (ppp) cc_final: 0.8039 (ppp) REVERT: G 115 LEU cc_start: 0.9329 (mp) cc_final: 0.8865 (mp) REVERT: G 379 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8528 (mm-30) REVERT: G 382 TYR cc_start: 0.8715 (m-10) cc_final: 0.8469 (m-10) REVERT: G 421 MET cc_start: 0.8129 (ptp) cc_final: 0.7907 (ptp) REVERT: G 476 ARG cc_start: 0.8793 (mtt90) cc_final: 0.8530 (mtt-85) REVERT: G 480 TYR cc_start: 0.8820 (p90) cc_final: 0.8509 (p90) REVERT: A 198 PHE cc_start: 0.6968 (m-80) cc_final: 0.6705 (m-80) REVERT: A 323 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7542 (pm20) REVERT: B 2 ASP cc_start: 0.8265 (t0) cc_final: 0.7915 (t0) REVERT: B 43 PHE cc_start: 0.8899 (m-10) cc_final: 0.8595 (m-80) REVERT: B 161 LEU cc_start: 0.9251 (tt) cc_final: 0.9008 (mt) REVERT: B 261 GLN cc_start: 0.8864 (mm110) cc_final: 0.8334 (tm-30) REVERT: B 279 MET cc_start: 0.9012 (ptp) cc_final: 0.8742 (ptp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0635 time to fit residues: 11.4209 Evaluate side-chains 94 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.061794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.043774 restraints weight = 60932.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045132 restraints weight = 35587.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.046050 restraints weight = 25101.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046691 restraints weight = 19973.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047050 restraints weight = 17175.449| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9145 Z= 0.144 Angle : 0.703 7.809 12481 Z= 0.339 Chirality : 0.047 0.302 1519 Planarity : 0.004 0.039 1505 Dihedral : 5.124 45.133 1133 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.18 % Favored : 92.72 % Rotamer: Outliers : 0.21 % Allowed : 1.58 % Favored : 98.21 % 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 are not related in a simple way. whole: -2.05 (0.25), residues: 1058 helix: 0.73 (0.31), residues: 292 sheet: -1.29 (0.32), residues: 268 loop : -2.76 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 486 TYR 0.027 0.002 TYR G 217 PHE 0.012 0.001 PHE G 92 TRP 0.018 0.001 TRP G 475 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9100) covalent geometry : angle 0.67625 / 0.33 (12364) SS BOND : bond 0.00337 / 0.22 ( 12) SS BOND : angle 1.59679 / 0.95 ( 24) hydrogen bonds : bond 0.03874 / 2.50 ( 304) hydrogen bonds : angle 5.64881 / 3.94 ( 828) Misc. bond : bond 0.00058 / 0.03 ( 2) link_ALPHA1-2 : bond 0.00319 / 0.17 ( 1) link_ALPHA1-2 : angle 1.71743 / 1.28 ( 3) link_ALPHA1-3 : bond 0.00424 / 0.22 ( 1) link_ALPHA1-3 : angle 1.71204 / 1.41 ( 3) link_ALPHA1-6 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-6 : angle 1.15356 / 0.87 ( 3) link_BETA1-4 : bond 0.00317 / 0.20 ( 12) link_BETA1-4 : angle 1.37135 / 0.89 ( 36) link_NAG-ASN : bond 0.00357 / 0.18 ( 16) link_NAG-ASN : angle 2.75586 / 1.82 ( 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 122 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: G 38 TYR cc_start: 0.7945 (p90) cc_final: 0.7736 (p90) REVERT: G 94 MET cc_start: 0.8829 (ppp) cc_final: 0.8568 (ppp) REVERT: G 115 LEU cc_start: 0.9126 (mp) cc_final: 0.8801 (mp) REVERT: G 379 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8594 (mm-30) REVERT: G 382 TYR cc_start: 0.8734 (m-10) cc_final: 0.8515 (m-10) REVERT: G 421 MET cc_start: 0.8269 (ptp) cc_final: 0.7945 (ptp) REVERT: G 480 TYR cc_start: 0.8802 (p90) cc_final: 0.8484 (p90) REVERT: A 74 LEU cc_start: 0.9370 (mt) cc_final: 0.9080 (mt) REVERT: A 276 LEU cc_start: 0.9397 (pt) cc_final: 0.9025 (tp) REVERT: A 323 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7430 (pm20) REVERT: B 2 ASP cc_start: 0.8361 (t0) cc_final: 0.8049 (t0) REVERT: B 33 LEU cc_start: 0.9399 (mm) cc_final: 0.9084 (mm) REVERT: B 43 PHE cc_start: 0.8926 (m-10) cc_final: 0.8585 (m-80) REVERT: B 74 ILE cc_start: 0.9464 (mt) cc_final: 0.9248 (tt) REVERT: B 161 LEU cc_start: 0.9212 (tt) cc_final: 0.8964 (mt) REVERT: B 251 TYR cc_start: 0.9492 (t80) cc_final: 0.9080 (t80) REVERT: B 261 GLN cc_start: 0.8857 (mm110) cc_final: 0.8295 (tm-30) REVERT: B 279 MET cc_start: 0.8964 (ptp) cc_final: 0.8633 (ptp) REVERT: B 287 MET cc_start: 0.9446 (mtm) cc_final: 0.9088 (mtm) outliers start: 2 outliers final: 1 residues processed: 120 average time/residue: 0.0638 time to fit residues: 11.8839 Evaluate side-chains 95 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 93 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 32 ASN G 279 ASN B 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.062705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.044692 restraints weight = 58636.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046055 restraints weight = 35743.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.047008 restraints weight = 25626.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047606 restraints weight = 20417.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.047978 restraints weight = 17554.650| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9145 Z= 0.111 Angle : 0.660 8.067 12481 Z= 0.319 Chirality : 0.046 0.288 1519 Planarity : 0.004 0.054 1505 Dihedral : 4.793 33.934 1133 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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 are not related in a simple way. whole: -1.92 (0.25), residues: 1058 helix: 0.84 (0.31), residues: 298 sheet: -1.31 (0.33), residues: 250 loop : -2.64 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 304 TYR 0.020 0.001 TYR G 217 PHE 0.017 0.001 PHE A 198 TRP 0.016 0.001 TRP G 475 HIS 0.013 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9100) covalent geometry : angle 0.63693 / 0.31 (12364) SS BOND : bond 0.00233 / 0.16 ( 12) SS BOND : angle 1.54055 / 1.13 ( 24) hydrogen bonds : bond 0.03606 / 2.32 ( 304) hydrogen bonds : angle 5.38510 / 3.74 ( 828) Misc. bond : bond 0.00042 / 0.02 ( 2) link_ALPHA1-2 : bond 0.00158 / 0.08 ( 1) link_ALPHA1-2 : angle 1.70352 / 1.31 ( 3) link_ALPHA1-3 : bond 0.00517 / 0.27 ( 1) link_ALPHA1-3 : angle 1.55039 / 1.33 ( 3) link_ALPHA1-6 : bond 0.00342 / 0.18 ( 1) link_ALPHA1-6 : angle 1.22766 / 0.99 ( 3) link_BETA1-4 : bond 0.00342 / 0.22 ( 12) link_BETA1-4 : angle 1.21808 / 0.78 ( 36) link_NAG-ASN : bond 0.00398 / 0.21 ( 16) link_NAG-ASN : angle 2.48546 / 1.65 ( 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 121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 94 MET cc_start: 0.8771 (ppp) cc_final: 0.8296 (ppp) REVERT: G 115 LEU cc_start: 0.9287 (mp) cc_final: 0.8782 (mp) REVERT: G 259 LEU cc_start: 0.9323 (tt) cc_final: 0.9041 (tt) REVERT: G 379 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8668 (mm-30) REVERT: G 382 TYR cc_start: 0.8825 (m-10) cc_final: 0.8561 (m-10) REVERT: G 421 MET cc_start: 0.8341 (ptp) cc_final: 0.7989 (ptp) REVERT: G 480 TYR cc_start: 0.8796 (p90) cc_final: 0.8459 (p90) REVERT: A 276 LEU cc_start: 0.9423 (pt) cc_final: 0.9015 (tp) REVERT: A 306 TRP cc_start: 0.7828 (m100) cc_final: 0.7614 (t-100) REVERT: A 323 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7463 (pm20) REVERT: B 2 ASP cc_start: 0.8406 (t0) cc_final: 0.8101 (t0) REVERT: B 33 LEU cc_start: 0.9261 (mm) cc_final: 0.9040 (mm) REVERT: B 43 PHE cc_start: 0.8937 (m-10) cc_final: 0.8589 (m-80) REVERT: B 74 ILE cc_start: 0.9441 (mt) cc_final: 0.9238 (tt) REVERT: B 251 TYR cc_start: 0.9544 (t80) cc_final: 0.9164 (t80) REVERT: B 261 GLN cc_start: 0.8898 (mm110) cc_final: 0.8438 (tm-30) REVERT: B 279 MET cc_start: 0.8899 (ptp) cc_final: 0.8624 (ptp) REVERT: B 287 MET cc_start: 0.9454 (mtm) cc_final: 0.9030 (ptt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0618 time to fit residues: 11.3761 Evaluate side-chains 95 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 229 ASN ** G 279 ASN ** 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 = 0.3493 r_free = 0.3493 target = 0.061889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043706 restraints weight = 61570.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.045146 restraints weight = 35954.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046091 restraints weight = 25272.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.046743 restraints weight = 19994.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047151 restraints weight = 17075.545| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9145 Z= 0.129 Angle : 0.675 10.302 12481 Z= 0.322 Chirality : 0.046 0.287 1519 Planarity : 0.004 0.057 1505 Dihedral : 4.792 34.036 1133 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.25), residues: 1058 helix: 0.86 (0.31), residues: 294 sheet: -1.18 (0.33), residues: 252 loop : -2.53 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 476 TYR 0.021 0.002 TYR G 217 PHE 0.019 0.001 PHE A 198 TRP 0.027 0.001 TRP G 475 HIS 0.003 0.001 HIS G 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9100) covalent geometry : angle 0.65329 / 0.32 (12364) SS BOND : bond 0.00270 / 0.18 ( 12) SS BOND : angle 1.27851 / 0.90 ( 24) hydrogen bonds : bond 0.03531 / 2.26 ( 304) hydrogen bonds : angle 5.30266 / 3.70 ( 828) Misc. bond : bond 0.00043 / 0.02 ( 2) link_ALPHA1-2 : bond 0.00022 / 0.01 ( 1) link_ALPHA1-2 : angle 1.75601 / 1.32 ( 3) link_ALPHA1-3 : bond 0.00425 / 0.22 ( 1) link_ALPHA1-3 : angle 1.62743 / 1.36 ( 3) link_ALPHA1-6 : bond 0.00551 / 0.29 ( 1) link_ALPHA1-6 : angle 1.30020 / 0.97 ( 3) link_BETA1-4 : bond 0.00333 / 0.21 ( 12) link_BETA1-4 : angle 1.36277 / 0.89 ( 36) link_NAG-ASN : bond 0.00340 / 0.17 ( 16) link_NAG-ASN : angle 2.45614 / 1.67 ( 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 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 94 MET cc_start: 0.8901 (ppp) cc_final: 0.8441 (ppp) REVERT: G 115 LEU cc_start: 0.9168 (mp) cc_final: 0.8779 (mp) REVERT: G 421 MET cc_start: 0.8308 (ptp) cc_final: 0.8044 (ptp) REVERT: G 480 TYR cc_start: 0.8708 (p90) cc_final: 0.8415 (p90) REVERT: A 114 LEU cc_start: 0.8774 (tp) cc_final: 0.8421 (mt) REVERT: A 276 LEU cc_start: 0.9494 (pt) cc_final: 0.8994 (tp) REVERT: A 306 TRP cc_start: 0.7925 (m100) cc_final: 0.7715 (t-100) REVERT: A 323 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7489 (pm20) REVERT: B 2 ASP cc_start: 0.8460 (t0) cc_final: 0.8149 (t0) REVERT: B 33 LEU cc_start: 0.9442 (mm) cc_final: 0.8966 (mm) REVERT: B 43 PHE cc_start: 0.8973 (m-10) cc_final: 0.8632 (m-80) REVERT: B 261 GLN cc_start: 0.8910 (mm110) cc_final: 0.8327 (tm-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0716 time to fit residues: 12.6738 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 : 0.344 ------------------------------------------------------------------------------- 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: 0.8980 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044028 restraints weight = 58680.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.045409 restraints weight = 35327.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046326 restraints weight = 25216.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.046896 restraints weight = 20083.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.047332 restraints weight = 17279.131| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9145 Z= 0.114 Angle : 0.677 9.806 12481 Z= 0.325 Chirality : 0.046 0.307 1519 Planarity : 0.004 0.051 1505 Dihedral : 4.714 30.179 1133 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.25), residues: 1058 helix: 0.85 (0.31), residues: 298 sheet: -1.10 (0.33), residues: 254 loop : -2.45 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 476 TYR 0.021 0.001 TYR B 37 PHE 0.020 0.001 PHE A 198 TRP 0.017 0.001 TRP G 475 HIS 0.002 0.001 HIS G 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9100) covalent geometry : angle 0.65417 / 0.32 (12364) SS BOND : bond 0.00254 / 0.16 ( 12) SS BOND : angle 1.95327 / 1.22 ( 24) hydrogen bonds : bond 0.03646 / 2.42 ( 304) hydrogen bonds : angle 5.22381 / 3.65 ( 828) Misc. bond : bond 0.00040 / 0.02 ( 2) link_ALPHA1-2 : bond 0.00142 / 0.07 ( 1) link_ALPHA1-2 : angle 1.61223 / 1.23 ( 3) link_ALPHA1-3 : bond 0.00432 / 0.23 ( 1) link_ALPHA1-3 : angle 1.58442 / 1.38 ( 3) link_ALPHA1-6 : bond 0.00400 / 0.21 ( 1) link_ALPHA1-6 : angle 1.20814 / 0.96 ( 3) link_BETA1-4 : bond 0.00310 / 0.20 ( 12) link_BETA1-4 : angle 1.21029 / 0.78 ( 36) link_NAG-ASN : bond 0.00363 / 0.19 ( 16) link_NAG-ASN : angle 2.36456 / 1.59 ( 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 110 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: G 94 MET cc_start: 0.8794 (ppp) cc_final: 0.8309 (ppp) REVERT: G 115 LEU cc_start: 0.9069 (mp) cc_final: 0.8736 (mp) REVERT: G 421 MET cc_start: 0.8349 (ptp) cc_final: 0.7819 (mpp) REVERT: G 480 TYR cc_start: 0.8565 (p90) cc_final: 0.8273 (p90) REVERT: A 56 ASP cc_start: 0.8404 (t70) cc_final: 0.8197 (t0) REVERT: A 235 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9174 (tm-30) REVERT: A 276 LEU cc_start: 0.9441 (pt) cc_final: 0.8798 (tp) REVERT: A 323 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7504 (pm20) REVERT: B 2 ASP cc_start: 0.8292 (t0) cc_final: 0.7985 (t0) REVERT: B 43 PHE cc_start: 0.8969 (m-10) cc_final: 0.8615 (m-80) REVERT: B 251 TYR cc_start: 0.9429 (t80) cc_final: 0.9124 (t80) REVERT: B 255 LEU cc_start: 0.9619 (tt) cc_final: 0.9233 (mt) REVERT: B 261 GLN cc_start: 0.8885 (mm110) cc_final: 0.8414 (tm-30) REVERT: B 279 MET cc_start: 0.8803 (ptp) cc_final: 0.8553 (ptp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0701 time to fit residues: 12.2259 Evaluate side-chains 91 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 6.9990 chunk 73 optimal weight: 50.0000 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.058806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.041262 restraints weight = 61701.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042543 restraints weight = 36566.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043489 restraints weight = 25976.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044071 restraints weight = 20489.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.044456 restraints weight = 17535.969| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.7514 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= 0.224 Angle : 0.770 9.635 12481 Z= 0.370 Chirality : 0.048 0.317 1519 Planarity : 0.005 0.052 1505 Dihedral : 5.054 37.022 1133 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.26 % Favored : 90.64 % 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 are not related in a simple way. whole: -1.88 (0.25), residues: 1058 helix: 0.68 (0.30), residues: 296 sheet: -1.16 (0.30), residues: 286 loop : -2.60 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 476 TYR 0.028 0.002 TYR G 217 PHE 0.018 0.002 PHE A 198 TRP 0.029 0.002 TRP G 475 HIS 0.006 0.002 HIS G 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 ( 9100) covalent geometry : angle 0.74340 / 0.36 (12364) SS BOND : bond 0.00386 / 0.24 ( 12) SS BOND : angle 1.87429 / 1.13 ( 24) hydrogen bonds : bond 0.03845 / 2.48 ( 304) hydrogen bonds : angle 5.54319 / 3.87 ( 828) Misc. bond : bond 0.00072 / 0.04 ( 2) link_ALPHA1-2 : bond 0.00285 / 0.15 ( 1) link_ALPHA1-2 : angle 1.76942 / 1.26 ( 3) link_ALPHA1-3 : bond 0.00063 / 0.03 ( 1) link_ALPHA1-3 : angle 1.96088 / 1.64 ( 3) link_ALPHA1-6 : bond 0.00434 / 0.23 ( 1) link_ALPHA1-6 : angle 1.36837 / 0.88 ( 3) link_BETA1-4 : bond 0.00418 / 0.26 ( 12) link_BETA1-4 : angle 1.65315 / 1.08 ( 36) link_NAG-ASN : bond 0.00413 / 0.26 ( 16) link_NAG-ASN : angle 2.74202 / 1.85 ( 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 102 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 94 MET cc_start: 0.9012 (ppp) cc_final: 0.8588 (ppp) REVERT: G 382 TYR cc_start: 0.8759 (m-10) cc_final: 0.8465 (m-10) REVERT: G 421 MET cc_start: 0.8393 (ptp) cc_final: 0.7763 (ptp) REVERT: G 447 LEU cc_start: 0.9387 (mt) cc_final: 0.9024 (mt) REVERT: G 480 TYR cc_start: 0.8841 (p90) cc_final: 0.8535 (p90) REVERT: A 235 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9139 (tm-30) REVERT: A 276 LEU cc_start: 0.9594 (pt) cc_final: 0.9091 (mm) REVERT: A 323 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7671 (pm20) REVERT: B 2 ASP cc_start: 0.8399 (t0) cc_final: 0.8158 (t0) REVERT: B 33 LEU cc_start: 0.9459 (mm) cc_final: 0.8602 (pp) REVERT: B 37 TYR cc_start: 0.9296 (m-10) cc_final: 0.9083 (m-80) REVERT: B 43 PHE cc_start: 0.8993 (m-10) cc_final: 0.8635 (m-80) REVERT: B 161 LEU cc_start: 0.9263 (tt) cc_final: 0.8985 (mt) REVERT: B 251 TYR cc_start: 0.9516 (t80) cc_final: 0.9301 (t80) REVERT: B 261 GLN cc_start: 0.8902 (mm110) cc_final: 0.8545 (tm-30) REVERT: B 287 MET cc_start: 0.9659 (mtm) cc_final: 0.9350 (mtm) REVERT: B 291 CYS cc_start: 0.9670 (p) cc_final: 0.9469 (p) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0758 time to fit residues: 11.9417 Evaluate side-chains 82 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.059686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.041942 restraints weight = 60407.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.043311 restraints weight = 35794.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.044246 restraints weight = 25287.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.044847 restraints weight = 19913.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045223 restraints weight = 17023.705| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.7662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9145 Z= 0.143 Angle : 0.703 11.565 12481 Z= 0.335 Chirality : 0.047 0.331 1519 Planarity : 0.004 0.049 1505 Dihedral : 4.902 31.356 1133 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.18 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.25), residues: 1058 helix: 0.78 (0.30), residues: 297 sheet: -1.21 (0.30), residues: 286 loop : -2.54 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 476 TYR 0.022 0.002 TYR G 217 PHE 0.016 0.001 PHE A 198 TRP 0.021 0.002 TRP A 306 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9100) covalent geometry : angle 0.67989 / 0.33 (12364) SS BOND : bond 0.00308 / 0.18 ( 12) SS BOND : angle 1.51295 / 0.93 ( 24) hydrogen bonds : bond 0.03689 / 2.42 ( 304) hydrogen bonds : angle 5.32961 / 3.75 ( 828) Misc. bond : bond 0.00059 / 0.03 ( 2) link_ALPHA1-2 : bond 0.00136 / 0.07 ( 1) link_ALPHA1-2 : angle 1.67690 / 1.22 ( 3) link_ALPHA1-3 : bond 0.00281 / 0.15 ( 1) link_ALPHA1-3 : angle 1.74821 / 1.53 ( 3) link_ALPHA1-6 : bond 0.00389 / 0.20 ( 1) link_ALPHA1-6 : angle 1.20819 / 0.96 ( 3) link_BETA1-4 : bond 0.00269 / 0.17 ( 12) link_BETA1-4 : angle 1.32519 / 0.84 ( 36) link_NAG-ASN : bond 0.00354 / 0.17 ( 16) link_NAG-ASN : angle 2.56754 / 1.74 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.88 seconds wall clock time: 29 minutes 26.25 seconds (1766.25 seconds total)