Starting phenix.real_space_refine on Thu Feb 5 09:34:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lh9_63090/02_2026/9lh9_63090.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lh9_63090/02_2026/9lh9_63090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lh9_63090/02_2026/9lh9_63090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lh9_63090/02_2026/9lh9_63090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lh9_63090/02_2026/9lh9_63090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lh9_63090/02_2026/9lh9_63090.map" } resolution = 2.98 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= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10558 2.51 5 N 2603 2.21 5 O 2948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16224 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3274 Chain: "B" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "C" Number of atoms: 3186 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3179 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 400, 3179 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 3257 Chain: "D" Number of atoms: 3195 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3188 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 400, 3188 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 3268 Chain: "E" Number of atoms: 3201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3274 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.42 Number of scatterers: 16224 At special positions: 0 Unit cell: (92.92, 92.92, 168.67, 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 115 16.00 O 2948 8.00 N 2603 7.00 C 10558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 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=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 602 " - " ASN A 46 " " NAG B 602 " - " ASN B 46 " " NAG C 602 " - " ASN C 46 " " NAG D 601 " - " ASN D 46 " " NAG E 601 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 20 sheets defined 43.6% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.732A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.662A pdb=" N LEU A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 260 through 281 Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 431 through 489 removed outlier: 3.616A pdb=" N LYS A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.832A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.687A pdb=" N CYS B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 260 through 281 Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 321 through 325 removed outlier: 4.118A pdb=" N GLY B 325 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 431 through 489 removed outlier: 4.323A pdb=" N LEU B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.522A pdb=" N ALA B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.820A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.731A pdb=" N CYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 260 through 281 removed outlier: 3.910A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 431 through 490 removed outlier: 4.375A pdb=" N LYS C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.673A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 260 through 281 Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 337 removed outlier: 3.855A pdb=" N ASN D 337 " --> pdb=" O VAL D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 431 through 489 removed outlier: 4.002A pdb=" N ILE D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.566A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 237 through 248 removed outlier: 3.601A pdb=" N CYS E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.733A pdb=" N PHE E 252 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 282 removed outlier: 4.005A pdb=" N LEU E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'E' and resid 337 through 344 Processing helix chain 'E' and resid 431 through 489 removed outlier: 3.651A pdb=" N LYS E 435 " --> pdb=" O PRO E 431 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.858A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N THR A 83 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N TYR A 54 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.468A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.468A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.788A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TRP B 77 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLN B 79 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER B 58 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N SER B 81 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER B 56 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N THR B 83 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N TYR B 54 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.586A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.586A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.646A pdb=" N VAL C 71 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP C 64 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR C 52 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.561A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.561A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 208 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 removed outlier: 7.098A pdb=" N VAL D 71 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN D 75 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.002A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 5.002A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.880A pdb=" N VAL E 71 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP E 64 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN E 75 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR E 83 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR E 52 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.971A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.971A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2573 1.32 - 1.45: 4685 1.45 - 1.58: 9241 1.58 - 1.71: 6 1.71 - 1.85: 170 Bond restraints: 16675 Sorted by residual: bond pdb=" C6 NCT C 601 " pdb=" N2 NCT C 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C6 NCT B 601 " pdb=" N2 NCT B 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.623 -0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" C6 NCT B 601 " pdb=" C7 NCT B 601 " ideal model delta sigma weight residual 1.536 1.368 0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" C6 NCT C 601 " pdb=" C7 NCT C 601 " ideal model delta sigma weight residual 1.536 1.369 0.167 2.00e-02 2.50e+03 7.01e+01 ... (remaining 16670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 22220 2.08 - 4.16: 409 4.16 - 6.25: 109 6.25 - 8.33: 11 8.33 - 10.41: 6 Bond angle restraints: 22755 Sorted by residual: angle pdb=" C ASP B 451 " pdb=" N GLU B 452 " pdb=" CA GLU B 452 " ideal model delta sigma weight residual 120.31 114.86 5.45 1.52e+00 4.33e-01 1.28e+01 angle pdb=" N GLY A 144 " pdb=" CA GLY A 144 " pdb=" C GLY A 144 " ideal model delta sigma weight residual 110.91 115.95 -5.04 1.49e+00 4.50e-01 1.15e+01 angle pdb=" CA LYS E 435 " pdb=" CB LYS E 435 " pdb=" CG LYS E 435 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" C PRO D 202 " pdb=" N GLY D 203 " pdb=" CA GLY D 203 " ideal model delta sigma weight residual 122.47 119.52 2.95 8.90e-01 1.26e+00 1.10e+01 angle pdb=" C VAL E 132 " pdb=" N ASN E 133 " pdb=" CA ASN E 133 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 ... (remaining 22750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 9111 22.38 - 44.76: 748 44.76 - 67.14: 138 67.14 - 89.52: 27 89.52 - 111.90: 16 Dihedral angle restraints: 10040 sinusoidal: 4145 harmonic: 5895 Sorted by residual: dihedral pdb=" CA CYS D 212 " pdb=" C CYS D 212 " pdb=" N CYS D 213 " pdb=" CA CYS D 213 " ideal model delta harmonic sigma weight residual -180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CB CYS C 150 " pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " pdb=" CB CYS C 164 " ideal model delta sinusoidal sigma weight residual 93.00 46.21 46.79 1 1.00e+01 1.00e-02 3.03e+01 dihedral pdb=" CA CYS E 212 " pdb=" C CYS E 212 " pdb=" N CYS E 213 " pdb=" CA CYS E 213 " ideal model delta harmonic sigma weight residual -180.00 -153.47 -26.53 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 10037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2456 0.088 - 0.175: 137 0.175 - 0.263: 7 0.263 - 0.351: 2 0.351 - 0.438: 1 Chirality restraints: 2603 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 133 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 133 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2600 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 191 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO C 192 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " 0.026 2.00e-02 2.50e+03 2.39e-02 7.15e+00 pdb=" CG ASN E 133 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " -0.025 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 191 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO E 192 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 192 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 192 " 0.036 5.00e-02 4.00e+02 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4237 2.81 - 3.33: 14450 3.33 - 3.85: 26466 3.85 - 4.38: 29678 4.38 - 4.90: 53074 Nonbonded interactions: 127905 Sorted by model distance: nonbonded pdb=" OE2 GLU C 41 " pdb=" OH TYR C 86 " model vdw 2.286 3.040 nonbonded pdb=" OG SER C 81 " pdb=" NE2BHIS C 137 " model vdw 2.293 3.120 nonbonded pdb=" NH1 ARG B 332 " pdb=" OE2 GLU B 459 " model vdw 2.316 3.120 nonbonded pdb=" O PRO E 431 " pdb=" NZ LYS E 435 " model vdw 2.316 3.120 nonbonded pdb=" O SER D 172 " pdb=" NE ARG E 101 " model vdw 2.320 3.120 ... (remaining 127900 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 'A' and (resid 23 through 136 or resid 138 through 329 or (resid 330 and \ (name N or name CA or name C or name O or name CB )) or resid 331 through 346 or \ (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 8 through 502)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 through 502)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 329 or (resid 330 and \ (name N or name CA or name C or name O or name CB )) or resid 331 through 502)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 329 or (resid 330 and \ (name N or name CA or name C or name O or name CB )) or resid 331 through 346 or \ (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 8 through 502)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.330 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 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 : 0.008 0.172 16700 Z= 0.384 Angle : 0.730 11.257 22820 Z= 0.340 Chirality : 0.045 0.438 2603 Planarity : 0.005 0.071 2834 Dihedral : 17.151 111.895 6200 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.40 % Allowed : 17.04 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.18 (0.19), residues: 1985 helix: 2.40 (0.18), residues: 807 sheet: 0.27 (0.25), residues: 430 loop : -0.72 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 208 TYR 0.020 0.001 TYR E 296 PHE 0.016 0.001 PHE E 342 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 318 Details of bonding type rmsd covalent geometry : bond 0.00785 (16675) covalent geometry : angle 0.71337 (22755) SS BOND : bond 0.00765 ( 10) SS BOND : angle 1.62193 ( 20) hydrogen bonds : bond 0.08970 ( 855) hydrogen bonds : angle 4.79306 ( 2760) link_BETA1-4 : bond 0.00281 ( 5) link_BETA1-4 : angle 0.75033 ( 15) link_NAG-ASN : bond 0.00146 ( 10) link_NAG-ASN : angle 4.22094 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 271 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LYS cc_start: 0.9370 (mmtm) cc_final: 0.8778 (mptt) REVERT: A 439 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8996 (mm-30) REVERT: B 80 MET cc_start: 0.8815 (mtm) cc_final: 0.8560 (mtm) REVERT: B 237 LEU cc_start: 0.8784 (tt) cc_final: 0.8574 (mp) REVERT: B 296 TYR cc_start: 0.8491 (t80) cc_final: 0.8258 (t80) REVERT: B 302 ILE cc_start: 0.9259 (mm) cc_final: 0.9050 (pp) REVERT: B 338 TRP cc_start: 0.8591 (m-10) cc_final: 0.8322 (m100) REVERT: B 432 ASP cc_start: 0.9210 (m-30) cc_final: 0.8852 (p0) REVERT: B 435 LYS cc_start: 0.9430 (mtmt) cc_final: 0.8745 (mtmm) REVERT: B 437 LEU cc_start: 0.8974 (tt) cc_final: 0.7537 (tt) REVERT: B 441 ARG cc_start: 0.8920 (mtm-85) cc_final: 0.8381 (ptp90) REVERT: C 243 LEU cc_start: 0.8931 (mt) cc_final: 0.8710 (tp) REVERT: C 342 PHE cc_start: 0.8462 (t80) cc_final: 0.7709 (m-10) REVERT: C 454 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8495 (tm-30) REVERT: D 330 TRP cc_start: 0.7321 (m100) cc_final: 0.6989 (t-100) REVERT: E 247 LEU cc_start: 0.9536 (tp) cc_final: 0.9332 (tt) REVERT: E 342 PHE cc_start: 0.8957 (t80) cc_final: 0.8729 (t80) REVERT: E 441 ARG cc_start: 0.9134 (ttp-170) cc_final: 0.8927 (ttm-80) outliers start: 7 outliers final: 4 residues processed: 275 average time/residue: 0.4395 time to fit residues: 137.1572 Evaluate side-chains 210 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 210 TYR Chi-restraints excluded: chain E residue 437 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 236 ASN A 450 GLN B 236 ASN D 116 ASN D 450 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.081041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.065271 restraints weight = 62188.836| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.98 r_work: 0.2714 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16700 Z= 0.135 Angle : 0.665 11.236 22820 Z= 0.313 Chirality : 0.046 0.526 2603 Planarity : 0.005 0.060 2834 Dihedral : 10.283 72.469 2525 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.83 % Allowed : 17.72 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.30 (0.19), residues: 1985 helix: 2.38 (0.18), residues: 811 sheet: 0.50 (0.25), residues: 436 loop : -0.64 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 441 TYR 0.022 0.001 TYR D 442 PHE 0.017 0.001 PHE A 478 TRP 0.012 0.001 TRP A 196 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00305 (16675) covalent geometry : angle 0.64113 (22755) SS BOND : bond 0.00843 ( 10) SS BOND : angle 2.25414 ( 20) hydrogen bonds : bond 0.05052 ( 855) hydrogen bonds : angle 4.21473 ( 2760) link_BETA1-4 : bond 0.00528 ( 5) link_BETA1-4 : angle 2.25838 ( 15) link_NAG-ASN : bond 0.00164 ( 10) link_NAG-ASN : angle 4.37695 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8293 (t80) REVERT: A 435 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8623 (mptt) REVERT: A 454 GLU cc_start: 0.8708 (tp30) cc_final: 0.8417 (tp30) REVERT: B 296 TYR cc_start: 0.8357 (t80) cc_final: 0.7921 (t80) REVERT: B 302 ILE cc_start: 0.9047 (mm) cc_final: 0.8766 (pp) REVERT: B 338 TRP cc_start: 0.8644 (m-10) cc_final: 0.8282 (m100) REVERT: B 432 ASP cc_start: 0.9319 (m-30) cc_final: 0.8844 (p0) REVERT: B 435 LYS cc_start: 0.9136 (mtmt) cc_final: 0.8438 (mtmm) REVERT: B 439 GLU cc_start: 0.8821 (mp0) cc_final: 0.8307 (mp0) REVERT: C 243 LEU cc_start: 0.8784 (mt) cc_final: 0.8521 (tp) REVERT: C 454 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8582 (tm-30) REVERT: D 330 TRP cc_start: 0.7554 (m100) cc_final: 0.7166 (t-100) REVERT: E 283 MET cc_start: 0.8958 (mmp) cc_final: 0.8462 (mmm) REVERT: E 342 PHE cc_start: 0.9137 (t80) cc_final: 0.8838 (t80) REVERT: E 441 ARG cc_start: 0.9136 (ttp-170) cc_final: 0.8891 (ttm110) REVERT: E 454 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8573 (pp20) outliers start: 50 outliers final: 33 residues processed: 241 average time/residue: 0.4551 time to fit residues: 124.5620 Evaluate side-chains 230 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 166 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.061220 restraints weight = 95999.364| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.81 r_work: 0.2617 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16700 Z= 0.252 Angle : 0.705 11.728 22820 Z= 0.340 Chirality : 0.048 0.564 2603 Planarity : 0.005 0.056 2834 Dihedral : 7.703 48.282 2523 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.79 % Allowed : 17.72 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.22 (0.19), residues: 1985 helix: 2.30 (0.18), residues: 806 sheet: 0.41 (0.25), residues: 451 loop : -0.61 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 347 TYR 0.026 0.001 TYR D 115 PHE 0.016 0.001 PHE B 462 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00586 (16675) covalent geometry : angle 0.67884 (22755) SS BOND : bond 0.00820 ( 10) SS BOND : angle 2.25550 ( 20) hydrogen bonds : bond 0.05832 ( 855) hydrogen bonds : angle 4.42745 ( 2760) link_BETA1-4 : bond 0.00423 ( 5) link_BETA1-4 : angle 2.12000 ( 15) link_NAG-ASN : bond 0.00593 ( 10) link_NAG-ASN : angle 4.80132 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8218 (t80) REVERT: A 435 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8712 (mptt) REVERT: A 454 GLU cc_start: 0.8784 (tp30) cc_final: 0.8481 (tp30) REVERT: B 302 ILE cc_start: 0.9043 (mm) cc_final: 0.8730 (pp) REVERT: B 338 TRP cc_start: 0.8790 (m-10) cc_final: 0.8326 (m100) REVERT: B 432 ASP cc_start: 0.9346 (m-30) cc_final: 0.8941 (p0) REVERT: B 435 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8393 (mtmm) REVERT: B 439 GLU cc_start: 0.8810 (mp0) cc_final: 0.8312 (mp0) REVERT: C 454 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8629 (tm-30) REVERT: C 476 SER cc_start: 0.9188 (t) cc_final: 0.8829 (p) REVERT: D 330 TRP cc_start: 0.7719 (m100) cc_final: 0.7304 (t-100) REVERT: E 336 LEU cc_start: 0.9244 (mm) cc_final: 0.9038 (mm) REVERT: E 342 PHE cc_start: 0.9145 (t80) cc_final: 0.8885 (t80) REVERT: E 441 ARG cc_start: 0.9144 (ttp-170) cc_final: 0.8925 (ttm110) REVERT: E 454 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8715 (pp20) REVERT: E 468 ASP cc_start: 0.8698 (m-30) cc_final: 0.8468 (t0) outliers start: 67 outliers final: 34 residues processed: 242 average time/residue: 0.3978 time to fit residues: 110.7164 Evaluate side-chains 238 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 477 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 157 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 127 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN D 116 ASN E 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.066414 restraints weight = 61194.510| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.00 r_work: 0.2709 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16700 Z= 0.119 Angle : 0.645 11.783 22820 Z= 0.303 Chirality : 0.046 0.619 2603 Planarity : 0.004 0.051 2834 Dihedral : 6.550 39.728 2523 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.83 % Allowed : 19.14 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.35 (0.19), residues: 1985 helix: 2.41 (0.18), residues: 811 sheet: 0.56 (0.26), residues: 436 loop : -0.62 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 347 TYR 0.020 0.001 TYR B 296 PHE 0.013 0.001 PHE A 478 TRP 0.015 0.001 TRP D 176 HIS 0.003 0.000 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00264 (16675) covalent geometry : angle 0.61367 (22755) SS BOND : bond 0.00816 ( 10) SS BOND : angle 2.24906 ( 20) hydrogen bonds : bond 0.04948 ( 855) hydrogen bonds : angle 4.11197 ( 2760) link_BETA1-4 : bond 0.00438 ( 5) link_BETA1-4 : angle 2.47103 ( 15) link_NAG-ASN : bond 0.00373 ( 10) link_NAG-ASN : angle 4.95423 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8160 (t80) REVERT: B 302 ILE cc_start: 0.8980 (mm) cc_final: 0.8650 (pp) REVERT: B 338 TRP cc_start: 0.8798 (m-10) cc_final: 0.8355 (m100) REVERT: B 432 ASP cc_start: 0.9255 (m-30) cc_final: 0.8821 (p0) REVERT: B 435 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8355 (mtmm) REVERT: B 439 GLU cc_start: 0.8793 (mp0) cc_final: 0.8239 (mp0) REVERT: C 267 THR cc_start: 0.8693 (m) cc_final: 0.8480 (p) REVERT: C 271 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8845 (m) REVERT: C 454 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8541 (tm-30) REVERT: D 302 ILE cc_start: 0.9173 (mm) cc_final: 0.8801 (pt) REVERT: D 330 TRP cc_start: 0.7653 (m100) cc_final: 0.7223 (t-100) REVERT: E 260 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8176 (mt-10) REVERT: E 342 PHE cc_start: 0.9076 (t80) cc_final: 0.8832 (t80) REVERT: E 438 GLU cc_start: 0.8746 (tp30) cc_final: 0.8488 (tp30) REVERT: E 441 ARG cc_start: 0.9107 (ttp-170) cc_final: 0.8896 (ttm110) REVERT: E 454 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8656 (pp20) outliers start: 50 outliers final: 24 residues processed: 236 average time/residue: 0.4108 time to fit residues: 111.1378 Evaluate side-chains 230 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 49 optimal weight: 0.0770 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 127 optimal weight: 0.0270 chunk 144 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN D 116 ASN E 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.065127 restraints weight = 88082.744| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.75 r_work: 0.2664 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16700 Z= 0.137 Angle : 0.639 11.854 22820 Z= 0.304 Chirality : 0.046 0.597 2603 Planarity : 0.004 0.050 2834 Dihedral : 6.262 38.313 2521 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.89 % Allowed : 19.88 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.39 (0.19), residues: 1985 helix: 2.42 (0.18), residues: 813 sheet: 0.61 (0.26), residues: 436 loop : -0.58 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 347 TYR 0.022 0.001 TYR E 296 PHE 0.012 0.001 PHE B 462 TRP 0.016 0.001 TRP D 176 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00313 (16675) covalent geometry : angle 0.60762 (22755) SS BOND : bond 0.00826 ( 10) SS BOND : angle 2.23268 ( 20) hydrogen bonds : bond 0.04929 ( 855) hydrogen bonds : angle 4.09094 ( 2760) link_BETA1-4 : bond 0.00212 ( 5) link_BETA1-4 : angle 2.48514 ( 15) link_NAG-ASN : bond 0.00142 ( 10) link_NAG-ASN : angle 4.91744 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8162 (t80) REVERT: A 296 TYR cc_start: 0.8302 (t80) cc_final: 0.7622 (t80) REVERT: B 302 ILE cc_start: 0.9007 (mm) cc_final: 0.8664 (pp) REVERT: B 338 TRP cc_start: 0.8822 (m-10) cc_final: 0.8359 (m100) REVERT: B 432 ASP cc_start: 0.9257 (m-30) cc_final: 0.8814 (p0) REVERT: B 435 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8465 (mmtt) REVERT: B 439 GLU cc_start: 0.8818 (mp0) cc_final: 0.8253 (mp0) REVERT: C 64 ASP cc_start: 0.8706 (t0) cc_final: 0.8367 (t0) REVERT: D 302 ILE cc_start: 0.9176 (mm) cc_final: 0.8912 (pt) REVERT: D 330 TRP cc_start: 0.7684 (m100) cc_final: 0.7275 (t-100) REVERT: E 260 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8292 (mt-10) REVERT: E 342 PHE cc_start: 0.9054 (t80) cc_final: 0.8804 (t80) REVERT: E 438 GLU cc_start: 0.8760 (tp30) cc_final: 0.8477 (tp30) REVERT: E 441 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8899 (ttm110) REVERT: E 454 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8699 (pp20) outliers start: 51 outliers final: 29 residues processed: 227 average time/residue: 0.4386 time to fit residues: 113.7879 Evaluate side-chains 234 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 441 ARG Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 59 optimal weight: 0.3980 chunk 164 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 72 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.065682 restraints weight = 80214.800| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.44 r_work: 0.2684 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16700 Z= 0.136 Angle : 0.651 11.995 22820 Z= 0.307 Chirality : 0.047 0.612 2603 Planarity : 0.004 0.050 2834 Dihedral : 6.079 37.315 2521 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.72 % Allowed : 20.39 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.42 (0.19), residues: 1985 helix: 2.43 (0.18), residues: 816 sheet: 0.57 (0.25), residues: 442 loop : -0.54 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 347 TYR 0.021 0.001 TYR E 296 PHE 0.013 0.001 PHE A 478 TRP 0.020 0.001 TRP D 176 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00312 (16675) covalent geometry : angle 0.61924 (22755) SS BOND : bond 0.00816 ( 10) SS BOND : angle 2.23035 ( 20) hydrogen bonds : bond 0.04885 ( 855) hydrogen bonds : angle 4.06876 ( 2760) link_BETA1-4 : bond 0.00256 ( 5) link_BETA1-4 : angle 2.46174 ( 15) link_NAG-ASN : bond 0.00167 ( 10) link_NAG-ASN : angle 4.97713 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8186 (t80) REVERT: A 296 TYR cc_start: 0.8274 (t80) cc_final: 0.7632 (t80) REVERT: B 295 GLN cc_start: 0.8751 (mt0) cc_final: 0.8540 (mt0) REVERT: B 338 TRP cc_start: 0.8795 (m-10) cc_final: 0.8343 (m100) REVERT: B 435 LYS cc_start: 0.8999 (mtmt) cc_final: 0.8409 (mmtt) REVERT: B 439 GLU cc_start: 0.8918 (mp0) cc_final: 0.8362 (mp0) REVERT: C 64 ASP cc_start: 0.8678 (t0) cc_final: 0.8381 (t0) REVERT: D 302 ILE cc_start: 0.9188 (mm) cc_final: 0.8816 (pt) REVERT: D 330 TRP cc_start: 0.7680 (m100) cc_final: 0.7251 (t-100) REVERT: D 345 MET cc_start: 0.8690 (mtm) cc_final: 0.8303 (mtp) REVERT: E 260 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8201 (mt-10) REVERT: E 342 PHE cc_start: 0.9053 (t80) cc_final: 0.8807 (t80) REVERT: E 438 GLU cc_start: 0.8741 (tp30) cc_final: 0.8463 (tp30) REVERT: E 441 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8867 (ttm110) REVERT: E 452 GLU cc_start: 0.8307 (pp20) cc_final: 0.8090 (pp20) outliers start: 48 outliers final: 26 residues processed: 228 average time/residue: 0.4582 time to fit residues: 118.9786 Evaluate side-chains 231 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 441 ARG Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 6.9990 chunk 55 optimal weight: 0.0000 chunk 97 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.082082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.066099 restraints weight = 77833.235| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.38 r_work: 0.2693 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16700 Z= 0.128 Angle : 0.644 12.017 22820 Z= 0.305 Chirality : 0.046 0.609 2603 Planarity : 0.004 0.052 2834 Dihedral : 5.893 35.869 2521 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.43 % Allowed : 21.12 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.44 (0.19), residues: 1985 helix: 2.44 (0.18), residues: 816 sheet: 0.58 (0.25), residues: 442 loop : -0.53 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 347 TYR 0.027 0.001 TYR E 296 PHE 0.010 0.001 PHE D 157 TRP 0.024 0.001 TRP D 176 HIS 0.002 0.000 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00292 (16675) covalent geometry : angle 0.61261 (22755) SS BOND : bond 0.00824 ( 10) SS BOND : angle 2.23690 ( 20) hydrogen bonds : bond 0.04741 ( 855) hydrogen bonds : angle 4.00883 ( 2760) link_BETA1-4 : bond 0.00235 ( 5) link_BETA1-4 : angle 2.38681 ( 15) link_NAG-ASN : bond 0.00215 ( 10) link_NAG-ASN : angle 5.00182 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8187 (t80) REVERT: A 296 TYR cc_start: 0.8276 (t80) cc_final: 0.7621 (t80) REVERT: B 295 GLN cc_start: 0.8818 (mt0) cc_final: 0.8613 (mt0) REVERT: B 302 ILE cc_start: 0.8924 (mp) cc_final: 0.8619 (pp) REVERT: B 338 TRP cc_start: 0.8863 (m-10) cc_final: 0.8397 (m100) REVERT: B 435 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8393 (mmtt) REVERT: B 439 GLU cc_start: 0.8960 (mp0) cc_final: 0.8381 (mp0) REVERT: C 64 ASP cc_start: 0.8700 (t0) cc_final: 0.8435 (t0) REVERT: C 275 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8146 (t80) REVERT: D 302 ILE cc_start: 0.9190 (mm) cc_final: 0.8921 (pt) REVERT: D 330 TRP cc_start: 0.7666 (m100) cc_final: 0.7236 (t-100) REVERT: D 345 MET cc_start: 0.8674 (mtm) cc_final: 0.8346 (mtp) REVERT: E 260 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8162 (mt-10) REVERT: E 342 PHE cc_start: 0.9054 (t80) cc_final: 0.8813 (t80) REVERT: E 438 GLU cc_start: 0.8728 (tp30) cc_final: 0.8439 (tp30) REVERT: E 441 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8895 (ttm110) REVERT: E 452 GLU cc_start: 0.8284 (pp20) cc_final: 0.8054 (pp20) outliers start: 43 outliers final: 31 residues processed: 226 average time/residue: 0.4307 time to fit residues: 111.4168 Evaluate side-chains 231 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 441 ARG Chi-restraints excluded: chain E residue 468 ASP Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 10 optimal weight: 0.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.080087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.063676 restraints weight = 81879.283| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.59 r_work: 0.2669 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16700 Z= 0.148 Angle : 0.653 12.252 22820 Z= 0.309 Chirality : 0.047 0.625 2603 Planarity : 0.004 0.060 2834 Dihedral : 5.776 34.925 2521 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.38 % Allowed : 21.46 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.46 (0.19), residues: 1985 helix: 2.48 (0.18), residues: 814 sheet: 0.57 (0.25), residues: 442 loop : -0.52 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 347 TYR 0.024 0.001 TYR E 296 PHE 0.012 0.001 PHE A 478 TRP 0.030 0.001 TRP D 176 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00345 (16675) covalent geometry : angle 0.62105 (22755) SS BOND : bond 0.00811 ( 10) SS BOND : angle 2.22992 ( 20) hydrogen bonds : bond 0.04840 ( 855) hydrogen bonds : angle 4.04497 ( 2760) link_BETA1-4 : bond 0.00181 ( 5) link_BETA1-4 : angle 2.29150 ( 15) link_NAG-ASN : bond 0.00148 ( 10) link_NAG-ASN : angle 5.07418 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8260 (t80) REVERT: A 296 TYR cc_start: 0.8329 (t80) cc_final: 0.7663 (t80) REVERT: B 302 ILE cc_start: 0.8973 (mp) cc_final: 0.8664 (pp) REVERT: B 338 TRP cc_start: 0.8863 (m-10) cc_final: 0.8393 (m100) REVERT: B 435 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8349 (mmtt) REVERT: B 439 GLU cc_start: 0.8940 (mp0) cc_final: 0.8357 (mp0) REVERT: C 64 ASP cc_start: 0.8761 (t0) cc_final: 0.8490 (t0) REVERT: C 275 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8266 (t80) REVERT: D 176 TRP cc_start: 0.8552 (m-90) cc_final: 0.8346 (m-90) REVERT: D 302 ILE cc_start: 0.9196 (mm) cc_final: 0.8917 (pt) REVERT: D 330 TRP cc_start: 0.7679 (m100) cc_final: 0.7248 (t-100) REVERT: D 345 MET cc_start: 0.8653 (mtm) cc_final: 0.8373 (mtp) REVERT: E 342 PHE cc_start: 0.9033 (t80) cc_final: 0.8798 (t80) REVERT: E 438 GLU cc_start: 0.8756 (tp30) cc_final: 0.8482 (tp30) REVERT: E 452 GLU cc_start: 0.8338 (pp20) cc_final: 0.8097 (pp20) outliers start: 42 outliers final: 30 residues processed: 219 average time/residue: 0.4694 time to fit residues: 117.1193 Evaluate side-chains 228 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 132 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 55 optimal weight: 0.0060 chunk 149 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.080188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.063769 restraints weight = 73402.930| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.23 r_work: 0.2650 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16700 Z= 0.183 Angle : 0.685 12.666 22820 Z= 0.327 Chirality : 0.048 0.661 2603 Planarity : 0.004 0.074 2834 Dihedral : 5.672 32.823 2521 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.21 % Allowed : 21.80 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.47 (0.19), residues: 1985 helix: 2.48 (0.18), residues: 811 sheet: 0.54 (0.25), residues: 457 loop : -0.49 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 441 TYR 0.029 0.001 TYR E 296 PHE 0.011 0.001 PHE D 157 TRP 0.028 0.001 TRP D 176 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00426 (16675) covalent geometry : angle 0.65334 (22755) SS BOND : bond 0.00805 ( 10) SS BOND : angle 2.23849 ( 20) hydrogen bonds : bond 0.05242 ( 855) hydrogen bonds : angle 4.17227 ( 2760) link_BETA1-4 : bond 0.00175 ( 5) link_BETA1-4 : angle 2.11812 ( 15) link_NAG-ASN : bond 0.00197 ( 10) link_NAG-ASN : angle 5.23690 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8247 (t80) REVERT: A 296 TYR cc_start: 0.8326 (t80) cc_final: 0.7584 (t80) REVERT: B 80 MET cc_start: 0.9264 (mtm) cc_final: 0.9000 (mtm) REVERT: B 338 TRP cc_start: 0.8867 (m-10) cc_final: 0.8380 (m100) REVERT: B 435 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8310 (mmtt) REVERT: B 439 GLU cc_start: 0.8949 (mp0) cc_final: 0.8349 (mp0) REVERT: C 64 ASP cc_start: 0.8723 (t0) cc_final: 0.8451 (t0) REVERT: C 275 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8240 (t80) REVERT: D 302 ILE cc_start: 0.9188 (mm) cc_final: 0.8808 (pt) REVERT: D 330 TRP cc_start: 0.7669 (m100) cc_final: 0.7241 (t-100) REVERT: D 345 MET cc_start: 0.8662 (mtm) cc_final: 0.8313 (mtp) REVERT: E 342 PHE cc_start: 0.9025 (t80) cc_final: 0.8788 (t80) REVERT: E 438 GLU cc_start: 0.8735 (tp30) cc_final: 0.8512 (tp30) REVERT: E 452 GLU cc_start: 0.8335 (pp20) cc_final: 0.8104 (pp20) outliers start: 39 outliers final: 28 residues processed: 221 average time/residue: 0.4764 time to fit residues: 119.8803 Evaluate side-chains 226 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 166 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 12 optimal weight: 0.0270 chunk 152 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.062898 restraints weight = 72530.538| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.21 r_work: 0.2649 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 16700 Z= 0.200 Angle : 0.858 59.064 22820 Z= 0.463 Chirality : 0.049 0.658 2603 Planarity : 0.005 0.079 2834 Dihedral : 5.682 32.808 2519 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.87 % Allowed : 22.42 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.47 (0.19), residues: 1985 helix: 2.49 (0.18), residues: 811 sheet: 0.54 (0.25), residues: 457 loop : -0.49 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 441 TYR 0.026 0.001 TYR E 296 PHE 0.011 0.001 PHE D 157 TRP 0.131 0.002 TRP E 176 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00443 (16675) covalent geometry : angle 0.83343 (22755) SS BOND : bond 0.00816 ( 10) SS BOND : angle 2.22401 ( 20) hydrogen bonds : bond 0.05180 ( 855) hydrogen bonds : angle 4.16934 ( 2760) link_BETA1-4 : bond 0.00227 ( 5) link_BETA1-4 : angle 2.17828 ( 15) link_NAG-ASN : bond 0.00162 ( 10) link_NAG-ASN : angle 5.22279 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8239 (t80) REVERT: A 296 TYR cc_start: 0.8312 (t80) cc_final: 0.7569 (t80) REVERT: B 80 MET cc_start: 0.9262 (mtm) cc_final: 0.8994 (mtm) REVERT: B 302 ILE cc_start: 0.8928 (mp) cc_final: 0.8619 (pp) REVERT: B 338 TRP cc_start: 0.8870 (m-10) cc_final: 0.8383 (m100) REVERT: B 435 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8307 (mmtt) REVERT: B 439 GLU cc_start: 0.8944 (mp0) cc_final: 0.8347 (mp0) REVERT: C 64 ASP cc_start: 0.8706 (t0) cc_final: 0.8446 (t0) REVERT: C 275 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8235 (t80) REVERT: D 116 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8240 (p0) REVERT: D 302 ILE cc_start: 0.9113 (mm) cc_final: 0.8813 (pt) REVERT: D 330 TRP cc_start: 0.7665 (m100) cc_final: 0.7240 (t-100) REVERT: D 345 MET cc_start: 0.8661 (mtm) cc_final: 0.8318 (mtp) REVERT: E 342 PHE cc_start: 0.9029 (t80) cc_final: 0.8793 (t80) REVERT: E 452 GLU cc_start: 0.8324 (pp20) cc_final: 0.8090 (pp20) outliers start: 33 outliers final: 27 residues processed: 207 average time/residue: 0.4829 time to fit residues: 114.3319 Evaluate side-chains 224 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 187 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.062533 restraints weight = 79246.032| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 4.46 r_work: 0.2641 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 16700 Z= 0.200 Angle : 0.858 59.195 22820 Z= 0.463 Chirality : 0.049 0.658 2603 Planarity : 0.005 0.079 2834 Dihedral : 5.681 32.808 2519 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.64 % Allowed : 22.65 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.47 (0.19), residues: 1985 helix: 2.49 (0.18), residues: 811 sheet: 0.54 (0.25), residues: 457 loop : -0.49 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 441 TYR 0.026 0.001 TYR E 296 PHE 0.011 0.001 PHE D 157 TRP 0.131 0.002 TRP E 176 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00443 (16675) covalent geometry : angle 0.83352 (22755) SS BOND : bond 0.00815 ( 10) SS BOND : angle 2.22402 ( 20) hydrogen bonds : bond 0.05180 ( 855) hydrogen bonds : angle 4.16934 ( 2760) link_BETA1-4 : bond 0.00222 ( 5) link_BETA1-4 : angle 2.17428 ( 15) link_NAG-ASN : bond 0.00162 ( 10) link_NAG-ASN : angle 5.22277 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4748.17 seconds wall clock time: 81 minutes 44.82 seconds (4904.82 seconds total)