Starting phenix.real_space_refine on Thu Feb 5 09:36:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lha_63091/02_2026/9lha_63091.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lha_63091/02_2026/9lha_63091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lha_63091/02_2026/9lha_63091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lha_63091/02_2026/9lha_63091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lha_63091/02_2026/9lha_63091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lha_63091/02_2026/9lha_63091.map" } resolution = 2.96 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 10540 2.51 5 N 2606 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 13 residue(s): 0.01s 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: 16209 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" 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: "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: 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: "D" 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: "E" 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: "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: 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: "D" 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: "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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.37, per 1000 atoms: 0.45 Number of scatterers: 16209 At special positions: 0 Unit cell: (89.89, 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 2606 7.00 C 10540 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 601 " - " ASN C 46 " " NAG D 602 " - " 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: 1.40 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: 50 helices and 20 sheets defined 43.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.536A pdb=" N LYS A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 249 removed outlier: 5.172A pdb=" N ILE A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.550A pdb=" N LEU A 254 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' 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 removed outlier: 3.752A pdb=" N TRP A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 490 removed outlier: 4.179A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.704A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 249 removed outlier: 4.955A pdb=" N ILE B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.598A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 260 through 281 Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 431 through 490 removed outlier: 4.452A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 502 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.725A 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: 3.806A pdb=" N CYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.533A pdb=" N PHE C 252 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.657A pdb=" N GLY C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 281 removed outlier: 3.734A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 431 through 490 removed outlier: 3.695A pdb=" N LYS C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.262A 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: 3.647A 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 249 removed outlier: 3.564A pdb=" N CYS D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 260 through 283 removed outlier: 3.511A pdb=" N PHE D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 431 through 489 removed outlier: 3.628A pdb=" N LYS D 435 " --> pdb=" O PRO D 431 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 489 " --> pdb=" O GLY D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.662A 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: 3.518A pdb=" N CYS E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 252 removed outlier: 3.610A pdb=" N PHE E 252 " --> pdb=" O LEU E 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 249 through 252' Processing helix chain 'E' and resid 260 through 281 removed outlier: 4.056A pdb=" N LEU E 278 " --> pdb=" O VAL E 274 " (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 490 removed outlier: 3.803A pdb=" N ILE E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 480 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA E 490 " --> pdb=" O ILE E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 removed outlier: 4.708A pdb=" N THR A 83 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A 52 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 66 removed outlier: 7.386A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 76 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 144 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.640A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.955A 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: 3.640A pdb=" N GLY A 169 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.610A 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 removed outlier: 3.553A pdb=" N VAL B 100 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 66 removed outlier: 5.832A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.626A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.889A 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: 4.626A 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 removed outlier: 3.793A pdb=" N TRP C 82 " --> pdb=" O CYS C 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.793A pdb=" N TRP C 82 " --> pdb=" O CYS C 138 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 71 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP C 64 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 79 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 7.100A 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: 5.294A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 7.051A 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: 5.294A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 removed outlier: 4.628A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 66 removed outlier: 7.535A pdb=" N LEU D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N TRP D 77 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN D 75 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 76 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.726A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.975A 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: 4.726A 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: 6.992A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N THR E 83 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N TYR E 54 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.524A 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: 6.954A 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 114 917 hydrogen bonds defined for protein. 2664 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: 2.97 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2572 1.31 - 1.44: 4636 1.44 - 1.57: 9270 1.57 - 1.70: 6 1.70 - 1.83: 170 Bond restraints: 16654 Sorted by residual: bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.628 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" C6 NCT B 601 " pdb=" N2 NCT B 601 " ideal model delta sigma weight residual 1.452 1.628 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" C6 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.627 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" C6 NCT B 601 " pdb=" C7 NCT B 601 " ideal model delta sigma weight residual 1.536 1.371 0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" C6 NCT A 601 " pdb=" C7 NCT A 601 " ideal model delta sigma weight residual 1.536 1.371 0.165 2.00e-02 2.50e+03 6.79e+01 ... (remaining 16649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 22204 1.95 - 3.89: 402 3.89 - 5.84: 96 5.84 - 7.79: 14 7.79 - 9.73: 5 Bond angle restraints: 22721 Sorted by residual: angle pdb=" C SER E 271 " pdb=" CA SER E 271 " pdb=" CB SER E 271 " ideal model delta sigma weight residual 110.88 105.69 5.19 1.57e+00 4.06e-01 1.09e+01 angle pdb=" N THR E 267 " pdb=" CA THR E 267 " pdb=" C THR E 267 " ideal model delta sigma weight residual 111.14 107.59 3.55 1.08e+00 8.57e-01 1.08e+01 angle pdb=" C3 NAG I 1 " pdb=" C4 NAG I 1 " pdb=" C5 NAG I 1 " ideal model delta sigma weight residual 109.38 119.11 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" N LEU E 269 " pdb=" CA LEU E 269 " pdb=" C LEU E 269 " ideal model delta sigma weight residual 111.14 107.66 3.48 1.08e+00 8.57e-01 1.04e+01 angle pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" C5 NAG G 1 " ideal model delta sigma weight residual 109.38 118.93 -9.55 3.00e+00 1.11e-01 1.01e+01 ... (remaining 22716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.51: 8929 20.51 - 41.02: 911 41.02 - 61.53: 158 61.53 - 82.04: 35 82.04 - 102.55: 11 Dihedral angle restraints: 10044 sinusoidal: 4149 harmonic: 5895 Sorted by residual: dihedral pdb=" CB CYS A 150 " pdb=" SG CYS A 150 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual 93.00 48.71 44.29 1 1.00e+01 1.00e-02 2.73e+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 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA CYS C 212 " pdb=" C CYS C 212 " pdb=" N CYS C 213 " pdb=" CA CYS C 213 " ideal model delta harmonic sigma weight residual 180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 10041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2324 0.064 - 0.128: 247 0.128 - 0.191: 27 0.191 - 0.255: 2 0.255 - 0.319: 3 Chirality restraints: 2603 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 133 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+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 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+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 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 2600 not shown) Planarity restraints: 2843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 191 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO E 192 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 192 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 192 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 327 " -0.042 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO E 328 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 328 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 328 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 157 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO E 158 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 158 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 158 " -0.032 5.00e-02 4.00e+02 ... (remaining 2840 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4895 2.83 - 3.35: 14295 3.35 - 3.87: 26530 3.87 - 4.38: 29530 4.38 - 4.90: 52477 Nonbonded interactions: 127727 Sorted by model distance: nonbonded pdb=" OE2 GLU D 67 " pdb=" NH2 ARG D 228 " model vdw 2.313 3.120 nonbonded pdb=" O ALA E 455 " pdb=" OG SER E 458 " model vdw 2.319 3.040 nonbonded pdb=" OE2 GLU A 67 " pdb=" NH2 ARG A 228 " model vdw 2.320 3.120 nonbonded pdb=" OD2 ASP D 66 " pdb=" ND2 ASN D 69 " model vdw 2.326 3.120 nonbonded pdb=" NE ARG A 101 " pdb=" O SER E 172 " model vdw 2.328 3.120 ... (remaining 127722 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 136 or resid 138 through 502)) selection = (chain 'B' and (resid 23 through 136 or resid 138 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 502)) selection = (chain 'E' and (resid 23 through 136 or resid 138 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=0.38 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: 0.920 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.440 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 0.176 16679 Z= 0.387 Angle : 0.665 9.732 22786 Z= 0.312 Chirality : 0.043 0.319 2603 Planarity : 0.005 0.067 2833 Dihedral : 16.748 102.553 6204 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.17 % Allowed : 16.83 % Favored : 83.00 % 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: 1.25 (0.19), residues: 1985 helix: 2.48 (0.18), residues: 813 sheet: 0.15 (0.25), residues: 432 loop : -0.60 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 347 TYR 0.008 0.001 TYR C 442 PHE 0.016 0.001 PHE E 342 TRP 0.014 0.001 TRP B 156 HIS 0.004 0.000 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00762 (16654) covalent geometry : angle 0.65139 (22721) SS BOND : bond 0.00664 ( 10) SS BOND : angle 1.23223 ( 20) hydrogen bonds : bond 0.11876 ( 849) hydrogen bonds : angle 5.31832 ( 2664) link_BETA1-4 : bond 0.00332 ( 5) link_BETA1-4 : angle 0.46657 ( 15) link_NAG-ASN : bond 0.00243 ( 10) link_NAG-ASN : angle 3.67617 ( 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 298 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8516 (pt0) cc_final: 0.8053 (tm-30) REVERT: A 301 MET cc_start: 0.8883 (mmp) cc_final: 0.8590 (tpp) REVERT: A 316 GLN cc_start: 0.9109 (tt0) cc_final: 0.8766 (tp-100) REVERT: A 435 LYS cc_start: 0.9373 (mttm) cc_final: 0.9124 (mmmm) REVERT: A 437 LEU cc_start: 0.9408 (tp) cc_final: 0.9068 (tt) REVERT: A 441 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8781 (mtm-85) REVERT: A 454 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8791 (tm-30) REVERT: B 453 SER cc_start: 0.8708 (m) cc_final: 0.8177 (p) REVERT: B 488 MET cc_start: 0.8518 (mmm) cc_final: 0.8242 (mmm) REVERT: C 160 ASP cc_start: 0.8072 (m-30) cc_final: 0.7840 (m-30) REVERT: C 435 LYS cc_start: 0.9374 (mttp) cc_final: 0.8818 (ptpp) REVERT: C 451 ASP cc_start: 0.9216 (m-30) cc_final: 0.8863 (m-30) REVERT: C 457 CYS cc_start: 0.9085 (m) cc_final: 0.8793 (m) REVERT: C 468 ASP cc_start: 0.8859 (t0) cc_final: 0.8658 (t0) REVERT: C 488 MET cc_start: 0.8650 (tpp) cc_final: 0.7720 (tmm) REVERT: D 245 SER cc_start: 0.9440 (t) cc_final: 0.9201 (p) REVERT: D 302 ILE cc_start: 0.9416 (mt) cc_final: 0.9212 (mp) REVERT: D 454 GLU cc_start: 0.9045 (tp30) cc_final: 0.8220 (tm-30) REVERT: D 471 CYS cc_start: 0.9198 (m) cc_final: 0.8799 (t) REVERT: D 476 SER cc_start: 0.8982 (m) cc_final: 0.8774 (p) REVERT: E 182 MET cc_start: 0.8511 (ttt) cc_final: 0.8265 (ttp) REVERT: E 204 LYS cc_start: 0.9238 (ttpp) cc_final: 0.9035 (mppt) REVERT: E 338 TRP cc_start: 0.8643 (m-10) cc_final: 0.7008 (t60) REVERT: E 439 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8847 (mm-30) outliers start: 3 outliers final: 2 residues processed: 296 average time/residue: 0.4416 time to fit residues: 150.5349 Evaluate side-chains 228 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 274 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 450 GLN C 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.081120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.064253 restraints weight = 83604.763| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.61 r_work: 0.2668 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16679 Z= 0.125 Angle : 0.633 14.549 22786 Z= 0.299 Chirality : 0.043 0.443 2603 Planarity : 0.005 0.057 2833 Dihedral : 8.546 68.360 2522 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.38 % Allowed : 19.60 % Favored : 78.02 % 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: 1.41 (0.19), residues: 1985 helix: 2.56 (0.18), residues: 815 sheet: 0.34 (0.25), residues: 432 loop : -0.55 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.018 0.001 TYR D 151 PHE 0.013 0.001 PHE B 157 TRP 0.018 0.001 TRP E 176 HIS 0.005 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00278 (16654) covalent geometry : angle 0.61054 (22721) SS BOND : bond 0.00766 ( 10) SS BOND : angle 1.64012 ( 20) hydrogen bonds : bond 0.04867 ( 849) hydrogen bonds : angle 4.33131 ( 2664) link_BETA1-4 : bond 0.00421 ( 5) link_BETA1-4 : angle 1.85623 ( 15) link_NAG-ASN : bond 0.00568 ( 10) link_NAG-ASN : angle 4.35441 ( 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 293 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8585 (pt0) cc_final: 0.8080 (tm-30) REVERT: A 296 TYR cc_start: 0.8459 (t80) cc_final: 0.8211 (t80) REVERT: A 454 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8715 (tp30) REVERT: B 275 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7648 (t80) REVERT: B 453 SER cc_start: 0.8344 (m) cc_final: 0.7955 (p) REVERT: B 488 MET cc_start: 0.8506 (mmm) cc_final: 0.8232 (mmm) REVERT: C 160 ASP cc_start: 0.8127 (m-30) cc_final: 0.7643 (m-30) REVERT: C 244 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8532 (mp) REVERT: C 488 MET cc_start: 0.8558 (tpp) cc_final: 0.7423 (tmm) REVERT: D 245 SER cc_start: 0.9414 (t) cc_final: 0.9137 (p) REVERT: D 454 GLU cc_start: 0.9030 (tp30) cc_final: 0.8275 (tm-30) REVERT: D 471 CYS cc_start: 0.9099 (m) cc_final: 0.8685 (t) REVERT: E 182 MET cc_start: 0.8867 (ttt) cc_final: 0.8630 (ttm) REVERT: E 204 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8763 (mppt) REVERT: E 276 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8106 (ttp) REVERT: E 301 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8463 (mtt) REVERT: E 338 TRP cc_start: 0.8719 (m-10) cc_final: 0.7212 (t60) REVERT: E 439 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9011 (mm-30) outliers start: 42 outliers final: 13 residues processed: 262 average time/residue: 0.4170 time to fit residues: 127.1107 Evaluate side-chains 244 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 478 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 86 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 450 GLN B 49 GLN C 163 HIS E 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.077944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.061101 restraints weight = 95107.037| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.81 r_work: 0.2594 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16679 Z= 0.213 Angle : 0.665 14.097 22786 Z= 0.317 Chirality : 0.046 0.506 2603 Planarity : 0.004 0.052 2833 Dihedral : 6.737 59.847 2519 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.29 % Allowed : 19.15 % Favored : 77.56 % 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: 1.44 (0.19), residues: 1985 helix: 2.48 (0.18), residues: 815 sheet: 0.28 (0.25), residues: 465 loop : -0.36 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 347 TYR 0.011 0.001 TYR D 296 PHE 0.012 0.001 PHE D 157 TRP 0.028 0.001 TRP E 176 HIS 0.005 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00495 (16654) covalent geometry : angle 0.63926 (22721) SS BOND : bond 0.00738 ( 10) SS BOND : angle 1.54709 ( 20) hydrogen bonds : bond 0.05393 ( 849) hydrogen bonds : angle 4.33258 ( 2664) link_BETA1-4 : bond 0.00440 ( 5) link_BETA1-4 : angle 1.85471 ( 15) link_NAG-ASN : bond 0.00294 ( 10) link_NAG-ASN : angle 4.84712 ( 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 290 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8706 (pt0) cc_final: 0.8079 (tm-30) REVERT: A 296 TYR cc_start: 0.8587 (t80) cc_final: 0.7932 (t80) REVERT: A 437 LEU cc_start: 0.9270 (tt) cc_final: 0.9001 (tm) REVERT: A 454 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8798 (tp30) REVERT: B 275 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 453 SER cc_start: 0.8454 (m) cc_final: 0.8083 (p) REVERT: B 488 MET cc_start: 0.8617 (mmm) cc_final: 0.8350 (mmm) REVERT: C 104 ASP cc_start: 0.8955 (t0) cc_final: 0.8702 (t0) REVERT: C 160 ASP cc_start: 0.8264 (m-30) cc_final: 0.7708 (m-30) REVERT: C 459 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: C 468 ASP cc_start: 0.9025 (t70) cc_final: 0.8716 (t0) REVERT: C 488 MET cc_start: 0.8564 (tpp) cc_final: 0.7461 (tmm) REVERT: D 245 SER cc_start: 0.9416 (t) cc_final: 0.9182 (p) REVERT: D 454 GLU cc_start: 0.9067 (tp30) cc_final: 0.8368 (tm-30) REVERT: E 152 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9123 (mp) REVERT: E 276 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8159 (ttp) REVERT: E 301 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8544 (mtt) REVERT: E 439 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9039 (mm-30) outliers start: 58 outliers final: 26 residues processed: 252 average time/residue: 0.4232 time to fit residues: 123.6166 Evaluate side-chains 248 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 478 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 450 GLN 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 = 0.078957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.062450 restraints weight = 79147.808| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.42 r_work: 0.2635 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16679 Z= 0.146 Angle : 0.630 13.824 22786 Z= 0.296 Chirality : 0.045 0.513 2603 Planarity : 0.004 0.047 2833 Dihedral : 6.057 53.329 2519 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.95 % Allowed : 19.89 % Favored : 77.17 % 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: 1.49 (0.19), residues: 1985 helix: 2.52 (0.18), residues: 815 sheet: 0.29 (0.25), residues: 465 loop : -0.31 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 347 TYR 0.019 0.001 TYR D 151 PHE 0.012 0.001 PHE B 157 TRP 0.028 0.001 TRP E 176 HIS 0.002 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00334 (16654) covalent geometry : angle 0.60250 (22721) SS BOND : bond 0.00736 ( 10) SS BOND : angle 1.51411 ( 20) hydrogen bonds : bond 0.05003 ( 849) hydrogen bonds : angle 4.14347 ( 2664) link_BETA1-4 : bond 0.00383 ( 5) link_BETA1-4 : angle 1.69914 ( 15) link_NAG-ASN : bond 0.00167 ( 10) link_NAG-ASN : angle 4.82619 ( 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 285 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 TYR cc_start: 0.8530 (t80) cc_final: 0.8117 (t80) REVERT: A 437 LEU cc_start: 0.9244 (tt) cc_final: 0.8958 (tm) REVERT: A 454 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8785 (tp30) REVERT: B 275 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7765 (t80) REVERT: B 488 MET cc_start: 0.8604 (mmm) cc_final: 0.8341 (mmm) REVERT: C 104 ASP cc_start: 0.8887 (t0) cc_final: 0.8655 (t0) REVERT: C 160 ASP cc_start: 0.8187 (m-30) cc_final: 0.7673 (m-30) REVERT: C 244 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8532 (mp) REVERT: C 468 ASP cc_start: 0.8991 (t70) cc_final: 0.8637 (t0) REVERT: C 488 MET cc_start: 0.8579 (tpp) cc_final: 0.7473 (tmm) REVERT: D 245 SER cc_start: 0.9402 (t) cc_final: 0.9157 (p) REVERT: D 454 GLU cc_start: 0.9069 (tp30) cc_final: 0.8355 (tm-30) REVERT: E 182 MET cc_start: 0.8891 (ttt) cc_final: 0.8618 (ttp) REVERT: E 276 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8205 (ttp) REVERT: E 301 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8548 (mtt) REVERT: E 327 MET cc_start: 0.8568 (mtp) cc_final: 0.8028 (ttm) REVERT: E 439 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9028 (mm-30) outliers start: 52 outliers final: 24 residues processed: 254 average time/residue: 0.4157 time to fit residues: 122.3534 Evaluate side-chains 247 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 478 PHE 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 35 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 45 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.062149 restraints weight = 77223.996| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.39 r_work: 0.2603 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16679 Z= 0.223 Angle : 0.669 14.500 22786 Z= 0.320 Chirality : 0.046 0.520 2603 Planarity : 0.004 0.045 2833 Dihedral : 5.725 41.382 2519 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.06 % Allowed : 20.34 % Favored : 76.60 % 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: 1.45 (0.19), residues: 1985 helix: 2.43 (0.18), residues: 815 sheet: 0.29 (0.25), residues: 465 loop : -0.28 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.013 0.001 TYR D 296 PHE 0.013 0.001 PHE D 157 TRP 0.034 0.001 TRP E 176 HIS 0.003 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00520 (16654) covalent geometry : angle 0.64140 (22721) SS BOND : bond 0.00718 ( 10) SS BOND : angle 1.46697 ( 20) hydrogen bonds : bond 0.05486 ( 849) hydrogen bonds : angle 4.29048 ( 2664) link_BETA1-4 : bond 0.00363 ( 5) link_BETA1-4 : angle 1.81795 ( 15) link_NAG-ASN : bond 0.00277 ( 10) link_NAG-ASN : angle 5.00718 ( 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 272 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 LEU cc_start: 0.9267 (tt) cc_final: 0.9010 (tm) REVERT: A 454 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8772 (tp30) REVERT: B 120 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8652 (mm-30) REVERT: B 275 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7831 (t80) REVERT: B 488 MET cc_start: 0.8656 (mmm) cc_final: 0.8391 (mmm) REVERT: C 104 ASP cc_start: 0.8950 (t0) cc_final: 0.8725 (t0) REVERT: C 160 ASP cc_start: 0.8283 (m-30) cc_final: 0.7727 (m-30) REVERT: C 244 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8568 (mp) REVERT: C 468 ASP cc_start: 0.9011 (t70) cc_final: 0.8724 (t0) REVERT: C 488 MET cc_start: 0.8588 (tpp) cc_final: 0.7451 (tmm) REVERT: D 245 SER cc_start: 0.9411 (t) cc_final: 0.9175 (p) REVERT: D 454 GLU cc_start: 0.9086 (tp30) cc_final: 0.8378 (tm-30) REVERT: E 182 MET cc_start: 0.8933 (ttt) cc_final: 0.8695 (ttm) REVERT: E 276 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8124 (ttp) outliers start: 54 outliers final: 27 residues processed: 240 average time/residue: 0.4247 time to fit residues: 117.3371 Evaluate side-chains 240 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 478 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.062847 restraints weight = 73192.551| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 4.29 r_work: 0.2617 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16679 Z= 0.180 Angle : 0.653 13.905 22786 Z= 0.310 Chirality : 0.046 0.534 2603 Planarity : 0.004 0.045 2833 Dihedral : 5.545 37.313 2519 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.78 % Allowed : 20.85 % Favored : 76.37 % 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: 1.49 (0.19), residues: 1985 helix: 2.44 (0.18), residues: 815 sheet: 0.36 (0.25), residues: 459 loop : -0.26 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.020 0.001 TYR A 296 PHE 0.011 0.001 PHE B 157 TRP 0.034 0.001 TRP E 176 HIS 0.003 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00419 (16654) covalent geometry : angle 0.62551 (22721) SS BOND : bond 0.00715 ( 10) SS BOND : angle 1.47400 ( 20) hydrogen bonds : bond 0.05333 ( 849) hydrogen bonds : angle 4.23125 ( 2664) link_BETA1-4 : bond 0.00336 ( 5) link_BETA1-4 : angle 1.70091 ( 15) link_NAG-ASN : bond 0.00148 ( 10) link_NAG-ASN : angle 5.01004 ( 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 265 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 296 TYR cc_start: 0.8559 (t80) cc_final: 0.8353 (t80) REVERT: A 437 LEU cc_start: 0.9248 (tt) cc_final: 0.8993 (tm) REVERT: A 454 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8767 (tp30) REVERT: B 120 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8567 (mm-30) REVERT: B 121 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7912 (ptt90) REVERT: B 275 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7823 (t80) REVERT: B 470 LEU cc_start: 0.8955 (mp) cc_final: 0.8706 (mt) REVERT: B 488 MET cc_start: 0.8637 (mmm) cc_final: 0.8367 (mmm) REVERT: C 104 ASP cc_start: 0.8885 (t0) cc_final: 0.8678 (t0) REVERT: C 160 ASP cc_start: 0.8265 (m-30) cc_final: 0.7705 (m-30) REVERT: C 244 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8561 (mp) REVERT: C 468 ASP cc_start: 0.9015 (t70) cc_final: 0.8700 (t0) REVERT: C 488 MET cc_start: 0.8588 (tpp) cc_final: 0.7471 (tmm) REVERT: D 245 SER cc_start: 0.9386 (t) cc_final: 0.9146 (p) REVERT: D 454 GLU cc_start: 0.9097 (tp30) cc_final: 0.8400 (tm-30) REVERT: E 182 MET cc_start: 0.8922 (ttt) cc_final: 0.8699 (ttm) REVERT: E 276 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8158 (ttp) REVERT: E 327 MET cc_start: 0.8532 (mtp) cc_final: 0.8043 (ttm) outliers start: 49 outliers final: 31 residues processed: 240 average time/residue: 0.4372 time to fit residues: 120.5409 Evaluate side-chains 246 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 478 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 0.0000 chunk 190 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.081874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.065374 restraints weight = 78924.240| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 4.53 r_work: 0.2672 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16679 Z= 0.114 Angle : 0.619 15.003 22786 Z= 0.291 Chirality : 0.044 0.528 2603 Planarity : 0.004 0.044 2833 Dihedral : 5.359 36.203 2519 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.93 % Allowed : 21.53 % Favored : 76.54 % 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: 1.57 (0.19), residues: 1985 helix: 2.52 (0.18), residues: 817 sheet: 0.58 (0.25), residues: 430 loop : -0.36 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.020 0.001 TYR A 296 PHE 0.012 0.001 PHE B 157 TRP 0.035 0.001 TRP E 176 HIS 0.002 0.000 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00253 (16654) covalent geometry : angle 0.59229 (22721) SS BOND : bond 0.00761 ( 10) SS BOND : angle 1.47662 ( 20) hydrogen bonds : bond 0.04564 ( 849) hydrogen bonds : angle 3.97365 ( 2664) link_BETA1-4 : bond 0.00412 ( 5) link_BETA1-4 : angle 1.77116 ( 15) link_NAG-ASN : bond 0.00359 ( 10) link_NAG-ASN : angle 4.70611 ( 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 272 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 LEU cc_start: 0.9243 (tt) cc_final: 0.8954 (tm) REVERT: A 454 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8736 (tp30) REVERT: B 275 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7770 (t80) REVERT: B 301 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8405 (mpp) REVERT: B 339 CYS cc_start: 0.8830 (m) cc_final: 0.8588 (m) REVERT: B 488 MET cc_start: 0.8610 (mmm) cc_final: 0.8322 (mmm) REVERT: C 104 ASP cc_start: 0.8917 (t0) cc_final: 0.8715 (t0) REVERT: C 160 ASP cc_start: 0.8174 (m-30) cc_final: 0.7709 (m-30) REVERT: C 244 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8554 (mp) REVERT: C 275 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8309 (t80) REVERT: C 297 PHE cc_start: 0.8746 (m-80) cc_final: 0.8426 (m-80) REVERT: C 468 ASP cc_start: 0.9017 (t70) cc_final: 0.8743 (t0) REVERT: C 488 MET cc_start: 0.8561 (tpp) cc_final: 0.7376 (tmm) REVERT: D 197 ASP cc_start: 0.8601 (t0) cc_final: 0.7770 (p0) REVERT: D 245 SER cc_start: 0.9364 (t) cc_final: 0.9096 (p) REVERT: D 454 GLU cc_start: 0.9039 (tp30) cc_final: 0.8363 (tm-30) REVERT: E 182 MET cc_start: 0.8928 (ttt) cc_final: 0.8720 (ttm) REVERT: E 327 MET cc_start: 0.8534 (mtp) cc_final: 0.8043 (ttm) outliers start: 34 outliers final: 22 residues processed: 252 average time/residue: 0.3813 time to fit residues: 111.0122 Evaluate side-chains 248 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.079946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.063504 restraints weight = 74627.542| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 4.35 r_work: 0.2662 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16679 Z= 0.137 Angle : 0.646 15.688 22786 Z= 0.301 Chirality : 0.045 0.522 2603 Planarity : 0.004 0.043 2833 Dihedral : 5.246 35.968 2519 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.93 % Allowed : 22.10 % Favored : 75.98 % 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: 1.62 (0.19), residues: 1985 helix: 2.54 (0.18), residues: 817 sheet: 0.66 (0.26), residues: 423 loop : -0.33 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.023 0.001 TYR A 296 PHE 0.011 0.001 PHE B 157 TRP 0.031 0.001 TRP E 176 HIS 0.002 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00319 (16654) covalent geometry : angle 0.62026 (22721) SS BOND : bond 0.00743 ( 10) SS BOND : angle 1.43261 ( 20) hydrogen bonds : bond 0.04681 ( 849) hydrogen bonds : angle 3.97934 ( 2664) link_BETA1-4 : bond 0.00309 ( 5) link_BETA1-4 : angle 1.82151 ( 15) link_NAG-ASN : bond 0.00161 ( 10) link_NAG-ASN : angle 4.70208 ( 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 262 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 LEU cc_start: 0.9221 (tt) cc_final: 0.8941 (tm) REVERT: A 454 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8739 (tp30) REVERT: B 275 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7811 (t80) REVERT: B 301 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8413 (mpp) REVERT: B 339 CYS cc_start: 0.8805 (m) cc_final: 0.8537 (m) REVERT: B 488 MET cc_start: 0.8608 (mmm) cc_final: 0.8319 (mmm) REVERT: C 104 ASP cc_start: 0.8899 (t0) cc_final: 0.8683 (t0) REVERT: C 160 ASP cc_start: 0.8168 (m-30) cc_final: 0.7692 (m-30) REVERT: C 244 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8539 (mp) REVERT: C 275 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8337 (t80) REVERT: C 297 PHE cc_start: 0.8749 (m-80) cc_final: 0.8421 (m-80) REVERT: C 468 ASP cc_start: 0.9033 (t70) cc_final: 0.8656 (t0) REVERT: C 488 MET cc_start: 0.8540 (tpp) cc_final: 0.7366 (tmm) REVERT: D 197 ASP cc_start: 0.8546 (t0) cc_final: 0.7688 (p0) REVERT: D 245 SER cc_start: 0.9373 (t) cc_final: 0.9126 (p) REVERT: D 454 GLU cc_start: 0.9041 (tp30) cc_final: 0.8344 (tm-30) REVERT: D 471 CYS cc_start: 0.9144 (m) cc_final: 0.8569 (t) REVERT: E 182 MET cc_start: 0.8908 (ttt) cc_final: 0.8679 (ttm) REVERT: E 327 MET cc_start: 0.8559 (mtp) cc_final: 0.8033 (ttm) outliers start: 34 outliers final: 22 residues processed: 245 average time/residue: 0.4024 time to fit residues: 114.6032 Evaluate side-chains 244 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 135 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 183 optimal weight: 0.0030 chunk 52 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 147 optimal weight: 0.7980 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.062432 restraints weight = 87691.250| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 4.72 r_work: 0.2628 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16679 Z= 0.161 Angle : 0.651 15.610 22786 Z= 0.307 Chirality : 0.046 0.527 2603 Planarity : 0.004 0.044 2833 Dihedral : 5.240 35.360 2519 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.87 % Allowed : 22.15 % Favored : 75.98 % 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: 1.63 (0.19), residues: 1985 helix: 2.50 (0.18), residues: 817 sheet: 0.54 (0.26), residues: 456 loop : -0.20 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.016 0.001 TYR D 296 PHE 0.012 0.001 PHE D 157 TRP 0.033 0.001 TRP E 176 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00375 (16654) covalent geometry : angle 0.62507 (22721) SS BOND : bond 0.00723 ( 10) SS BOND : angle 1.44230 ( 20) hydrogen bonds : bond 0.04909 ( 849) hydrogen bonds : angle 4.04351 ( 2664) link_BETA1-4 : bond 0.00329 ( 5) link_BETA1-4 : angle 1.76876 ( 15) link_NAG-ASN : bond 0.00139 ( 10) link_NAG-ASN : angle 4.79624 ( 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 250 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 LEU cc_start: 0.9212 (tt) cc_final: 0.8956 (tm) REVERT: A 454 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8741 (tp30) REVERT: B 275 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7790 (t80) REVERT: B 301 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8438 (mpp) REVERT: B 339 CYS cc_start: 0.8825 (m) cc_final: 0.8573 (m) REVERT: B 488 MET cc_start: 0.8627 (mmm) cc_final: 0.8368 (mmm) REVERT: C 104 ASP cc_start: 0.8927 (t0) cc_final: 0.8713 (t0) REVERT: C 160 ASP cc_start: 0.8197 (m-30) cc_final: 0.7714 (m-30) REVERT: C 244 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8568 (mp) REVERT: C 468 ASP cc_start: 0.9006 (t70) cc_final: 0.8748 (t0) REVERT: C 488 MET cc_start: 0.8553 (tpp) cc_final: 0.7381 (tmm) REVERT: D 245 SER cc_start: 0.9378 (t) cc_final: 0.9134 (p) REVERT: D 278 LEU cc_start: 0.8160 (tp) cc_final: 0.7914 (tt) REVERT: D 281 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8510 (pp20) REVERT: D 454 GLU cc_start: 0.9054 (tp30) cc_final: 0.8360 (tm-30) REVERT: E 182 MET cc_start: 0.8910 (ttt) cc_final: 0.8683 (ttm) REVERT: E 276 MET cc_start: 0.8626 (ttt) cc_final: 0.8320 (tmm) REVERT: E 327 MET cc_start: 0.8587 (mtp) cc_final: 0.8030 (ttm) outliers start: 33 outliers final: 22 residues processed: 232 average time/residue: 0.4357 time to fit residues: 116.4644 Evaluate side-chains 237 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 473 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN D 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.081191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.065234 restraints weight = 80436.499| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.50 r_work: 0.2657 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16679 Z= 0.127 Angle : 0.648 15.616 22786 Z= 0.302 Chirality : 0.045 0.525 2603 Planarity : 0.004 0.045 2833 Dihedral : 5.205 34.864 2519 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.64 % Allowed : 22.32 % Favored : 76.03 % 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: 1.60 (0.19), residues: 1985 helix: 2.53 (0.18), residues: 814 sheet: 0.64 (0.27), residues: 403 loop : -0.30 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.023 0.001 TYR A 296 PHE 0.012 0.001 PHE B 157 TRP 0.034 0.001 TRP E 176 HIS 0.002 0.000 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00292 (16654) covalent geometry : angle 0.62267 (22721) SS BOND : bond 0.00740 ( 10) SS BOND : angle 1.45171 ( 20) hydrogen bonds : bond 0.04658 ( 849) hydrogen bonds : angle 3.95242 ( 2664) link_BETA1-4 : bond 0.00323 ( 5) link_BETA1-4 : angle 1.73942 ( 15) link_NAG-ASN : bond 0.00236 ( 10) link_NAG-ASN : angle 4.71578 ( 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 257 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 LEU cc_start: 0.9205 (tt) cc_final: 0.8966 (tm) REVERT: A 454 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8724 (tp30) REVERT: B 275 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7824 (t80) REVERT: B 301 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8407 (mpp) REVERT: B 339 CYS cc_start: 0.8827 (m) cc_final: 0.8576 (m) REVERT: B 488 MET cc_start: 0.8618 (mmm) cc_final: 0.8365 (mmm) REVERT: C 104 ASP cc_start: 0.8892 (t0) cc_final: 0.8678 (t0) REVERT: C 160 ASP cc_start: 0.8079 (m-30) cc_final: 0.7616 (m-30) REVERT: C 244 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8544 (mp) REVERT: C 468 ASP cc_start: 0.9058 (t70) cc_final: 0.8765 (t0) REVERT: C 488 MET cc_start: 0.8539 (tpp) cc_final: 0.7374 (tmm) REVERT: D 245 SER cc_start: 0.9343 (t) cc_final: 0.9093 (p) REVERT: D 278 LEU cc_start: 0.8101 (tp) cc_final: 0.7853 (tt) REVERT: D 281 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8502 (pp20) REVERT: D 454 GLU cc_start: 0.9061 (tp30) cc_final: 0.8374 (tm-30) REVERT: D 471 CYS cc_start: 0.9120 (m) cc_final: 0.8591 (t) REVERT: E 182 MET cc_start: 0.8912 (ttt) cc_final: 0.8695 (ttm) REVERT: E 276 MET cc_start: 0.8618 (ttt) cc_final: 0.8293 (OUTLIER) REVERT: E 327 MET cc_start: 0.8551 (mtp) cc_final: 0.8043 (ttm) outliers start: 29 outliers final: 20 residues processed: 240 average time/residue: 0.4052 time to fit residues: 112.9739 Evaluate side-chains 238 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 476 SER Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 473 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 40 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 176 optimal weight: 0.0170 chunk 188 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 24 optimal weight: 0.0470 chunk 61 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.081076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.065204 restraints weight = 74076.608| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.32 r_work: 0.2693 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16679 Z= 0.114 Angle : 0.639 15.221 22786 Z= 0.298 Chirality : 0.045 0.514 2603 Planarity : 0.004 0.044 2833 Dihedral : 5.116 34.651 2519 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.36 % Allowed : 22.78 % Favored : 75.86 % 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: 1.58 (0.19), residues: 1985 helix: 2.56 (0.18), residues: 814 sheet: 0.76 (0.28), residues: 352 loop : -0.37 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 347 TYR 0.018 0.001 TYR D 296 PHE 0.011 0.001 PHE B 157 TRP 0.032 0.001 TRP E 176 HIS 0.002 0.000 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00257 (16654) covalent geometry : angle 0.61498 (22721) SS BOND : bond 0.00758 ( 10) SS BOND : angle 1.44154 ( 20) hydrogen bonds : bond 0.04371 ( 849) hydrogen bonds : angle 3.87842 ( 2664) link_BETA1-4 : bond 0.00429 ( 5) link_BETA1-4 : angle 1.80374 ( 15) link_NAG-ASN : bond 0.00305 ( 10) link_NAG-ASN : angle 4.57647 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5124.33 seconds wall clock time: 88 minutes 14.26 seconds (5294.26 seconds total)