Starting phenix.real_space_refine on Sun Jun 15 04:36:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtr_34265/06_2025/8gtr_34265_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtr_34265/06_2025/8gtr_34265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gtr_34265/06_2025/8gtr_34265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtr_34265/06_2025/8gtr_34265.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtr_34265/06_2025/8gtr_34265_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtr_34265/06_2025/8gtr_34265_neut.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 98 5.16 5 C 11221 2.51 5 N 2660 2.21 5 O 2989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16975 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 8.52, per 1000 atoms: 0.50 Number of scatterers: 16975 At special positions: 0 Unit cell: (119.28, 120.345, 118.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 7 15.00 O 2989 8.00 N 2660 7.00 C 11221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 261 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 261 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 261 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 261 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 242 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 71 " " NAG B 401 " - " ASN B 71 " " NAG C 401 " - " ASN C 71 " " NAG D 402 " - " ASN D 71 " " NAG E 402 " - " ASN E 71 " " NAG F 402 " - " ASN F 71 " " NAG G 402 " - " ASN G 71 " Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.5 seconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4228 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 7 sheets defined 75.0% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.667A pdb=" N LEU A 28 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 57 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 105 through 122 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.690A pdb=" N LEU A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 132 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 159 removed outlier: 3.799A pdb=" N GLN A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 204 through 231 Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.185A pdb=" N ASP A 251 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 294 Proline residue: A 285 - end of helix removed outlier: 4.234A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 324 through 336 removed outlier: 4.098A pdb=" N VAL A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.589A pdb=" N ASP A 354 " --> pdb=" O CYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.667A pdb=" N LEU B 28 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 57 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 105 through 122 Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.690A pdb=" N LEU B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 132 " --> pdb=" O TRP B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 159 removed outlier: 3.800A pdb=" N GLN B 159 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 204 through 231 Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.185A pdb=" N ASP B 251 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 294 Proline residue: B 285 - end of helix removed outlier: 4.233A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 336 removed outlier: 4.098A pdb=" N VAL B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 removed outlier: 3.589A pdb=" N ASP B 354 " --> pdb=" O CYS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.668A pdb=" N LEU C 28 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 57 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 105 through 122 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 122 through 132 removed outlier: 3.689A pdb=" N LEU C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 132 " --> pdb=" O TRP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 159 removed outlier: 3.799A pdb=" N GLN C 159 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 204 through 231 Processing helix chain 'C' and resid 247 through 252 removed outlier: 4.184A pdb=" N ASP C 251 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 294 Proline residue: C 285 - end of helix removed outlier: 4.234A pdb=" N LEU C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 324 through 336 removed outlier: 4.098A pdb=" N VAL C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 354 removed outlier: 3.589A pdb=" N ASP C 354 " --> pdb=" O CYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.667A pdb=" N LEU D 28 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 57 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 105 through 122 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 122 through 132 removed outlier: 3.689A pdb=" N LEU D 126 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 132 " --> pdb=" O TRP D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 159 removed outlier: 3.800A pdb=" N GLN D 159 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 204 through 231 Processing helix chain 'D' and resid 247 through 252 removed outlier: 4.185A pdb=" N ASP D 251 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 294 Proline residue: D 285 - end of helix removed outlier: 4.234A pdb=" N LEU D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 324 through 336 removed outlier: 4.098A pdb=" N VAL D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 354 removed outlier: 3.589A pdb=" N ASP D 354 " --> pdb=" O CYS D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.667A pdb=" N LEU E 28 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 57 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 105 through 122 Proline residue: E 111 - end of helix Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.690A pdb=" N LEU E 126 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 132 " --> pdb=" O TRP E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 159 removed outlier: 3.799A pdb=" N GLN E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'E' and resid 204 through 231 Processing helix chain 'E' and resid 247 through 252 removed outlier: 4.185A pdb=" N ASP E 251 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 294 Proline residue: E 285 - end of helix removed outlier: 4.234A pdb=" N LEU E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 308 through 315 Processing helix chain 'E' and resid 324 through 336 removed outlier: 4.098A pdb=" N VAL E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 354 removed outlier: 3.588A pdb=" N ASP E 354 " --> pdb=" O CYS E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 373 Processing helix chain 'F' and resid 24 through 28 removed outlier: 3.667A pdb=" N LEU F 28 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 57 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 105 through 122 Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 122 through 132 removed outlier: 3.690A pdb=" N LEU F 126 " --> pdb=" O TYR F 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA F 132 " --> pdb=" O TRP F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 159 removed outlier: 3.799A pdb=" N GLN F 159 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 204 through 231 Processing helix chain 'F' and resid 247 through 252 removed outlier: 4.185A pdb=" N ASP F 251 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 294 Proline residue: F 285 - end of helix removed outlier: 4.234A pdb=" N LEU F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 301 through 306 Processing helix chain 'F' and resid 308 through 315 Processing helix chain 'F' and resid 324 through 336 removed outlier: 4.097A pdb=" N VAL F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 354 removed outlier: 3.588A pdb=" N ASP F 354 " --> pdb=" O CYS F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 373 Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.667A pdb=" N LEU G 28 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 57 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 105 through 122 Proline residue: G 111 - end of helix Processing helix chain 'G' and resid 122 through 132 removed outlier: 3.689A pdb=" N LEU G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA G 132 " --> pdb=" O TRP G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 159 removed outlier: 3.800A pdb=" N GLN G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'G' and resid 204 through 231 Processing helix chain 'G' and resid 247 through 252 removed outlier: 4.185A pdb=" N ASP G 251 " --> pdb=" O LEU G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 294 Proline residue: G 285 - end of helix removed outlier: 4.234A pdb=" N LEU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 308 through 315 Processing helix chain 'G' and resid 324 through 336 removed outlier: 4.097A pdb=" N VAL G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 354 removed outlier: 3.589A pdb=" N ASP G 354 " --> pdb=" O CYS G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 65 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 65 through 66 1113 hydrogen bonds defined for protein. 3234 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: 5.69 Time building geometry restraints manager: 6.07 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: 2513 1.31 - 1.44: 4641 1.44 - 1.56: 10024 1.56 - 1.69: 14 1.69 - 1.82: 140 Bond restraints: 17332 Sorted by residual: bond pdb=" C30 PTY A 402 " pdb=" O4 PTY A 402 " ideal model delta sigma weight residual 1.331 1.401 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C30 PTY G 401 " pdb=" O4 PTY G 401 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C30 PTY C 402 " pdb=" O4 PTY C 402 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C30 PTY F 401 " pdb=" O4 PTY F 401 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C30 PTY D 401 " pdb=" O4 PTY D 401 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 17327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 23372 3.36 - 6.72: 141 6.72 - 10.07: 42 10.07 - 13.43: 7 13.43 - 16.79: 7 Bond angle restraints: 23569 Sorted by residual: angle pdb=" O11 PTY E 401 " pdb=" P1 PTY E 401 " pdb=" O14 PTY E 401 " ideal model delta sigma weight residual 92.90 109.69 -16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PTY G 401 " pdb=" P1 PTY G 401 " pdb=" O14 PTY G 401 " ideal model delta sigma weight residual 92.90 109.68 -16.78 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PTY A 402 " pdb=" P1 PTY A 402 " pdb=" O14 PTY A 402 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O11 PTY D 401 " pdb=" P1 PTY D 401 " pdb=" O14 PTY D 401 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O11 PTY B 402 " pdb=" P1 PTY B 402 " pdb=" O14 PTY B 402 " ideal model delta sigma weight residual 92.90 109.67 -16.77 3.00e+00 1.11e-01 3.12e+01 ... (remaining 23564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.46: 9534 18.46 - 36.92: 763 36.92 - 55.38: 182 55.38 - 73.84: 21 73.84 - 92.30: 28 Dihedral angle restraints: 10528 sinusoidal: 4095 harmonic: 6433 Sorted by residual: dihedral pdb=" CA GLU B 339 " pdb=" C GLU B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLU E 339 " pdb=" C GLU E 339 " pdb=" N LEU E 340 " pdb=" CA LEU E 340 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLU A 339 " pdb=" C GLU A 339 " pdb=" N LEU A 340 " pdb=" CA LEU A 340 " ideal model delta harmonic sigma weight residual 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 10525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2020 0.033 - 0.065: 641 0.065 - 0.098: 194 0.098 - 0.130: 57 0.130 - 0.163: 14 Chirality restraints: 2926 Sorted by residual: chirality pdb=" CA ILE F 244 " pdb=" N ILE F 244 " pdb=" C ILE F 244 " pdb=" CB ILE F 244 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA ILE B 244 " pdb=" N ILE B 244 " pdb=" C ILE B 244 " pdb=" CB ILE B 244 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 2923 not shown) Planarity restraints: 2814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 234 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C VAL F 234 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL F 234 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE F 235 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 234 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C VAL D 234 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL D 234 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE D 235 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 234 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL G 234 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL G 234 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE G 235 " -0.009 2.00e-02 2.50e+03 ... (remaining 2811 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3640 2.78 - 3.31: 17025 3.31 - 3.84: 27059 3.84 - 4.37: 28088 4.37 - 4.90: 49635 Nonbonded interactions: 125447 Sorted by model distance: nonbonded pdb=" O ILE E 341 " pdb=" OG SER E 344 " model vdw 2.256 3.040 nonbonded pdb=" O ILE F 341 " pdb=" OG SER F 344 " model vdw 2.256 3.040 nonbonded pdb=" O ILE A 341 " pdb=" OG SER A 344 " model vdw 2.257 3.040 nonbonded pdb=" O ILE B 341 " pdb=" OG SER B 344 " model vdw 2.257 3.040 nonbonded pdb=" O ILE G 341 " pdb=" OG SER G 344 " model vdw 2.257 3.040 ... (remaining 125442 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: 0.08 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 373) selection = (chain 'B' and resid 24 through 373) selection = (chain 'C' and resid 24 through 373) selection = (chain 'D' and resid 24 through 373) selection = (chain 'E' and resid 24 through 373) selection = (chain 'F' and resid 24 through 373) selection = (chain 'G' and resid 24 through 373) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.620 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 : 0.004 0.070 17353 Z= 0.180 Angle : 0.784 16.790 23618 Z= 0.342 Chirality : 0.039 0.163 2926 Planarity : 0.003 0.026 2807 Dihedral : 14.856 92.301 6258 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 2100 helix: 1.78 (0.14), residues: 1428 sheet: -1.33 (0.43), residues: 119 loop : -0.64 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 297 HIS 0.003 0.001 HIS F 229 PHE 0.027 0.001 PHE G 368 TYR 0.009 0.001 TYR D 226 ARG 0.001 0.000 ARG C 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 7) link_NAG-ASN : angle 2.63765 ( 21) hydrogen bonds : bond 0.13278 ( 1113) hydrogen bonds : angle 5.48457 ( 3234) SS BOND : bond 0.00192 ( 14) SS BOND : angle 0.78048 ( 28) covalent geometry : bond 0.00353 (17332) covalent geometry : angle 0.78044 (23569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 2.081 Fit side-chains REVERT: B 121 MET cc_start: 0.6121 (mmp) cc_final: 0.5731 (mmp) REVERT: F 121 MET cc_start: 0.6556 (mmp) cc_final: 0.6053 (mmp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2485 time to fit residues: 59.1122 Evaluate side-chains 89 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 54 optimal weight: 0.0060 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.0570 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS E 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.126932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.102067 restraints weight = 35013.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104511 restraints weight = 19948.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.106137 restraints weight = 13460.639| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17353 Z= 0.142 Angle : 0.670 10.746 23618 Z= 0.314 Chirality : 0.040 0.151 2926 Planarity : 0.003 0.026 2807 Dihedral : 10.143 65.241 2660 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.37 % Allowed : 6.46 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 2100 helix: 1.93 (0.14), residues: 1421 sheet: -1.30 (0.43), residues: 119 loop : -0.12 (0.31), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 85 HIS 0.002 0.001 HIS A 90 PHE 0.028 0.002 PHE E 368 TYR 0.011 0.001 TYR C 226 ARG 0.001 0.000 ARG E 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 7) link_NAG-ASN : angle 3.02387 ( 21) hydrogen bonds : bond 0.03628 ( 1113) hydrogen bonds : angle 4.11702 ( 3234) SS BOND : bond 0.00416 ( 14) SS BOND : angle 0.94597 ( 28) covalent geometry : bond 0.00317 (17332) covalent geometry : angle 0.66404 (23569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 2.232 Fit side-chains REVERT: B 101 MET cc_start: 0.7980 (tpp) cc_final: 0.7667 (tpp) REVERT: E 101 MET cc_start: 0.7887 (tpp) cc_final: 0.7588 (tpp) REVERT: G 324 ASN cc_start: 0.8684 (p0) cc_final: 0.8460 (p0) outliers start: 25 outliers final: 22 residues processed: 117 average time/residue: 0.2414 time to fit residues: 47.6192 Evaluate side-chains 106 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 56 optimal weight: 0.0670 chunk 116 optimal weight: 0.0470 chunk 41 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 0.0270 chunk 158 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.132000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107782 restraints weight = 33892.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110389 restraints weight = 18570.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.112125 restraints weight = 12104.250| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17353 Z= 0.112 Angle : 0.609 9.769 23618 Z= 0.287 Chirality : 0.038 0.170 2926 Planarity : 0.003 0.024 2807 Dihedral : 8.902 58.676 2660 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.66 % Allowed : 9.58 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 2100 helix: 2.10 (0.14), residues: 1442 sheet: -1.18 (0.43), residues: 119 loop : 0.18 (0.32), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 85 HIS 0.001 0.000 HIS B 90 PHE 0.008 0.001 PHE A 368 TYR 0.006 0.001 TYR E 226 ARG 0.002 0.000 ARG G 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 7) link_NAG-ASN : angle 2.61380 ( 21) hydrogen bonds : bond 0.03093 ( 1113) hydrogen bonds : angle 3.84767 ( 3234) SS BOND : bond 0.00073 ( 14) SS BOND : angle 0.34166 ( 28) covalent geometry : bond 0.00220 (17332) covalent geometry : angle 0.60414 (23569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.857 Fit side-chains REVERT: G 101 MET cc_start: 0.7983 (tpp) cc_final: 0.7721 (tpp) outliers start: 12 outliers final: 7 residues processed: 119 average time/residue: 0.2493 time to fit residues: 48.8757 Evaluate side-chains 96 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 50 optimal weight: 0.0030 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.127342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.103378 restraints weight = 34529.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104593 restraints weight = 19786.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105559 restraints weight = 14756.346| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17353 Z= 0.150 Angle : 0.659 9.974 23618 Z= 0.311 Chirality : 0.041 0.403 2926 Planarity : 0.003 0.024 2807 Dihedral : 8.205 57.347 2660 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.86 % Allowed : 11.33 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2100 helix: 1.93 (0.14), residues: 1442 sheet: 0.04 (0.46), residues: 84 loop : -0.44 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 85 HIS 0.003 0.001 HIS E 231 PHE 0.024 0.001 PHE A 368 TYR 0.010 0.001 TYR E 226 ARG 0.001 0.000 ARG C 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 7) link_NAG-ASN : angle 3.31121 ( 21) hydrogen bonds : bond 0.03526 ( 1113) hydrogen bonds : angle 3.81498 ( 3234) SS BOND : bond 0.00358 ( 14) SS BOND : angle 0.84932 ( 28) covalent geometry : bond 0.00334 (17332) covalent geometry : angle 0.65130 (23569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 2.123 Fit side-chains REVERT: B 39 LYS cc_start: 0.8364 (tmmt) cc_final: 0.8158 (ttpp) REVERT: B 147 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.5862 (tp) REVERT: C 217 LEU cc_start: 0.8380 (tp) cc_final: 0.8129 (tp) REVERT: E 101 MET cc_start: 0.7964 (tpp) cc_final: 0.7351 (tpp) REVERT: F 50 MET cc_start: 0.7189 (tpp) cc_final: 0.6970 (mpp) REVERT: G 101 MET cc_start: 0.8009 (tpp) cc_final: 0.7759 (tpp) REVERT: G 324 ASN cc_start: 0.8778 (p0) cc_final: 0.8568 (p0) outliers start: 34 outliers final: 24 residues processed: 125 average time/residue: 0.3006 time to fit residues: 60.5071 Evaluate side-chains 114 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 161 optimal weight: 0.0050 chunk 121 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN E 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.129847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107307 restraints weight = 34506.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107778 restraints weight = 21288.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108673 restraints weight = 14697.957| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17353 Z= 0.116 Angle : 0.627 10.092 23618 Z= 0.297 Chirality : 0.038 0.167 2926 Planarity : 0.003 0.024 2807 Dihedral : 7.714 54.271 2660 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.81 % Allowed : 12.81 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 2100 helix: 2.03 (0.14), residues: 1442 sheet: -0.90 (0.44), residues: 119 loop : -0.13 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 85 HIS 0.002 0.000 HIS A 91 PHE 0.026 0.001 PHE E 368 TYR 0.009 0.001 TYR G 195 ARG 0.001 0.000 ARG B 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00011 ( 7) link_NAG-ASN : angle 2.99946 ( 21) hydrogen bonds : bond 0.03177 ( 1113) hydrogen bonds : angle 3.68480 ( 3234) SS BOND : bond 0.00147 ( 14) SS BOND : angle 0.57230 ( 28) covalent geometry : bond 0.00238 (17332) covalent geometry : angle 0.62116 (23569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 2.292 Fit side-chains REVERT: B 147 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6149 (tp) REVERT: C 217 LEU cc_start: 0.8294 (tp) cc_final: 0.8047 (tp) REVERT: C 331 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8268 (tt) REVERT: F 50 MET cc_start: 0.7090 (tpp) cc_final: 0.6828 (mpp) REVERT: G 101 MET cc_start: 0.8030 (tpp) cc_final: 0.7717 (tpp) REVERT: G 324 ASN cc_start: 0.8734 (p0) cc_final: 0.8524 (p0) outliers start: 33 outliers final: 18 residues processed: 131 average time/residue: 0.2686 time to fit residues: 57.2177 Evaluate side-chains 108 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 134 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 174 optimal weight: 0.0570 chunk 172 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN D 237 GLN F 237 GLN G 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.127512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102233 restraints weight = 35374.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.104954 restraints weight = 19416.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106754 restraints weight = 12671.674| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17353 Z= 0.117 Angle : 0.630 10.059 23618 Z= 0.299 Chirality : 0.038 0.146 2926 Planarity : 0.003 0.022 2807 Dihedral : 7.258 50.347 2660 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.59 % Allowed : 14.12 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.19), residues: 2100 helix: 2.08 (0.14), residues: 1442 sheet: -0.84 (0.44), residues: 119 loop : -0.23 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 85 HIS 0.001 0.000 HIS E 231 PHE 0.024 0.001 PHE E 368 TYR 0.008 0.001 TYR E 226 ARG 0.002 0.000 ARG F 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00006 ( 7) link_NAG-ASN : angle 2.95404 ( 21) hydrogen bonds : bond 0.03121 ( 1113) hydrogen bonds : angle 3.64693 ( 3234) SS BOND : bond 0.00149 ( 14) SS BOND : angle 0.60660 ( 28) covalent geometry : bond 0.00245 (17332) covalent geometry : angle 0.62376 (23569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.905 Fit side-chains REVERT: C 217 LEU cc_start: 0.8282 (tp) cc_final: 0.8034 (tp) REVERT: F 50 MET cc_start: 0.7247 (tpp) cc_final: 0.7019 (mpp) REVERT: G 101 MET cc_start: 0.8022 (tpp) cc_final: 0.7697 (tpp) outliers start: 29 outliers final: 23 residues processed: 130 average time/residue: 0.2194 time to fit residues: 48.5463 Evaluate side-chains 111 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 121 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098177 restraints weight = 37638.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100689 restraints weight = 21369.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102420 restraints weight = 14379.177| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17353 Z= 0.122 Angle : 0.652 10.823 23618 Z= 0.306 Chirality : 0.039 0.270 2926 Planarity : 0.003 0.022 2807 Dihedral : 6.958 45.811 2660 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.97 % Allowed : 14.12 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 2100 helix: 2.06 (0.14), residues: 1442 sheet: -0.79 (0.45), residues: 119 loop : -0.31 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 85 HIS 0.002 0.000 HIS E 231 PHE 0.026 0.001 PHE E 368 TYR 0.008 0.001 TYR E 226 ARG 0.002 0.000 ARG C 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 7) link_NAG-ASN : angle 3.02148 ( 21) hydrogen bonds : bond 0.03156 ( 1113) hydrogen bonds : angle 3.64861 ( 3234) SS BOND : bond 0.00186 ( 14) SS BOND : angle 0.59757 ( 28) covalent geometry : bond 0.00260 (17332) covalent geometry : angle 0.64597 (23569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 2.144 Fit side-chains REVERT: B 147 LEU cc_start: 0.6622 (mm) cc_final: 0.5981 (tp) REVERT: C 217 LEU cc_start: 0.8297 (tp) cc_final: 0.8045 (tp) REVERT: F 50 MET cc_start: 0.7278 (tpp) cc_final: 0.7076 (mpp) REVERT: G 101 MET cc_start: 0.8100 (tpp) cc_final: 0.7830 (tpp) outliers start: 36 outliers final: 28 residues processed: 136 average time/residue: 0.2509 time to fit residues: 56.6269 Evaluate side-chains 120 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 180 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 115 optimal weight: 0.0270 chunk 203 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.122461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.097138 restraints weight = 37675.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099549 restraints weight = 21643.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.101301 restraints weight = 14701.449| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17353 Z= 0.136 Angle : 0.675 12.911 23618 Z= 0.318 Chirality : 0.041 0.494 2926 Planarity : 0.003 0.022 2807 Dihedral : 6.787 43.478 2660 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.03 % Allowed : 14.45 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 2100 helix: 2.01 (0.14), residues: 1442 sheet: -0.77 (0.46), residues: 119 loop : -0.38 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 297 HIS 0.002 0.001 HIS E 231 PHE 0.030 0.001 PHE E 368 TYR 0.009 0.001 TYR E 226 ARG 0.001 0.000 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 7) link_NAG-ASN : angle 3.20047 ( 21) hydrogen bonds : bond 0.03342 ( 1113) hydrogen bonds : angle 3.71851 ( 3234) SS BOND : bond 0.00250 ( 14) SS BOND : angle 0.75734 ( 28) covalent geometry : bond 0.00304 (17332) covalent geometry : angle 0.66802 (23569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 1.892 Fit side-chains REVERT: B 147 LEU cc_start: 0.6723 (mm) cc_final: 0.6066 (tp) REVERT: C 217 LEU cc_start: 0.8324 (tp) cc_final: 0.8099 (tp) outliers start: 37 outliers final: 31 residues processed: 130 average time/residue: 0.2186 time to fit residues: 48.6861 Evaluate side-chains 122 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 103 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.122927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098480 restraints weight = 37841.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.100481 restraints weight = 21283.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101651 restraints weight = 14493.172| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17353 Z= 0.128 Angle : 0.684 10.894 23618 Z= 0.324 Chirality : 0.040 0.221 2926 Planarity : 0.003 0.022 2807 Dihedral : 6.607 39.960 2660 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.03 % Allowed : 14.56 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 2100 helix: 2.02 (0.14), residues: 1442 sheet: -0.77 (0.45), residues: 119 loop : -0.40 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 297 HIS 0.002 0.000 HIS E 231 PHE 0.034 0.001 PHE E 368 TYR 0.008 0.001 TYR E 226 ARG 0.001 0.000 ARG F 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 7) link_NAG-ASN : angle 3.12604 ( 21) hydrogen bonds : bond 0.03277 ( 1113) hydrogen bonds : angle 3.68396 ( 3234) SS BOND : bond 0.00195 ( 14) SS BOND : angle 0.71044 ( 28) covalent geometry : bond 0.00277 (17332) covalent geometry : angle 0.67790 (23569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 1.860 Fit side-chains REVERT: C 217 LEU cc_start: 0.8319 (tp) cc_final: 0.8081 (tp) REVERT: G 369 MET cc_start: 0.6344 (ppp) cc_final: 0.6133 (ppp) outliers start: 37 outliers final: 31 residues processed: 129 average time/residue: 0.2206 time to fit residues: 49.0539 Evaluate side-chains 120 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 135 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.122390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099764 restraints weight = 37473.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099933 restraints weight = 22360.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100598 restraints weight = 16999.631| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17353 Z= 0.148 Angle : 0.730 14.341 23618 Z= 0.343 Chirality : 0.041 0.333 2926 Planarity : 0.003 0.023 2807 Dihedral : 6.576 39.370 2660 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.86 % Allowed : 14.78 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2100 helix: 1.94 (0.14), residues: 1442 sheet: 0.29 (0.47), residues: 84 loop : -0.87 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 297 HIS 0.002 0.001 HIS E 231 PHE 0.034 0.002 PHE E 368 TYR 0.010 0.001 TYR E 226 ARG 0.001 0.000 ARG F 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 7) link_NAG-ASN : angle 3.41623 ( 21) hydrogen bonds : bond 0.03521 ( 1113) hydrogen bonds : angle 3.73308 ( 3234) SS BOND : bond 0.00318 ( 14) SS BOND : angle 0.86308 ( 28) covalent geometry : bond 0.00333 (17332) covalent geometry : angle 0.72289 (23569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 2.861 Fit side-chains REVERT: C 217 LEU cc_start: 0.8379 (tp) cc_final: 0.8147 (tp) outliers start: 34 outliers final: 32 residues processed: 118 average time/residue: 0.2722 time to fit residues: 57.3763 Evaluate side-chains 121 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 203 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.125640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100467 restraints weight = 36180.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102958 restraints weight = 19952.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104881 restraints weight = 13247.628| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17353 Z= 0.123 Angle : 0.706 11.020 23618 Z= 0.333 Chirality : 0.040 0.222 2926 Planarity : 0.003 0.023 2807 Dihedral : 6.416 39.104 2660 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.75 % Allowed : 15.00 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 2100 helix: 2.05 (0.14), residues: 1442 sheet: -0.80 (0.45), residues: 119 loop : -0.46 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.001 0.000 HIS E 231 PHE 0.033 0.001 PHE E 368 TYR 0.008 0.001 TYR E 226 ARG 0.001 0.000 ARG F 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 7) link_NAG-ASN : angle 3.08084 ( 21) hydrogen bonds : bond 0.03247 ( 1113) hydrogen bonds : angle 3.63694 ( 3234) SS BOND : bond 0.00127 ( 14) SS BOND : angle 0.60246 ( 28) covalent geometry : bond 0.00257 (17332) covalent geometry : angle 0.70021 (23569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4897.19 seconds wall clock time: 89 minutes 18.36 seconds (5358.36 seconds total)