Starting phenix.real_space_refine on Sun Aug 24 04:19:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtr_34265/08_2025/8gtr_34265_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtr_34265/08_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_34265/08_2025/8gtr_34265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtr_34265/08_2025/8gtr_34265.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtr_34265/08_2025/8gtr_34265_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtr_34265/08_2025/8gtr_34265_neut.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 5, 'GLU:plan': 3, 'ASP:plan': 4, 'TYR:plan': 2, 'PHE:plan': 1, 'TRP:plan': 1} 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: 2.32, per 1000 atoms: 0.14 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: 1.14 Conformation dependent library (CDL) restraints added in 545.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 2.04 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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: 0.03 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 11.320 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (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 ARG 0.001 0.000 ARG C 156 TYR 0.009 0.001 TYR D 226 PHE 0.027 0.001 PHE G 368 TRP 0.008 0.001 TRP E 297 HIS 0.003 0.001 HIS F 229 Details of bonding type rmsd covalent geometry : bond 0.00353 (17332) covalent geometry : angle 0.78044 (23569) SS BOND : bond 0.00192 ( 14) SS BOND : angle 0.78048 ( 28) hydrogen bonds : bond 0.13278 ( 1113) hydrogen bonds : angle 5.48457 ( 3234) link_NAG-ASN : bond 0.00061 ( 7) link_NAG-ASN : angle 2.63765 ( 21) *********************** 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 : 0.625 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: 0.1078 time to fit residues: 25.5274 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 : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.122902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097360 restraints weight = 35532.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.099651 restraints weight = 20814.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101121 restraints weight = 14341.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.102223 restraints weight = 11279.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102609 restraints weight = 9612.993| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17353 Z= 0.240 Angle : 0.789 10.837 23618 Z= 0.375 Chirality : 0.043 0.149 2926 Planarity : 0.004 0.029 2807 Dihedral : 10.251 67.447 2660 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.37 % Allowed : 8.92 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.19), residues: 2100 helix: 1.56 (0.13), residues: 1421 sheet: -0.40 (0.47), residues: 84 loop : -0.72 (0.28), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.017 0.002 TYR C 226 PHE 0.034 0.002 PHE G 368 TRP 0.007 0.001 TRP B 85 HIS 0.004 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00561 (17332) covalent geometry : angle 0.77914 (23569) SS BOND : bond 0.00802 ( 14) SS BOND : angle 1.40228 ( 28) hydrogen bonds : bond 0.04309 ( 1113) hydrogen bonds : angle 4.38600 ( 3234) link_NAG-ASN : bond 0.00526 ( 7) link_NAG-ASN : angle 4.07991 ( 21) *********************** 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 116 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.564 Fit side-chains REVERT: B 101 MET cc_start: 0.8025 (tpp) cc_final: 0.7789 (tpp) REVERT: C 324 ASN cc_start: 0.8970 (p0) cc_final: 0.8766 (p0) REVERT: D 217 LEU cc_start: 0.8451 (tp) cc_final: 0.8235 (tp) REVERT: E 324 ASN cc_start: 0.8989 (p0) cc_final: 0.8781 (p0) REVERT: G 101 MET cc_start: 0.8059 (tpp) cc_final: 0.7824 (tpp) REVERT: G 324 ASN cc_start: 0.8803 (p0) cc_final: 0.8555 (p0) outliers start: 25 outliers final: 23 residues processed: 109 average time/residue: 0.0803 time to fit residues: 15.1694 Evaluate side-chains 102 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 264 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 163 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 157 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.129138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104240 restraints weight = 34509.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106803 restraints weight = 19036.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108513 restraints weight = 12541.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.109514 restraints weight = 9538.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.110288 restraints weight = 8055.458| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17353 Z= 0.122 Angle : 0.639 9.773 23618 Z= 0.304 Chirality : 0.038 0.152 2926 Planarity : 0.003 0.026 2807 Dihedral : 9.185 59.830 2660 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.15 % Allowed : 10.84 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.19), residues: 2100 helix: 1.87 (0.14), residues: 1442 sheet: -1.13 (0.44), residues: 119 loop : -0.13 (0.31), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 156 TYR 0.007 0.001 TYR E 226 PHE 0.011 0.001 PHE A 368 TRP 0.005 0.001 TRP C 85 HIS 0.001 0.000 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00252 (17332) covalent geometry : angle 0.63252 (23569) SS BOND : bond 0.00173 ( 14) SS BOND : angle 0.42635 ( 28) hydrogen bonds : bond 0.03508 ( 1113) hydrogen bonds : angle 3.97548 ( 3234) link_NAG-ASN : bond 0.00033 ( 7) link_NAG-ASN : angle 3.26638 ( 21) *********************** 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 121 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.402 Fit side-chains REVERT: C 324 ASN cc_start: 0.8788 (p0) cc_final: 0.8537 (p0) REVERT: E 369 MET cc_start: 0.6412 (ppp) cc_final: 0.6033 (ppp) REVERT: G 101 MET cc_start: 0.8019 (tpp) cc_final: 0.7748 (tpp) REVERT: G 369 MET cc_start: 0.5983 (ppp) cc_final: 0.5591 (ppp) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.0938 time to fit residues: 18.8044 Evaluate side-chains 102 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 223 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 282 ILE Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 223 THR 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 29 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 237 GLN C 237 GLN D 237 GLN E 237 GLN F 237 GLN G 237 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.126209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102217 restraints weight = 34896.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.103218 restraints weight = 20785.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.104329 restraints weight = 15204.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.104993 restraints weight = 11471.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105143 restraints weight = 10216.285| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17353 Z= 0.170 Angle : 0.688 10.064 23618 Z= 0.325 Chirality : 0.042 0.405 2926 Planarity : 0.003 0.027 2807 Dihedral : 8.677 59.849 2660 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.35 % Allowed : 12.53 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.19), residues: 2100 helix: 1.72 (0.14), residues: 1442 sheet: -0.28 (0.45), residues: 84 loop : -0.72 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 156 TYR 0.012 0.001 TYR E 226 PHE 0.010 0.001 PHE F 368 TRP 0.005 0.001 TRP F 85 HIS 0.003 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00390 (17332) covalent geometry : angle 0.67866 (23569) SS BOND : bond 0.00449 ( 14) SS BOND : angle 0.78469 ( 28) hydrogen bonds : bond 0.03841 ( 1113) hydrogen bonds : angle 3.99637 ( 3234) link_NAG-ASN : bond 0.00330 ( 7) link_NAG-ASN : angle 3.81693 ( 21) *********************** 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 142 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.601 Fit side-chains REVERT: B 39 LYS cc_start: 0.8460 (tmmt) cc_final: 0.8207 (ttpp) REVERT: C 39 LYS cc_start: 0.8215 (tmmt) cc_final: 0.8003 (ttpp) REVERT: C 324 ASN cc_start: 0.8905 (p0) cc_final: 0.8617 (p0) REVERT: E 101 MET cc_start: 0.7943 (tpp) cc_final: 0.7557 (tpp) REVERT: G 101 MET cc_start: 0.8018 (tpp) cc_final: 0.7804 (tpp) outliers start: 43 outliers final: 27 residues processed: 132 average time/residue: 0.0994 time to fit residues: 22.0044 Evaluate side-chains 112 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 311 PHE 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 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 242 CYS 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 242 CYS 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 108 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 chunk 169 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.127284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102040 restraints weight = 35070.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104687 restraints weight = 19250.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106470 restraints weight = 12632.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107613 restraints weight = 9538.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108133 restraints weight = 7989.391| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17353 Z= 0.118 Angle : 0.656 13.491 23618 Z= 0.307 Chirality : 0.041 0.408 2926 Planarity : 0.003 0.025 2807 Dihedral : 7.953 56.204 2660 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.75 % Allowed : 15.22 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.19), residues: 2100 helix: 1.96 (0.14), residues: 1442 sheet: -0.99 (0.44), residues: 119 loop : -0.26 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 156 TYR 0.006 0.001 TYR F 226 PHE 0.033 0.001 PHE G 368 TRP 0.006 0.001 TRP C 85 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00235 (17332) covalent geometry : angle 0.64970 (23569) SS BOND : bond 0.00141 ( 14) SS BOND : angle 0.43332 ( 28) hydrogen bonds : bond 0.03319 ( 1113) hydrogen bonds : angle 3.79450 ( 3234) link_NAG-ASN : bond 0.00078 ( 7) link_NAG-ASN : angle 3.13151 ( 21) *********************** 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 146 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.441 Fit side-chains REVERT: B 147 LEU cc_start: 0.6598 (mm) cc_final: 0.6052 (tp) REVERT: C 39 LYS cc_start: 0.8090 (tmmt) cc_final: 0.7890 (ttpp) REVERT: C 324 ASN cc_start: 0.8746 (p0) cc_final: 0.8517 (p0) REVERT: E 39 LYS cc_start: 0.8286 (tmmt) cc_final: 0.8065 (ttpp) REVERT: G 101 MET cc_start: 0.8002 (tpp) cc_final: 0.7712 (tpp) outliers start: 32 outliers final: 16 residues processed: 141 average time/residue: 0.1001 time to fit residues: 22.8521 Evaluate side-chains 109 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 206 VAL 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 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 282 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 232 LEU 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 140 optimal weight: 3.9990 chunk 93 optimal weight: 0.0030 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.126779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.101187 restraints weight = 35957.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103848 restraints weight = 19614.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105742 restraints weight = 12931.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106876 restraints weight = 9724.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107673 restraints weight = 8147.485| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17353 Z= 0.121 Angle : 0.663 12.907 23618 Z= 0.311 Chirality : 0.041 0.449 2926 Planarity : 0.003 0.025 2807 Dihedral : 7.452 53.187 2660 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.70 % Allowed : 16.09 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.19), residues: 2100 helix: 1.98 (0.14), residues: 1442 sheet: -0.91 (0.44), residues: 119 loop : -0.36 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 156 TYR 0.008 0.001 TYR E 226 PHE 0.025 0.001 PHE F 368 TRP 0.005 0.001 TRP C 85 HIS 0.002 0.000 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00258 (17332) covalent geometry : angle 0.65625 (23569) SS BOND : bond 0.00155 ( 14) SS BOND : angle 0.64357 ( 28) hydrogen bonds : bond 0.03266 ( 1113) hydrogen bonds : angle 3.75107 ( 3234) link_NAG-ASN : bond 0.00028 ( 7) link_NAG-ASN : angle 3.11963 ( 21) *********************** 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 139 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.655 Fit side-chains REVERT: B 147 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6122 (tp) REVERT: C 324 ASN cc_start: 0.8770 (p0) cc_final: 0.8534 (p0) REVERT: G 101 MET cc_start: 0.8068 (tpp) cc_final: 0.7782 (tpp) outliers start: 31 outliers final: 23 residues processed: 131 average time/residue: 0.0882 time to fit residues: 19.5051 Evaluate side-chains 115 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 CYS 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 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 242 CYS Chi-restraints excluded: chain E residue 281 THR 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 223 THR Chi-restraints excluded: chain G residue 232 LEU 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 202 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.123454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097683 restraints weight = 36342.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100210 restraints weight = 20426.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101867 restraints weight = 13681.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103087 restraints weight = 10526.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103627 restraints weight = 8858.157| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17353 Z= 0.146 Angle : 0.682 11.330 23618 Z= 0.322 Chirality : 0.041 0.484 2926 Planarity : 0.003 0.025 2807 Dihedral : 7.223 49.973 2660 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.08 % Allowed : 16.48 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.19), residues: 2100 helix: 1.91 (0.14), residues: 1442 sheet: -0.01 (0.46), residues: 84 loop : -0.80 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 156 TYR 0.010 0.001 TYR G 226 PHE 0.026 0.001 PHE F 368 TRP 0.004 0.001 TRP B 85 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00326 (17332) covalent geometry : angle 0.67410 (23569) SS BOND : bond 0.00316 ( 14) SS BOND : angle 0.81759 ( 28) hydrogen bonds : bond 0.03506 ( 1113) hydrogen bonds : angle 3.78524 ( 3234) link_NAG-ASN : bond 0.00204 ( 7) link_NAG-ASN : angle 3.42564 ( 21) *********************** 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 133 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.579 Fit side-chains REVERT: C 101 MET cc_start: 0.7928 (tpp) cc_final: 0.7680 (tpp) REVERT: C 324 ASN cc_start: 0.8821 (p0) cc_final: 0.8586 (p0) REVERT: F 50 MET cc_start: 0.7209 (tpp) cc_final: 0.6928 (mpp) REVERT: G 101 MET cc_start: 0.8113 (tpp) cc_final: 0.7863 (tpp) outliers start: 38 outliers final: 31 residues processed: 122 average time/residue: 0.0892 time to fit residues: 18.4427 Evaluate side-chains 121 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 242 CYS 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 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 242 CYS 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 198 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 173 optimal weight: 0.0170 chunk 163 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.125627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100461 restraints weight = 35856.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.103000 restraints weight = 20076.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104753 restraints weight = 13366.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.105772 restraints weight = 10142.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106533 restraints weight = 8579.251| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2062 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= 0.118 Angle : 0.663 14.648 23618 Z= 0.312 Chirality : 0.040 0.434 2926 Planarity : 0.003 0.025 2807 Dihedral : 6.817 44.227 2660 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.48 % Allowed : 17.24 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.19), residues: 2100 helix: 2.04 (0.14), residues: 1442 sheet: -0.91 (0.45), residues: 119 loop : -0.38 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.008 0.001 TYR E 226 PHE 0.024 0.001 PHE F 368 TRP 0.008 0.001 TRP E 297 HIS 0.001 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00242 (17332) covalent geometry : angle 0.65764 (23569) SS BOND : bond 0.00108 ( 14) SS BOND : angle 0.50883 ( 28) hydrogen bonds : bond 0.03172 ( 1113) hydrogen bonds : angle 3.70146 ( 3234) link_NAG-ASN : bond 0.00053 ( 7) link_NAG-ASN : angle 2.99346 ( 21) *********************** 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 132 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.440 Fit side-chains REVERT: B 147 LEU cc_start: 0.6573 (mm) cc_final: 0.5850 (tp) REVERT: C 324 ASN cc_start: 0.8762 (p0) cc_final: 0.8543 (p0) REVERT: F 50 MET cc_start: 0.7238 (tpp) cc_final: 0.6942 (mpp) outliers start: 27 outliers final: 23 residues processed: 130 average time/residue: 0.0853 time to fit residues: 19.0800 Evaluate side-chains 114 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 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 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 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 206 VAL 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 282 ILE 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 66 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 145 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.122033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096373 restraints weight = 37181.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098873 restraints weight = 21363.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100603 restraints weight = 14475.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101616 restraints weight = 11109.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102371 restraints weight = 9448.942| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17353 Z= 0.144 Angle : 0.716 14.378 23618 Z= 0.335 Chirality : 0.041 0.337 2926 Planarity : 0.003 0.025 2807 Dihedral : 6.704 41.680 2660 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.70 % Allowed : 18.12 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.19), residues: 2100 helix: 1.91 (0.14), residues: 1442 sheet: 0.07 (0.47), residues: 84 loop : -0.88 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 293 TYR 0.010 0.001 TYR E 226 PHE 0.030 0.001 PHE F 368 TRP 0.004 0.001 TRP G 297 HIS 0.002 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00321 (17332) covalent geometry : angle 0.70882 (23569) SS BOND : bond 0.00334 ( 14) SS BOND : angle 0.80627 ( 28) hydrogen bonds : bond 0.03476 ( 1113) hydrogen bonds : angle 3.75178 ( 3234) link_NAG-ASN : bond 0.00183 ( 7) link_NAG-ASN : angle 3.34935 ( 21) *********************** 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 126 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.700 Fit side-chains REVERT: A 121 MET cc_start: 0.6895 (mmp) cc_final: 0.6692 (mmp) REVERT: C 324 ASN cc_start: 0.8738 (p0) cc_final: 0.8499 (p0) REVERT: G 101 MET cc_start: 0.8081 (tpp) cc_final: 0.7828 (tpp) outliers start: 31 outliers final: 31 residues processed: 117 average time/residue: 0.0922 time to fit residues: 18.1663 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 : 0.436 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 187 optimal weight: 0.2980 chunk 160 optimal weight: 0.9990 chunk 15 optimal weight: 0.0050 chunk 175 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.126242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.101185 restraints weight = 35201.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103664 restraints weight = 19609.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105454 restraints weight = 13030.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106580 restraints weight = 9866.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107127 restraints weight = 8295.482| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17353 Z= 0.122 Angle : 0.711 15.431 23618 Z= 0.332 Chirality : 0.040 0.339 2926 Planarity : 0.003 0.024 2807 Dihedral : 6.482 38.395 2660 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.48 % Allowed : 18.23 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.19), residues: 2100 helix: 1.98 (0.14), residues: 1442 sheet: -0.90 (0.44), residues: 119 loop : -0.51 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 194 TYR 0.017 0.001 TYR E 195 PHE 0.031 0.001 PHE F 368 TRP 0.007 0.001 TRP G 297 HIS 0.001 0.000 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00255 (17332) covalent geometry : angle 0.70518 (23569) SS BOND : bond 0.00132 ( 14) SS BOND : angle 0.55828 ( 28) hydrogen bonds : bond 0.03250 ( 1113) hydrogen bonds : angle 3.68969 ( 3234) link_NAG-ASN : bond 0.00025 ( 7) link_NAG-ASN : angle 3.04105 ( 21) ********************** 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 124 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.409 Fit side-chains REVERT: A 121 MET cc_start: 0.6673 (mmp) cc_final: 0.6415 (mmp) REVERT: C 101 MET cc_start: 0.7842 (tpp) cc_final: 0.7543 (tpp) REVERT: C 324 ASN cc_start: 0.8743 (p0) cc_final: 0.8527 (p0) REVERT: E 139 ASP cc_start: 0.6595 (m-30) cc_final: 0.6225 (t0) REVERT: G 101 MET cc_start: 0.8020 (tpp) cc_final: 0.7763 (tpp) outliers start: 27 outliers final: 26 residues processed: 122 average time/residue: 0.0864 time to fit residues: 18.1125 Evaluate side-chains 122 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 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 232 LEU 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 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 282 ILE 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 183 optimal weight: 2.9990 chunk 204 optimal weight: 0.0870 chunk 114 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 0.0470 chunk 132 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.125020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099907 restraints weight = 36177.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102443 restraints weight = 20434.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104149 restraints weight = 13661.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.105285 restraints weight = 10423.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106042 restraints weight = 8773.566| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17353 Z= 0.118 Angle : 0.701 12.970 23618 Z= 0.328 Chirality : 0.040 0.314 2926 Planarity : 0.003 0.024 2807 Dihedral : 6.286 39.760 2660 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.42 % Allowed : 18.66 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.19), residues: 2100 helix: 2.04 (0.14), residues: 1442 sheet: -0.90 (0.44), residues: 119 loop : -0.50 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 293 TYR 0.018 0.001 TYR E 195 PHE 0.030 0.001 PHE F 368 TRP 0.006 0.001 TRP F 297 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00243 (17332) covalent geometry : angle 0.69572 (23569) SS BOND : bond 0.00118 ( 14) SS BOND : angle 0.53388 ( 28) hydrogen bonds : bond 0.03157 ( 1113) hydrogen bonds : angle 3.62787 ( 3234) link_NAG-ASN : bond 0.00046 ( 7) link_NAG-ASN : angle 2.89139 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2113.92 seconds wall clock time: 37 minutes 36.24 seconds (2256.24 seconds total)