Starting phenix.real_space_refine on Wed Mar 4 22:33:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtr_34265/03_2026/8gtr_34265_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtr_34265/03_2026/8gtr_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gtr_34265/03_2026/8gtr_34265_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtr_34265/03_2026/8gtr_34265_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gtr_34265/03_2026/8gtr_34265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtr_34265/03_2026/8gtr_34265.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16975 Number of models: 1 Model: "" Number of chains: 14 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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 Time building chain proxies: 3.93, per 1000 atoms: 0.23 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 B 84 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 261 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 261 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 261 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 261 " 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: 1.28 Conformation dependent library (CDL) restraints added in 497.5 milliseconds 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: 0.45 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: 2.49 Time building geometry restraints manager: 1.60 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: 0.02 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.820 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- 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 are 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 : 0.589 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: 0.1082 time to fit residues: 25.8867 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 : 0.528 ------------------------------------------------------------------------------- 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 are 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 : 0.575 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: 0.8234 (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: 0.0934 time to fit residues: 17.6077 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 : 0.640 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104235 restraints weight = 34509.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106802 restraints weight = 19031.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108515 restraints weight = 12547.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109637 restraints weight = 9532.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110237 restraints weight = 7984.473| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 are 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 : 0.600 Fit side-chains REVERT: C 324 ASN cc_start: 0.8785 (p0) cc_final: 0.8536 (p0) REVERT: E 369 MET cc_start: 0.6411 (ppp) cc_final: 0.6032 (ppp) REVERT: G 101 MET cc_start: 0.8019 (tpp) cc_final: 0.7747 (tpp) REVERT: G 369 MET cc_start: 0.5986 (ppp) cc_final: 0.5592 (ppp) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.0973 time to fit residues: 19.3563 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 : 0.488 ------------------------------------------------------------------------------- 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: 6.9990 chunk 164 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.126184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100961 restraints weight = 34973.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.103441 restraints weight = 19586.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.105142 restraints weight = 13055.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.106214 restraints weight = 9962.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106721 restraints weight = 8400.256| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17353 Z= 0.155 Angle : 0.672 9.969 23618 Z= 0.317 Chirality : 0.041 0.408 2926 Planarity : 0.003 0.027 2807 Dihedral : 8.555 59.527 2660 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.24 % Allowed : 12.53 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 2100 helix: 1.77 (0.14), residues: 1442 sheet: -0.23 (0.45), residues: 84 loop : -0.70 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 156 TYR 0.011 0.001 TYR E 226 PHE 0.009 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 0.00350 (17332) covalent geometry : angle 0.66301 (23569) SS BOND : bond 0.00383 ( 14) SS BOND : angle 0.72306 ( 28) hydrogen bonds : bond 0.03724 ( 1113) hydrogen bonds : angle 3.94931 ( 3234) link_NAG-ASN : bond 0.00263 ( 7) link_NAG-ASN : angle 3.68385 ( 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 141 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.652 Fit side-chains REVERT: B 39 LYS cc_start: 0.8394 (tmmt) cc_final: 0.8140 (ttpp) REVERT: C 39 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7948 (ttpp) REVERT: C 324 ASN cc_start: 0.8905 (p0) cc_final: 0.8608 (p0) REVERT: E 101 MET cc_start: 0.7951 (tpp) cc_final: 0.7525 (tpp) REVERT: G 101 MET cc_start: 0.8070 (tpp) cc_final: 0.7822 (tpp) REVERT: G 324 ASN cc_start: 0.8719 (p0) cc_final: 0.8510 (p0) REVERT: G 369 MET cc_start: 0.6270 (ppp) cc_final: 0.6061 (tmm) outliers start: 41 outliers final: 27 residues processed: 131 average time/residue: 0.1037 time to fit residues: 22.8199 Evaluate side-chains 115 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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: 0.5980 chunk 122 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 169 optimal weight: 0.0870 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.126837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.101576 restraints weight = 35422.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104162 restraints weight = 19541.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105838 restraints weight = 12907.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107043 restraints weight = 9815.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107800 restraints weight = 8268.500| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17353 Z= 0.115 Angle : 0.645 13.975 23618 Z= 0.301 Chirality : 0.041 0.416 2926 Planarity : 0.003 0.025 2807 Dihedral : 7.796 55.572 2660 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 are not related in a simple way. whole: 1.88 (0.19), residues: 2100 helix: 2.01 (0.14), residues: 1442 sheet: -0.94 (0.44), residues: 119 loop : -0.25 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 156 TYR 0.007 0.001 TYR F 226 PHE 0.028 0.001 PHE E 368 TRP 0.006 0.001 TRP D 85 HIS 0.001 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00231 (17332) covalent geometry : angle 0.63935 (23569) SS BOND : bond 0.00113 ( 14) SS BOND : angle 0.43248 ( 28) hydrogen bonds : bond 0.03242 ( 1113) hydrogen bonds : angle 3.76208 ( 3234) link_NAG-ASN : bond 0.00069 ( 7) link_NAG-ASN : angle 3.07196 ( 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 151 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.707 Fit side-chains REVERT: B 147 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.5966 (tp) REVERT: C 324 ASN cc_start: 0.8720 (p0) cc_final: 0.8498 (p0) REVERT: F 50 MET cc_start: 0.7270 (mpp) cc_final: 0.7029 (mmp) REVERT: G 101 MET cc_start: 0.8009 (tpp) cc_final: 0.7717 (tpp) REVERT: G 324 ASN cc_start: 0.8649 (p0) cc_final: 0.8423 (p0) outliers start: 32 outliers final: 16 residues processed: 145 average time/residue: 0.1017 time to fit residues: 24.1984 Evaluate side-chains 110 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 93 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.124162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.098382 restraints weight = 36343.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100924 restraints weight = 20403.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102726 restraints weight = 13606.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103754 restraints weight = 10381.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104552 restraints weight = 8781.218| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17353 Z= 0.134 Angle : 0.675 13.200 23618 Z= 0.318 Chirality : 0.041 0.427 2926 Planarity : 0.003 0.025 2807 Dihedral : 7.484 53.404 2660 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.24 % Allowed : 16.26 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.19), residues: 2100 helix: 1.95 (0.14), residues: 1442 sheet: -0.90 (0.45), residues: 119 loop : -0.43 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 75 TYR 0.012 0.001 TYR D 195 PHE 0.031 0.001 PHE C 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 0.00296 (17332) covalent geometry : angle 0.66839 (23569) SS BOND : bond 0.00308 ( 14) SS BOND : angle 0.76637 ( 28) hydrogen bonds : bond 0.03366 ( 1113) hydrogen bonds : angle 3.76990 ( 3234) link_NAG-ASN : bond 0.00131 ( 7) link_NAG-ASN : angle 3.28271 ( 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 143 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 102 time to evaluate : 0.563 Fit side-chains REVERT: B 147 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.5956 (tp) REVERT: C 324 ASN cc_start: 0.8800 (p0) cc_final: 0.8561 (p0) outliers start: 41 outliers final: 28 residues processed: 131 average time/residue: 0.1011 time to fit residues: 22.3279 Evaluate side-chains 121 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 147 LEU 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 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 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 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 282 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 172 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 overall best weight: 1.0940 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.123920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098275 restraints weight = 36297.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100842 restraints weight = 20350.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.102478 restraints weight = 13623.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.103723 restraints weight = 10456.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.104342 restraints weight = 8786.548| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17353 Z= 0.132 Angle : 0.661 11.828 23618 Z= 0.314 Chirality : 0.040 0.334 2926 Planarity : 0.003 0.025 2807 Dihedral : 7.151 49.275 2660 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.30 % Allowed : 16.26 % 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 are not related in a simple way. whole: 1.73 (0.19), residues: 2100 helix: 1.92 (0.14), residues: 1449 sheet: 0.07 (0.47), residues: 84 loop : -0.71 (0.29), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.009 0.001 TYR F 226 PHE 0.029 0.001 PHE G 368 TRP 0.005 0.001 TRP F 85 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00287 (17332) covalent geometry : angle 0.65383 (23569) SS BOND : bond 0.00248 ( 14) SS BOND : angle 0.71467 ( 28) hydrogen bonds : bond 0.03374 ( 1113) hydrogen bonds : angle 3.74649 ( 3234) link_NAG-ASN : bond 0.00109 ( 7) link_NAG-ASN : angle 3.28795 ( 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 143 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.625 Fit side-chains REVERT: B 147 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.5941 (tp) REVERT: C 101 MET cc_start: 0.7916 (tpp) cc_final: 0.7658 (tpp) REVERT: C 324 ASN cc_start: 0.8805 (p0) cc_final: 0.8589 (p0) REVERT: F 50 MET cc_start: 0.7325 (tpp) cc_final: 0.6964 (mpp) REVERT: G 101 MET cc_start: 0.8089 (tpp) cc_final: 0.7836 (tpp) outliers start: 42 outliers final: 32 residues processed: 132 average time/residue: 0.0992 time to fit residues: 22.4837 Evaluate side-chains 123 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 198 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 173 optimal weight: 0.0970 chunk 163 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 chunk 135 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.123437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098163 restraints weight = 37830.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100740 restraints weight = 21467.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102444 restraints weight = 14405.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.103592 restraints weight = 11018.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104145 restraints weight = 9301.732| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17353 Z= 0.118 Angle : 0.677 15.381 23618 Z= 0.315 Chirality : 0.040 0.489 2926 Planarity : 0.003 0.024 2807 Dihedral : 6.793 44.105 2660 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.53 % Allowed : 17.35 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.19), residues: 2100 helix: 2.00 (0.14), residues: 1449 sheet: -0.89 (0.45), residues: 119 loop : -0.28 (0.30), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 293 TYR 0.008 0.001 TYR E 226 PHE 0.032 0.001 PHE G 368 TRP 0.006 0.001 TRP E 297 HIS 0.001 0.000 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00244 (17332) covalent geometry : angle 0.67143 (23569) SS BOND : bond 0.00110 ( 14) SS BOND : angle 0.51332 ( 28) hydrogen bonds : bond 0.03168 ( 1113) hydrogen bonds : angle 3.70512 ( 3234) link_NAG-ASN : bond 0.00057 ( 7) link_NAG-ASN : angle 2.97733 ( 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: 28 poor density : 104 time to evaluate : 0.625 Fit side-chains REVERT: B 147 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6144 (tp) REVERT: C 324 ASN cc_start: 0.8568 (p0) cc_final: 0.8360 (p0) REVERT: F 50 MET cc_start: 0.7264 (tpp) cc_final: 0.6982 (mpp) REVERT: F 147 LEU cc_start: 0.6921 (mm) cc_final: 0.6195 (tp) outliers start: 28 outliers final: 23 residues processed: 131 average time/residue: 0.0918 time to fit residues: 20.8265 Evaluate side-chains 117 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 206 VAL 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 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 E residue 311 PHE 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=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: 3.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 156 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.120432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095657 restraints weight = 37492.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096736 restraints weight = 23686.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.098275 restraints weight = 16813.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098863 restraints weight = 12111.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098902 restraints weight = 11359.103| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17353 Z= 0.180 Angle : 0.747 12.779 23618 Z= 0.352 Chirality : 0.042 0.298 2926 Planarity : 0.003 0.024 2807 Dihedral : 6.903 42.899 2660 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.70 % Allowed : 18.17 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2100 helix: 1.73 (0.13), residues: 1449 sheet: -0.03 (0.46), residues: 84 loop : -0.89 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 293 TYR 0.012 0.001 TYR E 226 PHE 0.038 0.002 PHE G 368 TRP 0.006 0.001 TRP F 297 HIS 0.003 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00409 (17332) covalent geometry : angle 0.73878 (23569) SS BOND : bond 0.00515 ( 14) SS BOND : angle 0.97865 ( 28) hydrogen bonds : bond 0.03818 ( 1113) hydrogen bonds : angle 3.87844 ( 3234) link_NAG-ASN : bond 0.00349 ( 7) link_NAG-ASN : angle 3.74120 ( 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 129 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.660 Fit side-chains REVERT: C 101 MET cc_start: 0.7984 (tpp) cc_final: 0.7712 (tpp) REVERT: C 324 ASN cc_start: 0.8810 (p0) cc_final: 0.8593 (p0) REVERT: G 101 MET cc_start: 0.8147 (tpp) cc_final: 0.7909 (tpp) outliers start: 31 outliers final: 28 residues processed: 118 average time/residue: 0.1021 time to fit residues: 20.4119 Evaluate side-chains 118 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 232 LEU 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 281 THR Chi-restraints excluded: chain C residue 282 ILE 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 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: 3.9990 chunk 59 optimal weight: 7.9990 chunk 187 optimal weight: 0.0050 chunk 160 optimal weight: 0.0470 chunk 15 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.9896 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.123610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097931 restraints weight = 36598.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.100496 restraints weight = 20617.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.102139 restraints weight = 13805.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103343 restraints weight = 10613.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103973 restraints weight = 8941.432| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.003 0.037 17353 Z= 0.133 Angle : 0.742 15.119 23618 Z= 0.344 Chirality : 0.042 0.426 2926 Planarity : 0.003 0.024 2807 Dihedral : 6.692 39.086 2660 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.26 % Allowed : 18.99 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.19), residues: 2100 helix: 1.82 (0.14), residues: 1449 sheet: 0.18 (0.46), residues: 84 loop : -0.87 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 293 TYR 0.009 0.001 TYR E 226 PHE 0.037 0.001 PHE G 368 TRP 0.007 0.001 TRP G 297 HIS 0.002 0.000 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00287 (17332) covalent geometry : angle 0.73587 (23569) SS BOND : bond 0.00177 ( 14) SS BOND : angle 0.63226 ( 28) hydrogen bonds : bond 0.03504 ( 1113) hydrogen bonds : angle 3.79017 ( 3234) link_NAG-ASN : bond 0.00073 ( 7) link_NAG-ASN : angle 3.39949 ( 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 118 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.474 Fit side-chains REVERT: C 101 MET cc_start: 0.7919 (tpp) cc_final: 0.7650 (tpp) REVERT: C 324 ASN cc_start: 0.8771 (p0) cc_final: 0.8537 (p0) REVERT: G 101 MET cc_start: 0.8062 (tpp) cc_final: 0.7793 (tpp) outliers start: 23 outliers final: 23 residues processed: 117 average time/residue: 0.0960 time to fit residues: 19.4046 Evaluate side-chains 115 residues out of total 1988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 206 VAL 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 232 LEU Chi-restraints excluded: chain C residue 282 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 198 optimal weight: 0.5980 chunk 107 optimal weight: 0.0050 chunk 67 optimal weight: 0.0050 chunk 132 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 overall best weight: 0.7010 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.124787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099372 restraints weight = 36307.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101953 restraints weight = 20284.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103720 restraints weight = 13486.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104851 restraints weight = 10285.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105474 restraints weight = 8655.835| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17353 Z= 0.123 Angle : 0.708 13.682 23618 Z= 0.332 Chirality : 0.041 0.418 2926 Planarity : 0.003 0.024 2807 Dihedral : 6.445 39.003 2660 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.64 % Allowed : 18.66 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 2100 helix: 1.91 (0.14), residues: 1449 sheet: -0.81 (0.45), residues: 119 loop : -0.54 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 293 TYR 0.008 0.001 TYR E 226 PHE 0.036 0.001 PHE G 368 TRP 0.007 0.001 TRP G 297 HIS 0.002 0.000 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00257 (17332) covalent geometry : angle 0.70222 (23569) SS BOND : bond 0.00145 ( 14) SS BOND : angle 0.55476 ( 28) hydrogen bonds : bond 0.03283 ( 1113) hydrogen bonds : angle 3.70781 ( 3234) link_NAG-ASN : bond 0.00004 ( 7) link_NAG-ASN : angle 3.11979 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.62 seconds wall clock time: 40 minutes 6.29 seconds (2406.29 seconds total)