Starting phenix.real_space_refine on Thu Feb 5 08:33:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lh5_63084/02_2026/9lh5_63084.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lh5_63084/02_2026/9lh5_63084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lh5_63084/02_2026/9lh5_63084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lh5_63084/02_2026/9lh5_63084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lh5_63084/02_2026/9lh5_63084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lh5_63084/02_2026/9lh5_63084.map" } resolution = 2.61 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= 0.007 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10355 2.51 5 N 2535 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15930 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 3169 Chain: "B" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 3169 Chain: "C" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 3169 Chain: "D" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 3169 Chain: "E" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 393, 3096 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 3169 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.76, per 1000 atoms: 0.42 Number of scatterers: 15930 At special positions: 0 Unit cell: (96.96, 96.96, 156.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2940 8.00 N 2535 7.00 C 10355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.15 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.15 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.15 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.15 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.15 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 602 " - " ASN A 90 " " NAG B 602 " - " ASN B 90 " " NAG C 602 " - " ASN C 90 " " NAG D 602 " - " ASN D 90 " " NAG E 602 " - " ASN E 90 " " NAG F 1 " - " ASN A 46 " " NAG G 1 " - " ASN A 133 " " NAG H 1 " - " ASN B 46 " " NAG I 1 " - " ASN B 133 " " NAG J 1 " - " ASN C 46 " " NAG K 1 " - " ASN C 133 " " NAG L 1 " - " ASN D 46 " " NAG M 1 " - " ASN D 133 " " NAG N 1 " - " ASN E 46 " " NAG O 1 " - " ASN E 133 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3750 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 42.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.740A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 254 removed outlier: 4.612A pdb=" N ILE A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.710A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.029A pdb=" N ALA A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 317 Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.815A pdb=" N ILE A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 488 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.122A pdb=" N VAL A 497 " --> pdb=" O PHE A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.740A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 254 removed outlier: 4.612A pdb=" N ILE B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.710A pdb=" N ILE B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 removed outlier: 4.029A pdb=" N ALA B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 317 Processing helix chain 'B' and resid 328 through 342 removed outlier: 3.815A pdb=" N ILE B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 488 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.122A pdb=" N VAL B 497 " --> pdb=" O PHE B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.740A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 254 removed outlier: 4.612A pdb=" N ILE C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 258 through 276 removed outlier: 3.711A pdb=" N ILE C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 removed outlier: 4.029A pdb=" N ALA C 280 " --> pdb=" O MET C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 317 Processing helix chain 'C' and resid 328 through 342 removed outlier: 3.816A pdb=" N ILE C 334 " --> pdb=" O TRP C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 488 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.122A pdb=" N VAL C 497 " --> pdb=" O PHE C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.740A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 254 removed outlier: 4.612A pdb=" N ILE D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 258 through 276 removed outlier: 3.710A pdb=" N ILE D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 281 removed outlier: 4.029A pdb=" N ALA D 280 " --> pdb=" O MET D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 317 Processing helix chain 'D' and resid 328 through 342 removed outlier: 3.815A pdb=" N ILE D 334 " --> pdb=" O TRP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 488 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.122A pdb=" N VAL D 497 " --> pdb=" O PHE D 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.740A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 254 removed outlier: 4.612A pdb=" N ILE E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 258 through 276 removed outlier: 3.710A pdb=" N ILE E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 281 removed outlier: 4.030A pdb=" N ALA E 280 " --> pdb=" O MET E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 317 Processing helix chain 'E' and resid 328 through 342 removed outlier: 3.815A pdb=" N ILE E 334 " --> pdb=" O TRP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 488 Processing helix chain 'E' and resid 493 through 500 removed outlier: 4.123A pdb=" N VAL E 497 " --> pdb=" O PHE E 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 102 removed outlier: 4.085A pdb=" N HIS A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 removed outlier: 4.085A pdb=" N HIS A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR A 83 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N TYR A 54 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.744A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.744A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 102 removed outlier: 4.085A pdb=" N HIS B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 removed outlier: 4.085A pdb=" N HIS B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N TRP B 77 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLN B 79 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER B 58 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER B 81 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER B 56 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR B 83 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N TYR B 54 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.744A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.744A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.501A pdb=" N ASN C 133 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.501A pdb=" N ASN C 133 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N TRP C 77 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLN C 79 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER C 58 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER C 81 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N SER C 56 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR C 83 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N TYR C 54 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.745A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.745A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 102 removed outlier: 4.112A pdb=" N HIS D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 102 removed outlier: 4.112A pdb=" N HIS D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN D 75 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N TRP D 77 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLN D 79 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER D 58 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER D 81 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N SER D 56 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR D 83 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N TYR D 54 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.745A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.745A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 99 through 102 removed outlier: 4.083A pdb=" N HIS E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 102 removed outlier: 4.083A pdb=" N HIS E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR E 83 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N TYR E 54 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.743A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.743A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2817 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: 2.77 Time building geometry restraints manager: 1.79 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: 2535 1.31 - 1.44: 4480 1.44 - 1.57: 9180 1.57 - 1.70: 10 1.70 - 1.83: 145 Bond restraints: 16350 Sorted by residual: bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.626 -0.174 2.00e-02 2.50e+03 7.55e+01 bond pdb=" C6 NCT B 601 " pdb=" N2 NCT B 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" C6 NCT C 601 " pdb=" N2 NCT C 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C6 NCT E 601 " pdb=" N2 NCT E 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C6 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.45e+01 ... (remaining 16345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 21662 2.17 - 4.35: 516 4.35 - 6.52: 107 6.52 - 8.69: 15 8.69 - 10.87: 5 Bond angle restraints: 22305 Sorted by residual: angle pdb=" N ARG C 121 " pdb=" CA ARG C 121 " pdb=" C ARG C 121 " ideal model delta sigma weight residual 109.59 101.92 7.67 1.61e+00 3.86e-01 2.27e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.59 101.92 7.67 1.61e+00 3.86e-01 2.27e+01 angle pdb=" N ARG D 121 " pdb=" CA ARG D 121 " pdb=" C ARG D 121 " ideal model delta sigma weight residual 109.59 101.94 7.65 1.61e+00 3.86e-01 2.26e+01 angle pdb=" N ARG A 121 " pdb=" CA ARG A 121 " pdb=" C ARG A 121 " ideal model delta sigma weight residual 109.59 101.95 7.64 1.61e+00 3.86e-01 2.25e+01 angle pdb=" N ARG E 121 " pdb=" CA ARG E 121 " pdb=" C ARG E 121 " ideal model delta sigma weight residual 109.59 101.97 7.62 1.61e+00 3.86e-01 2.24e+01 ... (remaining 22300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 9010 23.43 - 46.86: 830 46.86 - 70.29: 120 70.29 - 93.72: 15 93.72 - 117.15: 40 Dihedral angle restraints: 10015 sinusoidal: 4215 harmonic: 5800 Sorted by residual: dihedral pdb=" CA CYS A 212 " pdb=" C CYS A 212 " pdb=" N CYS A 213 " pdb=" CA CYS A 213 " ideal model delta harmonic sigma weight residual 180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA CYS B 212 " pdb=" C CYS B 212 " pdb=" N CYS B 213 " pdb=" CA CYS B 213 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA CYS E 212 " pdb=" C CYS E 212 " pdb=" N CYS E 213 " pdb=" CA CYS E 213 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 10012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1629 0.033 - 0.066: 710 0.066 - 0.099: 170 0.099 - 0.132: 66 0.132 - 0.165: 35 Chirality restraints: 2610 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.94e+00 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.77e+00 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.58e+00 ... (remaining 2607 not shown) Planarity restraints: 2780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 217 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.17e+00 pdb=" N PRO C 218 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 218 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 218 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 217 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 218 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 217 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO E 218 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 218 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 218 " -0.037 5.00e-02 4.00e+02 ... (remaining 2777 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3365 2.78 - 3.31: 14257 3.31 - 3.84: 26460 3.84 - 4.37: 29617 4.37 - 4.90: 51657 Nonbonded interactions: 125356 Sorted by model distance: nonbonded pdb=" OG1 THR A 230 " pdb=" OD2 ASP A 500 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR D 230 " pdb=" OD2 ASP D 500 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR B 230 " pdb=" OD2 ASP B 500 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR E 230 " pdb=" OD2 ASP E 500 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR C 230 " pdb=" OD2 ASP C 500 " model vdw 2.253 3.040 ... (remaining 125351 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 136 or resid 138 through 602)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 602)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 602)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 602)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 602)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.29 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 19.420 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.010 0.174 16385 Z= 0.520 Angle : 0.813 10.868 22400 Z= 0.390 Chirality : 0.044 0.165 2610 Planarity : 0.006 0.067 2765 Dihedral : 18.953 117.145 6235 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.71 % Allowed : 16.70 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.28 (0.18), residues: 1950 helix: 0.61 (0.18), residues: 775 sheet: 0.51 (0.26), residues: 405 loop : -1.36 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 42 TYR 0.010 0.001 TYR C 217 PHE 0.011 0.001 PHE E 275 TRP 0.044 0.002 TRP D 156 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.01022 (16350) covalent geometry : angle 0.80985 (22305) SS BOND : bond 0.08185 ( 10) SS BOND : angle 1.68874 ( 20) hydrogen bonds : bond 0.11305 ( 855) hydrogen bonds : angle 5.82348 ( 2817) link_BETA1-4 : bond 0.00293 ( 10) link_BETA1-4 : angle 1.23098 ( 30) link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 1.36676 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.561 Fit side-chains REVERT: C 155 ARG cc_start: 0.7728 (ptt180) cc_final: 0.7500 (ptp90) REVERT: C 276 MET cc_start: 0.5668 (pp-130) cc_final: 0.5466 (ppp) REVERT: D 276 MET cc_start: 0.5879 (pp-130) cc_final: 0.5516 (ppp) REVERT: E 276 MET cc_start: 0.5802 (pp-130) cc_final: 0.5562 (ppp) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.6481 time to fit residues: 92.8841 Evaluate side-chains 122 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 275 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.097910 restraints weight = 48870.120| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.15 r_work: 0.2978 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16385 Z= 0.120 Angle : 0.641 9.189 22400 Z= 0.306 Chirality : 0.042 0.182 2610 Planarity : 0.005 0.061 2765 Dihedral : 12.109 78.149 2723 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.42 % Allowed : 18.41 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.02 (0.18), residues: 1950 helix: 0.89 (0.18), residues: 750 sheet: 0.66 (0.24), residues: 440 loop : -1.25 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 227 TYR 0.004 0.001 TYR E 37 PHE 0.012 0.001 PHE B 275 TRP 0.033 0.002 TRP D 156 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00265 (16350) covalent geometry : angle 0.63278 (22305) SS BOND : bond 0.00820 ( 10) SS BOND : angle 0.93811 ( 20) hydrogen bonds : bond 0.04132 ( 855) hydrogen bonds : angle 5.13383 ( 2817) link_BETA1-4 : bond 0.00161 ( 10) link_BETA1-4 : angle 1.87808 ( 30) link_NAG-ASN : bond 0.00105 ( 15) link_NAG-ASN : angle 1.80078 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.655 Fit side-chains REVERT: A 197 ASP cc_start: 0.8290 (t70) cc_final: 0.8051 (t70) REVERT: A 275 PHE cc_start: 0.5225 (OUTLIER) cc_final: 0.4820 (t80) REVERT: A 276 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.5520 (tmm) REVERT: B 197 ASP cc_start: 0.8167 (t70) cc_final: 0.7877 (t70) REVERT: B 275 PHE cc_start: 0.4921 (OUTLIER) cc_final: 0.4533 (t80) REVERT: B 276 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5676 (tmm) REVERT: C 155 ARG cc_start: 0.7280 (ptt180) cc_final: 0.7035 (ptp90) REVERT: C 208 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7518 (mmm-85) REVERT: C 275 PHE cc_start: 0.5350 (OUTLIER) cc_final: 0.4920 (t80) REVERT: C 276 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.5366 (ppp) REVERT: D 276 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.5484 (ppp) REVERT: E 155 ARG cc_start: 0.7772 (ptp-170) cc_final: 0.7471 (ptp90) REVERT: E 227 ARG cc_start: 0.7445 (ttp80) cc_final: 0.7156 (ttp80) REVERT: E 275 PHE cc_start: 0.5403 (OUTLIER) cc_final: 0.4979 (t80) REVERT: E 276 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5401 (ppp) outliers start: 24 outliers final: 4 residues processed: 147 average time/residue: 0.6537 time to fit residues: 106.0119 Evaluate side-chains 141 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 154 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.176377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093747 restraints weight = 49334.518| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.19 r_work: 0.2890 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16385 Z= 0.194 Angle : 0.677 8.572 22400 Z= 0.323 Chirality : 0.043 0.168 2610 Planarity : 0.005 0.061 2765 Dihedral : 9.602 56.777 2715 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.59 % Allowed : 18.64 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.12 (0.18), residues: 1950 helix: 1.05 (0.18), residues: 765 sheet: 0.63 (0.24), residues: 440 loop : -1.27 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.010 0.001 TYR A 115 PHE 0.014 0.001 PHE C 157 TRP 0.040 0.002 TRP E 156 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00461 (16350) covalent geometry : angle 0.66698 (22305) SS BOND : bond 0.00772 ( 10) SS BOND : angle 1.27530 ( 20) hydrogen bonds : bond 0.04392 ( 855) hydrogen bonds : angle 5.14603 ( 2817) link_BETA1-4 : bond 0.00348 ( 10) link_BETA1-4 : angle 2.23355 ( 30) link_NAG-ASN : bond 0.00236 ( 15) link_NAG-ASN : angle 1.88462 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.8188 (t70) cc_final: 0.7961 (t70) REVERT: A 275 PHE cc_start: 0.5307 (OUTLIER) cc_final: 0.4915 (t80) REVERT: A 276 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5657 (tmm) REVERT: B 197 ASP cc_start: 0.8099 (t70) cc_final: 0.7822 (t70) REVERT: B 275 PHE cc_start: 0.4903 (OUTLIER) cc_final: 0.4589 (t80) REVERT: B 276 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5483 (tmm) REVERT: C 80 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8330 (mtp) REVERT: C 275 PHE cc_start: 0.5201 (OUTLIER) cc_final: 0.4871 (t80) REVERT: C 276 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.5307 (ppp) REVERT: D 276 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.5298 (ppp) REVERT: E 155 ARG cc_start: 0.7594 (ptp-170) cc_final: 0.7308 (ptp90) REVERT: E 275 PHE cc_start: 0.5283 (OUTLIER) cc_final: 0.4980 (t80) REVERT: E 276 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.5360 (ppp) outliers start: 27 outliers final: 13 residues processed: 149 average time/residue: 0.6166 time to fit residues: 101.9525 Evaluate side-chains 147 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 188 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 164 optimal weight: 0.0010 chunk 104 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 overall best weight: 0.9748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN E 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.096935 restraints weight = 43940.755| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.98 r_work: 0.2965 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.197 16385 Z= 0.142 Angle : 0.657 17.639 22400 Z= 0.317 Chirality : 0.041 0.258 2610 Planarity : 0.005 0.058 2765 Dihedral : 8.620 66.203 2715 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.01 % Allowed : 18.17 % Favored : 79.82 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 1950 helix: 1.17 (0.18), residues: 765 sheet: 0.77 (0.24), residues: 440 loop : -1.21 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 208 TYR 0.006 0.001 TYR B 232 PHE 0.012 0.001 PHE A 275 TRP 0.036 0.002 TRP C 156 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00348 (16350) covalent geometry : angle 0.63576 (22305) SS BOND : bond 0.01348 ( 10) SS BOND : angle 4.27123 ( 20) hydrogen bonds : bond 0.04057 ( 855) hydrogen bonds : angle 4.98381 ( 2817) link_BETA1-4 : bond 0.00517 ( 10) link_BETA1-4 : angle 2.25335 ( 30) link_NAG-ASN : bond 0.00071 ( 15) link_NAG-ASN : angle 1.81866 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7925 (mt) REVERT: A 197 ASP cc_start: 0.8164 (t70) cc_final: 0.7934 (t70) REVERT: A 275 PHE cc_start: 0.5459 (OUTLIER) cc_final: 0.5076 (t80) REVERT: A 276 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5608 (tmm) REVERT: B 197 ASP cc_start: 0.8058 (t70) cc_final: 0.7745 (t70) REVERT: B 276 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.5484 (tmm) REVERT: C 60 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8008 (mt) REVERT: C 80 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: C 275 PHE cc_start: 0.5300 (OUTLIER) cc_final: 0.5034 (t80) REVERT: C 276 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.5362 (ppp) REVERT: D 219 ASP cc_start: 0.8139 (t70) cc_final: 0.7100 (p0) REVERT: D 276 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.5200 (ppp) REVERT: E 155 ARG cc_start: 0.7710 (ptp-170) cc_final: 0.7418 (ptp90) REVERT: E 275 PHE cc_start: 0.5445 (OUTLIER) cc_final: 0.5208 (t80) REVERT: E 276 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5395 (ppp) outliers start: 34 outliers final: 15 residues processed: 153 average time/residue: 0.5696 time to fit residues: 96.7366 Evaluate side-chains 156 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.172943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.091511 restraints weight = 38478.284| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.72 r_work: 0.2897 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 16385 Z= 0.369 Angle : 0.795 9.171 22400 Z= 0.382 Chirality : 0.048 0.244 2610 Planarity : 0.006 0.062 2765 Dihedral : 8.685 92.153 2713 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.42 % Allowed : 16.99 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 1950 helix: 1.12 (0.18), residues: 750 sheet: 0.52 (0.24), residues: 470 loop : -1.34 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 208 TYR 0.016 0.002 TYR A 115 PHE 0.026 0.002 PHE B 275 TRP 0.053 0.003 TRP C 156 HIS 0.006 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00903 (16350) covalent geometry : angle 0.78050 (22305) SS BOND : bond 0.01103 ( 10) SS BOND : angle 2.69982 ( 20) hydrogen bonds : bond 0.05024 ( 855) hydrogen bonds : angle 5.27272 ( 2817) link_BETA1-4 : bond 0.00220 ( 10) link_BETA1-4 : angle 2.65744 ( 30) link_NAG-ASN : bond 0.00483 ( 15) link_NAG-ASN : angle 2.09093 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8069 (mt) REVERT: A 275 PHE cc_start: 0.5385 (OUTLIER) cc_final: 0.5013 (t80) REVERT: A 276 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5681 (tmm) REVERT: A 473 MET cc_start: 0.7959 (ppp) cc_final: 0.7752 (pmm) REVERT: B 276 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5454 (tmm) REVERT: C 60 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8238 (mt) REVERT: C 80 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8462 (mtp) REVERT: C 275 PHE cc_start: 0.5458 (OUTLIER) cc_final: 0.5177 (t80) REVERT: C 276 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5314 (ppp) REVERT: D 60 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8138 (mt) REVERT: D 214 LYS cc_start: 0.8425 (tptt) cc_final: 0.8189 (tptt) REVERT: D 219 ASP cc_start: 0.8472 (t70) cc_final: 0.7362 (p0) REVERT: D 276 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.5284 (ppp) REVERT: E 60 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8218 (mt) REVERT: E 275 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.5210 (t80) REVERT: E 276 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5411 (ppp) outliers start: 58 outliers final: 29 residues processed: 172 average time/residue: 0.5936 time to fit residues: 113.4768 Evaluate side-chains 169 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 487 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.174658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.093063 restraints weight = 44772.170| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.94 r_work: 0.2912 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16385 Z= 0.210 Angle : 0.710 13.473 22400 Z= 0.343 Chirality : 0.043 0.267 2610 Planarity : 0.005 0.059 2765 Dihedral : 8.220 91.167 2713 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.42 % Allowed : 18.88 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 1950 helix: 1.18 (0.18), residues: 765 sheet: 0.56 (0.24), residues: 470 loop : -1.29 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.009 0.001 TYR A 115 PHE 0.022 0.001 PHE B 275 TRP 0.046 0.002 TRP D 156 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00500 (16350) covalent geometry : angle 0.69681 (22305) SS BOND : bond 0.01284 ( 10) SS BOND : angle 2.47038 ( 20) hydrogen bonds : bond 0.04550 ( 855) hydrogen bonds : angle 5.12276 ( 2817) link_BETA1-4 : bond 0.00310 ( 10) link_BETA1-4 : angle 2.39720 ( 30) link_NAG-ASN : bond 0.00173 ( 15) link_NAG-ASN : angle 1.99248 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 275 PHE cc_start: 0.5455 (OUTLIER) cc_final: 0.5099 (t80) REVERT: A 276 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5641 (tmm) REVERT: B 276 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5420 (tmm) REVERT: C 32 GLU cc_start: 0.7941 (tp30) cc_final: 0.7537 (tp30) REVERT: C 80 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8424 (mtp) REVERT: C 275 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.5223 (t80) REVERT: C 276 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.5291 (ppp) REVERT: C 473 MET cc_start: 0.7576 (ppp) cc_final: 0.7354 (pmm) REVERT: D 219 ASP cc_start: 0.8432 (t70) cc_final: 0.7599 (p0) REVERT: D 275 PHE cc_start: 0.5295 (OUTLIER) cc_final: 0.5089 (t80) REVERT: D 276 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.5210 (ppp) REVERT: E 60 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8185 (mt) REVERT: E 276 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.5462 (ppp) outliers start: 41 outliers final: 25 residues processed: 163 average time/residue: 0.5930 time to fit residues: 106.8341 Evaluate side-chains 160 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 52 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 113 optimal weight: 30.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094869 restraints weight = 39499.655| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.79 r_work: 0.2953 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16385 Z= 0.150 Angle : 0.672 13.148 22400 Z= 0.324 Chirality : 0.042 0.270 2610 Planarity : 0.005 0.058 2765 Dihedral : 7.766 91.865 2711 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.42 % Allowed : 18.94 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 1950 helix: 1.24 (0.18), residues: 770 sheet: 0.61 (0.24), residues: 440 loop : -1.17 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.007 0.001 TYR A 210 PHE 0.029 0.001 PHE E 275 TRP 0.045 0.002 TRP B 156 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00348 (16350) covalent geometry : angle 0.65974 (22305) SS BOND : bond 0.01304 ( 10) SS BOND : angle 2.20886 ( 20) hydrogen bonds : bond 0.04245 ( 855) hydrogen bonds : angle 4.96590 ( 2817) link_BETA1-4 : bond 0.00374 ( 10) link_BETA1-4 : angle 2.22510 ( 30) link_NAG-ASN : bond 0.00061 ( 15) link_NAG-ASN : angle 1.92325 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 275 PHE cc_start: 0.5478 (OUTLIER) cc_final: 0.5149 (t80) REVERT: A 276 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5777 (tmm) REVERT: B 276 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5535 (tmm) REVERT: C 32 GLU cc_start: 0.7939 (tp30) cc_final: 0.7547 (tp30) REVERT: C 80 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: C 275 PHE cc_start: 0.5452 (OUTLIER) cc_final: 0.5241 (t80) REVERT: C 276 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.5417 (ppp) REVERT: C 473 MET cc_start: 0.7613 (ppp) cc_final: 0.7369 (pmm) REVERT: D 219 ASP cc_start: 0.8171 (t70) cc_final: 0.7842 (p0) REVERT: D 276 MET cc_start: 0.5581 (OUTLIER) cc_final: 0.5123 (ppp) REVERT: E 60 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8179 (mt) REVERT: E 155 ARG cc_start: 0.7672 (ptp-170) cc_final: 0.7388 (ptp90) REVERT: E 276 MET cc_start: 0.5850 (OUTLIER) cc_final: 0.5558 (ppp) outliers start: 41 outliers final: 22 residues processed: 164 average time/residue: 0.6042 time to fit residues: 109.4814 Evaluate side-chains 159 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 107 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093660 restraints weight = 43441.214| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.93 r_work: 0.2924 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16385 Z= 0.195 Angle : 0.689 10.298 22400 Z= 0.332 Chirality : 0.042 0.267 2610 Planarity : 0.005 0.057 2765 Dihedral : 7.647 91.682 2709 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.36 % Allowed : 19.00 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 1950 helix: 1.25 (0.18), residues: 770 sheet: 0.63 (0.25), residues: 430 loop : -1.24 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 208 TYR 0.010 0.001 TYR A 210 PHE 0.029 0.001 PHE D 275 TRP 0.048 0.002 TRP D 156 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00466 (16350) covalent geometry : angle 0.67638 (22305) SS BOND : bond 0.01327 ( 10) SS BOND : angle 2.33211 ( 20) hydrogen bonds : bond 0.04353 ( 855) hydrogen bonds : angle 4.96824 ( 2817) link_BETA1-4 : bond 0.00246 ( 10) link_BETA1-4 : angle 2.17260 ( 30) link_NAG-ASN : bond 0.00165 ( 15) link_NAG-ASN : angle 1.93951 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8021 (mt) REVERT: A 275 PHE cc_start: 0.5485 (OUTLIER) cc_final: 0.5190 (t80) REVERT: A 276 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5695 (tmm) REVERT: B 214 LYS cc_start: 0.8585 (tptt) cc_final: 0.8372 (tptp) REVERT: B 276 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5533 (tmm) REVERT: C 32 GLU cc_start: 0.7945 (tp30) cc_final: 0.7546 (OUTLIER) REVERT: C 80 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: C 275 PHE cc_start: 0.5389 (OUTLIER) cc_final: 0.5185 (t80) REVERT: C 276 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.5460 (ppp) REVERT: C 473 MET cc_start: 0.7604 (ppp) cc_final: 0.7401 (pmm) REVERT: D 60 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8116 (mt) REVERT: D 219 ASP cc_start: 0.8197 (t70) cc_final: 0.7892 (p0) REVERT: D 276 MET cc_start: 0.5656 (OUTLIER) cc_final: 0.5273 (ppp) REVERT: E 60 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8210 (mt) REVERT: E 276 MET cc_start: 0.5855 (OUTLIER) cc_final: 0.5569 (ppp) outliers start: 40 outliers final: 26 residues processed: 163 average time/residue: 0.6076 time to fit residues: 109.7138 Evaluate side-chains 164 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.174859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093291 restraints weight = 43030.242| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.88 r_work: 0.2922 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 16385 Z= 0.211 Angle : 0.754 30.938 22400 Z= 0.362 Chirality : 0.043 0.268 2610 Planarity : 0.005 0.057 2765 Dihedral : 7.779 91.618 2709 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.06 % Allowed : 19.29 % Favored : 78.64 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.28 (0.18), residues: 1950 helix: 1.27 (0.18), residues: 770 sheet: 0.58 (0.25), residues: 440 loop : -1.21 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 208 TYR 0.009 0.001 TYR A 210 PHE 0.026 0.001 PHE D 275 TRP 0.053 0.002 TRP D 156 HIS 0.003 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00527 (16350) covalent geometry : angle 0.72916 (22305) SS BOND : bond 0.01711 ( 10) SS BOND : angle 5.36363 ( 20) hydrogen bonds : bond 0.04351 ( 855) hydrogen bonds : angle 4.95721 ( 2817) link_BETA1-4 : bond 0.00284 ( 10) link_BETA1-4 : angle 2.07480 ( 30) link_NAG-ASN : bond 0.00145 ( 15) link_NAG-ASN : angle 1.93636 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8044 (mt) REVERT: A 275 PHE cc_start: 0.5441 (OUTLIER) cc_final: 0.5163 (t80) REVERT: A 276 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5673 (tmm) REVERT: B 214 LYS cc_start: 0.8585 (tptt) cc_final: 0.8365 (tptp) REVERT: B 276 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5440 (tmm) REVERT: C 32 GLU cc_start: 0.7977 (tp30) cc_final: 0.7569 (OUTLIER) REVERT: C 80 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: C 276 MET cc_start: 0.5926 (OUTLIER) cc_final: 0.5496 (ppp) REVERT: D 60 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8122 (mt) REVERT: D 219 ASP cc_start: 0.8168 (t70) cc_final: 0.7929 (p0) REVERT: D 276 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.5281 (ppp) REVERT: E 60 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8217 (mt) REVERT: E 276 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5587 (ppp) outliers start: 35 outliers final: 23 residues processed: 153 average time/residue: 0.6017 time to fit residues: 101.6160 Evaluate side-chains 157 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 136 optimal weight: 0.0060 chunk 13 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.177074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097651 restraints weight = 36804.152| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.64 r_work: 0.2939 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 16385 Z= 0.140 Angle : 0.718 30.705 22400 Z= 0.345 Chirality : 0.041 0.272 2610 Planarity : 0.005 0.056 2765 Dihedral : 7.392 92.384 2707 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.59 % Allowed : 19.88 % Favored : 78.53 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.43 (0.19), residues: 1950 helix: 1.36 (0.18), residues: 770 sheet: 0.80 (0.25), residues: 440 loop : -1.18 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.007 0.001 TYR B 232 PHE 0.040 0.001 PHE C 275 TRP 0.038 0.002 TRP B 156 HIS 0.003 0.000 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00348 (16350) covalent geometry : angle 0.69385 (22305) SS BOND : bond 0.01622 ( 10) SS BOND : angle 5.27034 ( 20) hydrogen bonds : bond 0.03981 ( 855) hydrogen bonds : angle 4.80144 ( 2817) link_BETA1-4 : bond 0.00441 ( 10) link_BETA1-4 : angle 1.82584 ( 30) link_NAG-ASN : bond 0.00116 ( 15) link_NAG-ASN : angle 1.83551 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7911 (mt) REVERT: A 275 PHE cc_start: 0.5352 (OUTLIER) cc_final: 0.5136 (t80) REVERT: A 276 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5782 (tmm) REVERT: B 155 ARG cc_start: 0.7602 (ptp-170) cc_final: 0.7312 (ptp90) REVERT: B 214 LYS cc_start: 0.8632 (tptt) cc_final: 0.8390 (tptp) REVERT: B 276 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5365 (tmm) REVERT: C 32 GLU cc_start: 0.7851 (tp30) cc_final: 0.7475 (tp30) REVERT: C 276 MET cc_start: 0.5827 (OUTLIER) cc_final: 0.5511 (ppp) REVERT: D 276 MET cc_start: 0.5620 (OUTLIER) cc_final: 0.5238 (ppp) REVERT: E 155 ARG cc_start: 0.7746 (ptp-170) cc_final: 0.7389 (ttp-170) REVERT: E 219 ASP cc_start: 0.8154 (t0) cc_final: 0.6780 (p0) REVERT: E 276 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5548 (ppp) outliers start: 27 outliers final: 17 residues processed: 150 average time/residue: 0.7038 time to fit residues: 115.7705 Evaluate side-chains 151 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 276 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 90 optimal weight: 0.0470 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 69 optimal weight: 40.0000 chunk 159 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.177740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096952 restraints weight = 37618.817| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.73 r_work: 0.2973 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.195 16385 Z= 0.135 Angle : 0.705 31.123 22400 Z= 0.339 Chirality : 0.040 0.271 2610 Planarity : 0.005 0.056 2765 Dihedral : 7.254 92.304 2707 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.30 % Allowed : 20.29 % Favored : 78.41 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.52 (0.19), residues: 1950 helix: 1.40 (0.18), residues: 770 sheet: 0.95 (0.25), residues: 440 loop : -1.18 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.006 0.001 TYR B 232 PHE 0.032 0.001 PHE C 275 TRP 0.037 0.002 TRP B 156 HIS 0.003 0.000 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00335 (16350) covalent geometry : angle 0.68202 (22305) SS BOND : bond 0.01626 ( 10) SS BOND : angle 5.17560 ( 20) hydrogen bonds : bond 0.03857 ( 855) hydrogen bonds : angle 4.69974 ( 2817) link_BETA1-4 : bond 0.00352 ( 10) link_BETA1-4 : angle 1.72149 ( 30) link_NAG-ASN : bond 0.00062 ( 15) link_NAG-ASN : angle 1.75976 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6777.00 seconds wall clock time: 115 minutes 45.53 seconds (6945.53 seconds total)