Starting phenix.real_space_refine on Wed Jun 11 18:45:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsz_43512/06_2025/8vsz_43512.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsz_43512/06_2025/8vsz_43512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vsz_43512/06_2025/8vsz_43512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsz_43512/06_2025/8vsz_43512.map" model { file = "/net/cci-nas-00/data/ceres_data/8vsz_43512/06_2025/8vsz_43512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsz_43512/06_2025/8vsz_43512.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.039 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 65 5.16 5 C 8590 2.51 5 N 2100 2.21 5 O 2465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13220 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2580 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain breaks: 1 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D, F, I, H, J Time building chain proxies: 6.33, per 1000 atoms: 0.48 Number of scatterers: 13220 At special positions: 0 Unit cell: (93.225, 91.575, 120.45, 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 65 16.00 O 2465 8.00 N 2100 7.00 C 8590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 174 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied ALPHA1-4 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 196 " " NAG B 501 " - " ASN B 196 " " NAG C 501 " - " ASN C 196 " " NAG D 501 " - " ASN D 196 " " NAG E 501 " - " ASN E 196 " " NAG F 1 " - " ASN A 145 " " NAG G 1 " - " ASN B 145 " " NAG H 1 " - " ASN C 145 " " NAG I 1 " - " ASN D 145 " " NAG J 1 " - " ASN E 145 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 36.4% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 241 through 249 removed outlier: 4.050A pdb=" N PHE A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 263 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 270 through 296 removed outlier: 3.684A pdb=" N LEU A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 332 removed outlier: 3.609A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 removed outlier: 4.334A pdb=" N LEU A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 241 through 249 removed outlier: 4.050A pdb=" N PHE B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 263 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 270 through 296 removed outlier: 3.684A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 332 removed outlier: 3.608A pdb=" N VAL B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 4.334A pdb=" N LEU B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 241 through 249 removed outlier: 4.049A pdb=" N PHE C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 263 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 270 through 296 removed outlier: 3.684A pdb=" N LEU C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 332 removed outlier: 3.608A pdb=" N VAL C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 4.334A pdb=" N LEU C 420 " --> pdb=" O HIS C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 241 through 249 removed outlier: 4.050A pdb=" N PHE D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 263 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 270 through 296 removed outlier: 3.684A pdb=" N LEU D 296 " --> pdb=" O SER D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 332 removed outlier: 3.608A pdb=" N VAL D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.334A pdb=" N LEU D 420 " --> pdb=" O HIS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 437 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 241 through 249 removed outlier: 4.050A pdb=" N PHE E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 263 Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 270 through 296 removed outlier: 3.684A pdb=" N LEU E 296 " --> pdb=" O SER E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 332 removed outlier: 3.608A pdb=" N VAL E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 420 removed outlier: 4.333A pdb=" N LEU E 420 " --> pdb=" O HIS E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 437 Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.790A pdb=" N ILE A 140 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR A 83 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 72 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR A 85 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET A 93 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN A 62 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 130 removed outlier: 6.939A pdb=" N THR A 157 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 128 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A 155 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU A 130 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG A 153 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR A 83 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 72 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR A 85 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET A 93 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN A 62 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ARG A 200 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 67 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.790A pdb=" N ILE B 140 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 83 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 72 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 85 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET B 93 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN B 62 " --> pdb=" O MET B 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 130 removed outlier: 6.939A pdb=" N THR B 157 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER B 128 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR B 155 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU B 130 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG B 153 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 83 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 72 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 85 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET B 93 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN B 62 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ARG B 200 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 67 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AA9, first strand: chain 'C' and resid 105 through 107 removed outlier: 3.790A pdb=" N ILE C 140 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 83 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE C 72 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR C 85 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET C 93 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN C 62 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 130 removed outlier: 6.939A pdb=" N THR C 157 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER C 128 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR C 155 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU C 130 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG C 153 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 83 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE C 72 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR C 85 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET C 93 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN C 62 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ARG C 200 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 67 " --> pdb=" O ARG C 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AB4, first strand: chain 'D' and resid 105 through 107 removed outlier: 3.790A pdb=" N ILE D 140 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 83 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE D 72 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR D 85 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET D 93 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN D 62 " --> pdb=" O MET D 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 130 removed outlier: 6.939A pdb=" N THR D 157 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER D 128 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR D 155 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU D 130 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG D 153 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 83 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE D 72 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR D 85 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET D 93 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN D 62 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ARG D 200 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 67 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 120 through 122 Processing sheet with id=AB7, first strand: chain 'D' and resid 120 through 122 Processing sheet with id=AB8, first strand: chain 'E' and resid 105 through 107 removed outlier: 3.791A pdb=" N ILE E 140 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 83 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE E 72 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR E 85 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET E 93 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN E 62 " --> pdb=" O MET E 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 130 removed outlier: 6.938A pdb=" N THR E 157 " --> pdb=" O LYS E 126 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER E 128 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR E 155 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU E 130 " --> pdb=" O ARG E 153 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG E 153 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 83 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE E 72 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR E 85 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET E 93 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN E 62 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ARG E 200 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU E 67 " --> pdb=" O ARG E 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 120 through 122 Processing sheet with id=AC2, first strand: chain 'E' and resid 120 through 122 770 hydrogen bonds defined for protein. 2220 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: 4.50 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3999 1.34 - 1.46: 3293 1.46 - 1.58: 6148 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 13545 Sorted by residual: bond pdb=" C1 MAN J 4 " pdb=" C2 MAN J 4 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 MAN I 4 " pdb=" C2 MAN I 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 MAN G 4 " pdb=" C2 MAN G 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 MAN H 4 " pdb=" C2 MAN H 4 " ideal model delta sigma weight residual 1.526 1.557 -0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 13540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 17932 1.58 - 3.15: 366 3.15 - 4.73: 87 4.73 - 6.30: 40 6.30 - 7.88: 10 Bond angle restraints: 18435 Sorted by residual: angle pdb=" C LEU E 420 " pdb=" N LEU E 421 " pdb=" CA LEU E 421 " ideal model delta sigma weight residual 122.17 115.67 6.50 1.54e+00 4.22e-01 1.78e+01 angle pdb=" C LEU B 420 " pdb=" N LEU B 421 " pdb=" CA LEU B 421 " ideal model delta sigma weight residual 122.17 115.70 6.47 1.54e+00 4.22e-01 1.76e+01 angle pdb=" C LEU A 420 " pdb=" N LEU A 421 " pdb=" CA LEU A 421 " ideal model delta sigma weight residual 122.17 115.71 6.46 1.54e+00 4.22e-01 1.76e+01 angle pdb=" C LEU D 420 " pdb=" N LEU D 421 " pdb=" CA LEU D 421 " ideal model delta sigma weight residual 122.17 115.71 6.46 1.54e+00 4.22e-01 1.76e+01 angle pdb=" C LEU C 420 " pdb=" N LEU C 421 " pdb=" CA LEU C 421 " ideal model delta sigma weight residual 122.17 115.72 6.45 1.54e+00 4.22e-01 1.75e+01 ... (remaining 18430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 7084 21.90 - 43.80: 919 43.80 - 65.69: 117 65.69 - 87.59: 45 87.59 - 109.49: 25 Dihedral angle restraints: 8190 sinusoidal: 3510 harmonic: 4680 Sorted by residual: dihedral pdb=" CB CYS C 160 " pdb=" SG CYS C 160 " pdb=" SG CYS C 174 " pdb=" CB CYS C 174 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" CB CYS B 160 " pdb=" SG CYS B 160 " pdb=" SG CYS B 174 " pdb=" CB CYS B 174 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 174 " pdb=" CB CYS E 174 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 8187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1871 0.059 - 0.118: 274 0.118 - 0.178: 25 0.178 - 0.237: 5 0.237 - 0.296: 10 Chirality restraints: 2185 Sorted by residual: chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 196 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 196 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 196 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2182 not shown) Planarity restraints: 2245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 261 " 0.007 2.00e-02 2.50e+03 6.16e-03 9.49e-01 pdb=" CG TRP B 261 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 261 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 261 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 261 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 261 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 261 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 261 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 261 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 261 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 261 " 0.007 2.00e-02 2.50e+03 6.12e-03 9.36e-01 pdb=" CG TRP A 261 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 261 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 261 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 261 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 261 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 261 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 261 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 261 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 261 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 261 " -0.007 2.00e-02 2.50e+03 6.06e-03 9.18e-01 pdb=" CG TRP D 261 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP D 261 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 261 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 261 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 261 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 261 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 261 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 261 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 261 " 0.000 2.00e-02 2.50e+03 ... (remaining 2242 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2285 2.77 - 3.30: 12369 3.30 - 3.83: 22277 3.83 - 4.37: 25923 4.37 - 4.90: 44665 Nonbonded interactions: 107519 Sorted by model distance: nonbonded pdb=" OG SER B 180 " pdb=" O TYR B 183 " model vdw 2.233 3.040 nonbonded pdb=" OG SER D 180 " pdb=" O TYR D 183 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 180 " pdb=" O TYR C 183 " model vdw 2.233 3.040 nonbonded pdb=" OG SER E 180 " pdb=" O TYR E 183 " model vdw 2.233 3.040 nonbonded pdb=" OG SER A 180 " pdb=" O TYR A 183 " model vdw 2.234 3.040 ... (remaining 107514 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 31.640 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.003 0.032 13580 Z= 0.157 Angle : 0.664 7.879 18520 Z= 0.324 Chirality : 0.047 0.296 2185 Planarity : 0.002 0.023 2235 Dihedral : 19.650 109.487 5165 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.88 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 34.97 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1560 helix: 2.25 (0.24), residues: 490 sheet: -1.25 (0.28), residues: 320 loop : -1.69 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 261 HIS 0.004 0.001 HIS C 204 PHE 0.014 0.001 PHE E 318 TYR 0.011 0.001 TYR D 433 ARG 0.002 0.000 ARG C 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 10) link_NAG-ASN : angle 3.23518 ( 30) link_ALPHA1-4 : bond 0.00675 ( 5) link_ALPHA1-4 : angle 1.46442 ( 15) link_BETA1-4 : bond 0.00472 ( 10) link_BETA1-4 : angle 1.30839 ( 30) hydrogen bonds : bond 0.18703 ( 625) hydrogen bonds : angle 7.70836 ( 2220) SS BOND : bond 0.00162 ( 5) SS BOND : angle 0.33597 ( 10) covalent geometry : bond 0.00311 (13545) covalent geometry : angle 0.64952 (18435) Misc. bond : bond 0.00025 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.477 Fit side-chains REVERT: B 285 MET cc_start: 0.7070 (tpt) cc_final: 0.6792 (tpt) REVERT: D 304 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7370 (mtmm) REVERT: E 304 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7315 (mtmm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2440 time to fit residues: 46.7003 Evaluate side-chains 118 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 204 HIS C 204 HIS D 204 HIS E 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.237749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.204076 restraints weight = 13201.149| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.18 r_work: 0.3821 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13580 Z= 0.225 Angle : 0.720 6.968 18520 Z= 0.353 Chirality : 0.049 0.331 2185 Planarity : 0.004 0.028 2235 Dihedral : 11.534 79.943 2270 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.27 % Favored : 96.41 % Rotamer: Outliers : 3.71 % Allowed : 32.17 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1560 helix: 2.50 (0.24), residues: 495 sheet: -1.00 (0.26), residues: 315 loop : -1.83 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 261 HIS 0.005 0.001 HIS B 131 PHE 0.021 0.002 PHE D 316 TYR 0.016 0.002 TYR E 121 ARG 0.003 0.000 ARG B 153 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 10) link_NAG-ASN : angle 2.82557 ( 30) link_ALPHA1-4 : bond 0.00887 ( 5) link_ALPHA1-4 : angle 3.12734 ( 15) link_BETA1-4 : bond 0.00563 ( 10) link_BETA1-4 : angle 2.47789 ( 30) hydrogen bonds : bond 0.04781 ( 625) hydrogen bonds : angle 4.98249 ( 2220) SS BOND : bond 0.00563 ( 5) SS BOND : angle 1.42535 ( 10) covalent geometry : bond 0.00521 (13545) covalent geometry : angle 0.69921 (18435) Misc. bond : bond 0.00079 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 1.404 Fit side-chains REVERT: A 234 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8062 (tp) REVERT: A 318 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.6884 (p90) REVERT: C 295 SER cc_start: 0.5916 (OUTLIER) cc_final: 0.4900 (t) REVERT: C 304 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7248 (mtmt) REVERT: D 318 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7109 (p90) REVERT: E 295 SER cc_start: 0.6068 (OUTLIER) cc_final: 0.5167 (t) REVERT: E 304 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7323 (mtmt) outliers start: 53 outliers final: 26 residues processed: 193 average time/residue: 0.2643 time to fit residues: 79.1869 Evaluate side-chains 158 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 295 SER Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 63 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 78 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 0.0570 chunk 149 optimal weight: 9.9990 chunk 121 optimal weight: 40.0000 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.242581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.209761 restraints weight = 13401.101| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 1.21 r_work: 0.3883 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13580 Z= 0.118 Angle : 0.619 11.416 18520 Z= 0.296 Chirality : 0.043 0.261 2185 Planarity : 0.003 0.025 2235 Dihedral : 10.357 68.790 2270 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.76 % Favored : 96.92 % Rotamer: Outliers : 4.13 % Allowed : 32.52 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1560 helix: 2.55 (0.24), residues: 495 sheet: -0.85 (0.26), residues: 340 loop : -1.35 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 261 HIS 0.004 0.001 HIS A 204 PHE 0.019 0.001 PHE D 316 TYR 0.013 0.001 TYR C 433 ARG 0.003 0.000 ARG E 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 10) link_NAG-ASN : angle 2.24110 ( 30) link_ALPHA1-4 : bond 0.01156 ( 5) link_ALPHA1-4 : angle 1.75904 ( 15) link_BETA1-4 : bond 0.00568 ( 10) link_BETA1-4 : angle 2.72553 ( 30) hydrogen bonds : bond 0.04163 ( 625) hydrogen bonds : angle 4.22254 ( 2220) SS BOND : bond 0.00470 ( 5) SS BOND : angle 1.08776 ( 10) covalent geometry : bond 0.00242 (13545) covalent geometry : angle 0.60107 (18435) Misc. bond : bond 0.00046 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 1.466 Fit side-chains REVERT: A 295 SER cc_start: 0.5787 (OUTLIER) cc_final: 0.5138 (t) REVERT: A 318 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7048 (p90) REVERT: B 110 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6943 (mtm180) REVERT: B 295 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5486 (t) REVERT: B 304 LYS cc_start: 0.6844 (mtmt) cc_final: 0.6521 (mtmm) REVERT: C 110 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7041 (mtm180) REVERT: C 250 TYR cc_start: 0.6480 (m-80) cc_final: 0.6033 (m-80) REVERT: C 304 LYS cc_start: 0.7270 (mtmm) cc_final: 0.6741 (mtmt) REVERT: D 110 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6931 (mtm180) REVERT: D 295 SER cc_start: 0.6280 (OUTLIER) cc_final: 0.5508 (t) REVERT: D 318 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7163 (p90) REVERT: E 110 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6959 (mtt180) REVERT: E 304 LYS cc_start: 0.7551 (mtmm) cc_final: 0.6998 (mtmt) outliers start: 59 outliers final: 26 residues processed: 191 average time/residue: 0.2894 time to fit residues: 78.1916 Evaluate side-chains 172 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 316 PHE Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 99 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4523 r_free = 0.4523 target = 0.239763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.204602 restraints weight = 13131.324| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.33 r_work: 0.3818 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13580 Z= 0.150 Angle : 0.652 10.919 18520 Z= 0.310 Chirality : 0.045 0.247 2185 Planarity : 0.003 0.025 2235 Dihedral : 9.679 62.739 2270 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.82 % Favored : 96.86 % Rotamer: Outliers : 5.38 % Allowed : 31.05 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1560 helix: 2.53 (0.24), residues: 500 sheet: -0.72 (0.26), residues: 340 loop : -1.31 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 261 HIS 0.003 0.001 HIS B 131 PHE 0.018 0.002 PHE C 316 TYR 0.010 0.001 TYR D 121 ARG 0.004 0.000 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 10) link_NAG-ASN : angle 1.73395 ( 30) link_ALPHA1-4 : bond 0.01113 ( 5) link_ALPHA1-4 : angle 2.85443 ( 15) link_BETA1-4 : bond 0.00581 ( 10) link_BETA1-4 : angle 2.78284 ( 30) hydrogen bonds : bond 0.03895 ( 625) hydrogen bonds : angle 4.11651 ( 2220) SS BOND : bond 0.00536 ( 5) SS BOND : angle 1.28147 ( 10) covalent geometry : bond 0.00330 (13545) covalent geometry : angle 0.63416 (18435) Misc. bond : bond 0.00068 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 138 time to evaluate : 1.595 Fit side-chains REVERT: A 48 TYR cc_start: -0.0151 (OUTLIER) cc_final: -0.2362 (m-80) REVERT: A 234 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8111 (tp) REVERT: A 247 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7095 (tt) REVERT: A 318 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6953 (p90) REVERT: B 48 TYR cc_start: -0.0198 (OUTLIER) cc_final: -0.1517 (m-10) REVERT: B 105 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5416 (m-80) REVERT: B 110 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7028 (mtm180) REVERT: B 255 PHE cc_start: 0.5586 (OUTLIER) cc_final: 0.4770 (m-80) REVERT: B 304 LYS cc_start: 0.7340 (mtmt) cc_final: 0.6987 (mtmm) REVERT: C 48 TYR cc_start: 0.0195 (OUTLIER) cc_final: -0.2355 (m-80) REVERT: C 110 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7089 (mtm180) REVERT: C 304 LYS cc_start: 0.7642 (mtmm) cc_final: 0.7046 (mtmt) REVERT: D 48 TYR cc_start: 0.0204 (OUTLIER) cc_final: -0.1024 (m-10) REVERT: D 110 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7100 (mtm180) REVERT: D 318 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7112 (p90) REVERT: E 48 TYR cc_start: 0.0289 (OUTLIER) cc_final: -0.2696 (m-80) REVERT: E 110 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7216 (mtt180) REVERT: E 304 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7273 (mtmt) outliers start: 77 outliers final: 34 residues processed: 200 average time/residue: 0.2877 time to fit residues: 81.5790 Evaluate side-chains 181 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 316 PHE Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4899 r_free = 0.4899 target = 0.271004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.252426 restraints weight = 13631.108| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 0.67 r_work: 0.4444 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4238 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13580 Z= 0.158 Angle : 0.670 10.990 18520 Z= 0.316 Chirality : 0.045 0.242 2185 Planarity : 0.003 0.026 2235 Dihedral : 9.201 57.073 2270 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.82 % Favored : 96.86 % Rotamer: Outliers : 5.45 % Allowed : 30.98 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1560 helix: 2.60 (0.23), residues: 500 sheet: -0.74 (0.25), residues: 340 loop : -1.33 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 261 HIS 0.005 0.001 HIS C 131 PHE 0.026 0.002 PHE A 426 TYR 0.011 0.001 TYR C 433 ARG 0.008 0.000 ARG C 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 10) link_NAG-ASN : angle 1.72553 ( 30) link_ALPHA1-4 : bond 0.01052 ( 5) link_ALPHA1-4 : angle 2.73182 ( 15) link_BETA1-4 : bond 0.00615 ( 10) link_BETA1-4 : angle 2.80362 ( 30) hydrogen bonds : bond 0.03805 ( 625) hydrogen bonds : angle 4.00022 ( 2220) SS BOND : bond 0.00584 ( 5) SS BOND : angle 1.36605 ( 10) covalent geometry : bond 0.00351 (13545) covalent geometry : angle 0.65320 (18435) Misc. bond : bond 0.00071 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 140 time to evaluate : 1.545 Fit side-chains REVERT: A 48 TYR cc_start: 0.0664 (OUTLIER) cc_final: -0.1711 (m-80) REVERT: A 234 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7945 (tp) REVERT: A 318 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6165 (p90) REVERT: B 48 TYR cc_start: 0.0935 (OUTLIER) cc_final: -0.0687 (m-10) REVERT: B 110 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7013 (mtm180) REVERT: B 255 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.5012 (m-80) REVERT: C 48 TYR cc_start: 0.1381 (OUTLIER) cc_final: -0.1773 (m-80) REVERT: C 110 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7073 (mtm180) REVERT: C 255 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.4874 (m-80) REVERT: C 304 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7594 (mtmt) REVERT: D 48 TYR cc_start: 0.0950 (OUTLIER) cc_final: -0.0496 (m-10) REVERT: D 110 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7044 (mtm180) REVERT: D 318 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.6127 (p90) REVERT: E 48 TYR cc_start: 0.1040 (OUTLIER) cc_final: -0.2074 (m-80) REVERT: E 110 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7187 (mtt180) REVERT: E 304 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7587 (mtmt) outliers start: 78 outliers final: 43 residues processed: 205 average time/residue: 0.2538 time to fit residues: 76.0581 Evaluate side-chains 189 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 316 PHE Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 50.0000 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4524 r_free = 0.4524 target = 0.239898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200903 restraints weight = 13368.552| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.41 r_work: 0.3775 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13580 Z= 0.135 Angle : 0.651 11.052 18520 Z= 0.305 Chirality : 0.044 0.222 2185 Planarity : 0.003 0.026 2235 Dihedral : 8.691 53.612 2270 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.14 % Favored : 96.54 % Rotamer: Outliers : 5.59 % Allowed : 30.63 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1560 helix: 2.66 (0.24), residues: 500 sheet: -0.62 (0.25), residues: 340 loop : -1.32 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 261 HIS 0.002 0.001 HIS C 131 PHE 0.018 0.001 PHE A 426 TYR 0.012 0.001 TYR C 433 ARG 0.007 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 10) link_NAG-ASN : angle 1.52577 ( 30) link_ALPHA1-4 : bond 0.01188 ( 5) link_ALPHA1-4 : angle 2.59975 ( 15) link_BETA1-4 : bond 0.00634 ( 10) link_BETA1-4 : angle 2.85461 ( 30) hydrogen bonds : bond 0.03649 ( 625) hydrogen bonds : angle 3.82652 ( 2220) SS BOND : bond 0.00506 ( 5) SS BOND : angle 1.16606 ( 10) covalent geometry : bond 0.00296 (13545) covalent geometry : angle 0.63437 (18435) Misc. bond : bond 0.00060 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 141 time to evaluate : 1.490 Fit side-chains REVERT: A 48 TYR cc_start: 0.0404 (OUTLIER) cc_final: -0.1908 (m-80) REVERT: A 234 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7943 (tp) REVERT: A 318 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6527 (p90) REVERT: B 48 TYR cc_start: 0.0492 (OUTLIER) cc_final: -0.1337 (m-80) REVERT: B 110 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6974 (mtm180) REVERT: B 255 PHE cc_start: 0.5772 (OUTLIER) cc_final: 0.4807 (m-80) REVERT: B 304 LYS cc_start: 0.7687 (mtmm) cc_final: 0.7215 (mtmt) REVERT: C 48 TYR cc_start: 0.0785 (OUTLIER) cc_final: -0.2009 (m-80) REVERT: C 110 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7091 (mtm180) REVERT: C 172 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: C 255 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4668 (m-80) REVERT: C 304 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7362 (mtmt) REVERT: D 48 TYR cc_start: 0.0488 (OUTLIER) cc_final: -0.0873 (m-10) REVERT: D 110 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7090 (mtm180) REVERT: D 172 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: D 318 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6733 (p90) REVERT: E 48 TYR cc_start: 0.0692 (OUTLIER) cc_final: -0.2326 (m-80) REVERT: E 110 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7105 (mtt180) REVERT: E 255 PHE cc_start: 0.5679 (OUTLIER) cc_final: 0.4886 (m-80) REVERT: E 304 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7606 (mtmm) outliers start: 80 outliers final: 42 residues processed: 208 average time/residue: 0.2454 time to fit residues: 74.8623 Evaluate side-chains 195 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 136 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 316 PHE Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 125 optimal weight: 0.0470 overall best weight: 0.9082 ------------------------------------------------------------------------------- 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 = 0.4525 r_free = 0.4525 target = 0.240123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.218503 restraints weight = 13231.609| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 1.08 r_work: 0.3980 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13580 Z= 0.140 Angle : 0.661 11.015 18520 Z= 0.311 Chirality : 0.045 0.220 2185 Planarity : 0.003 0.026 2235 Dihedral : 8.422 51.612 2270 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.01 % Favored : 96.67 % Rotamer: Outliers : 4.55 % Allowed : 31.89 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1560 helix: 2.68 (0.24), residues: 500 sheet: -0.61 (0.25), residues: 340 loop : -1.32 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 261 HIS 0.003 0.001 HIS A 131 PHE 0.024 0.002 PHE A 99 TYR 0.012 0.001 TYR C 433 ARG 0.005 0.000 ARG E 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 10) link_NAG-ASN : angle 1.52625 ( 30) link_ALPHA1-4 : bond 0.01144 ( 5) link_ALPHA1-4 : angle 2.67934 ( 15) link_BETA1-4 : bond 0.00623 ( 10) link_BETA1-4 : angle 2.80228 ( 30) hydrogen bonds : bond 0.03623 ( 625) hydrogen bonds : angle 3.77159 ( 2220) SS BOND : bond 0.00514 ( 5) SS BOND : angle 2.40724 ( 10) covalent geometry : bond 0.00312 (13545) covalent geometry : angle 0.64322 (18435) Misc. bond : bond 0.00063 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 1.816 Fit side-chains REVERT: A 48 TYR cc_start: 0.0650 (OUTLIER) cc_final: -0.1756 (m-80) REVERT: A 234 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7837 (tp) REVERT: A 318 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.6219 (p90) REVERT: B 48 TYR cc_start: 0.0780 (OUTLIER) cc_final: -0.1116 (m-80) REVERT: B 110 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6880 (mtm180) REVERT: B 304 LYS cc_start: 0.7613 (mtmm) cc_final: 0.7187 (mtmt) REVERT: C 48 TYR cc_start: 0.1066 (OUTLIER) cc_final: -0.1846 (m-80) REVERT: C 110 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7081 (mtm180) REVERT: C 304 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7375 (mtmt) REVERT: D 48 TYR cc_start: 0.0776 (OUTLIER) cc_final: -0.0657 (m-10) REVERT: D 110 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6959 (mtm180) REVERT: D 318 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.6165 (p90) REVERT: E 48 TYR cc_start: 0.0944 (OUTLIER) cc_final: -0.2166 (m-80) REVERT: E 110 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7063 (mtt180) REVERT: E 255 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4852 (m-80) REVERT: E 304 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7564 (mtmm) outliers start: 65 outliers final: 44 residues processed: 194 average time/residue: 0.3462 time to fit residues: 99.0657 Evaluate side-chains 196 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 316 PHE Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.236191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.207791 restraints weight = 13247.717| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 0.96 r_work: 0.3898 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13580 Z= 0.263 Angle : 0.782 10.872 18520 Z= 0.374 Chirality : 0.050 0.246 2185 Planarity : 0.005 0.039 2235 Dihedral : 8.574 48.552 2270 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.23 % Favored : 95.45 % Rotamer: Outliers : 5.10 % Allowed : 31.82 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1560 helix: 2.64 (0.24), residues: 500 sheet: -0.87 (0.24), residues: 335 loop : -1.70 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 261 HIS 0.006 0.001 HIS A 131 PHE 0.025 0.003 PHE A 99 TYR 0.014 0.002 TYR B 309 ARG 0.005 0.001 ARG A 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 10) link_NAG-ASN : angle 1.77577 ( 30) link_ALPHA1-4 : bond 0.00776 ( 5) link_ALPHA1-4 : angle 3.75908 ( 15) link_BETA1-4 : bond 0.00513 ( 10) link_BETA1-4 : angle 2.59823 ( 30) hydrogen bonds : bond 0.03933 ( 625) hydrogen bonds : angle 4.32385 ( 2220) SS BOND : bond 0.00838 ( 5) SS BOND : angle 2.77706 ( 10) covalent geometry : bond 0.00620 (13545) covalent geometry : angle 0.76332 (18435) Misc. bond : bond 0.00102 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 140 time to evaluate : 1.494 Fit side-chains REVERT: A 48 TYR cc_start: -0.0200 (OUTLIER) cc_final: -0.2100 (m-80) REVERT: A 102 ASN cc_start: 0.6154 (p0) cc_final: 0.5645 (p0) REVERT: A 234 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8038 (tp) REVERT: A 318 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7224 (p90) REVERT: B 48 TYR cc_start: 0.0035 (OUTLIER) cc_final: -0.1387 (m-10) REVERT: B 102 ASN cc_start: 0.6165 (p0) cc_final: 0.5673 (p0) REVERT: B 110 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7298 (mtm180) REVERT: B 304 LYS cc_start: 0.7463 (mtmm) cc_final: 0.6992 (mtmt) REVERT: C 48 TYR cc_start: 0.0226 (OUTLIER) cc_final: -0.2380 (m-80) REVERT: C 102 ASN cc_start: 0.6078 (p0) cc_final: 0.5641 (p0) REVERT: C 110 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7507 (mtm180) REVERT: C 255 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5094 (m-80) REVERT: D 48 TYR cc_start: -0.0152 (OUTLIER) cc_final: -0.1365 (m-10) REVERT: D 110 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7256 (mtm180) REVERT: D 255 PHE cc_start: 0.6116 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: D 318 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7393 (p90) REVERT: E 48 TYR cc_start: 0.0030 (OUTLIER) cc_final: -0.1428 (m-10) REVERT: E 110 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7359 (mtt180) REVERT: E 255 PHE cc_start: 0.5880 (OUTLIER) cc_final: 0.5177 (m-80) REVERT: E 304 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7250 (mtmt) outliers start: 73 outliers final: 51 residues processed: 197 average time/residue: 0.2489 time to fit residues: 72.0885 Evaluate side-chains 200 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 316 PHE Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 133 optimal weight: 0.2980 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 99 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.238904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.208588 restraints weight = 13197.500| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 1.06 r_work: 0.3894 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13580 Z= 0.165 Angle : 0.697 11.165 18520 Z= 0.330 Chirality : 0.046 0.233 2185 Planarity : 0.003 0.027 2235 Dihedral : 8.167 46.159 2270 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.56 % Favored : 97.12 % Rotamer: Outliers : 4.48 % Allowed : 31.75 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1560 helix: 2.65 (0.24), residues: 500 sheet: -0.79 (0.24), residues: 335 loop : -1.60 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 261 HIS 0.004 0.001 HIS A 131 PHE 0.024 0.002 PHE A 99 TYR 0.012 0.001 TYR D 121 ARG 0.004 0.000 ARG C 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 10) link_NAG-ASN : angle 1.74742 ( 30) link_ALPHA1-4 : bond 0.01065 ( 5) link_ALPHA1-4 : angle 2.65618 ( 15) link_BETA1-4 : bond 0.00553 ( 10) link_BETA1-4 : angle 2.73364 ( 30) hydrogen bonds : bond 0.03677 ( 625) hydrogen bonds : angle 3.99935 ( 2220) SS BOND : bond 0.00625 ( 5) SS BOND : angle 2.16747 ( 10) covalent geometry : bond 0.00372 (13545) covalent geometry : angle 0.68054 (18435) Misc. bond : bond 0.00079 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 1.526 Fit side-chains REVERT: A 48 TYR cc_start: -0.0191 (OUTLIER) cc_final: -0.2160 (m-80) REVERT: A 102 ASN cc_start: 0.6173 (p0) cc_final: 0.5650 (p0) REVERT: A 234 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8001 (tp) REVERT: A 318 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7253 (p90) REVERT: B 48 TYR cc_start: -0.0244 (OUTLIER) cc_final: -0.1783 (m-80) REVERT: B 102 ASN cc_start: 0.6095 (p0) cc_final: 0.5579 (p0) REVERT: B 110 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7234 (mtm180) REVERT: C 48 TYR cc_start: 0.0117 (OUTLIER) cc_final: -0.2349 (m-80) REVERT: C 102 ASN cc_start: 0.6019 (p0) cc_final: 0.5583 (p0) REVERT: C 110 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7494 (mtm180) REVERT: C 255 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5045 (m-80) REVERT: D 48 TYR cc_start: -0.0098 (OUTLIER) cc_final: -0.1376 (m-10) REVERT: D 110 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7293 (mtm180) REVERT: D 255 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: D 318 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7424 (p90) REVERT: E 48 TYR cc_start: 0.0016 (OUTLIER) cc_final: -0.1422 (m-10) REVERT: E 102 ASN cc_start: 0.6144 (p0) cc_final: 0.5637 (p0) REVERT: E 110 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7239 (mtt180) REVERT: E 255 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5114 (m-80) REVERT: E 304 LYS cc_start: 0.7662 (mtmm) cc_final: 0.7386 (mtmm) outliers start: 64 outliers final: 46 residues processed: 190 average time/residue: 0.2442 time to fit residues: 68.6748 Evaluate side-chains 199 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 138 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 316 PHE Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.0270 chunk 98 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 overall best weight: 1.3640 ------------------------------------------------------------------------------- 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 = 0.4513 r_free = 0.4513 target = 0.238558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.207815 restraints weight = 13226.048| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.13 r_work: 0.3879 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13580 Z= 0.174 Angle : 0.696 11.081 18520 Z= 0.330 Chirality : 0.046 0.228 2185 Planarity : 0.003 0.028 2235 Dihedral : 7.837 44.947 2270 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.72 % Favored : 95.96 % Rotamer: Outliers : 4.41 % Allowed : 31.89 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1560 helix: 2.67 (0.24), residues: 500 sheet: -0.76 (0.24), residues: 335 loop : -1.59 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 261 HIS 0.004 0.001 HIS A 131 PHE 0.027 0.002 PHE C 99 TYR 0.011 0.001 TYR C 433 ARG 0.005 0.000 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 10) link_NAG-ASN : angle 1.48196 ( 30) link_ALPHA1-4 : bond 0.01005 ( 5) link_ALPHA1-4 : angle 2.85866 ( 15) link_BETA1-4 : bond 0.00535 ( 10) link_BETA1-4 : angle 2.69584 ( 30) hydrogen bonds : bond 0.03604 ( 625) hydrogen bonds : angle 3.94291 ( 2220) SS BOND : bond 0.00637 ( 5) SS BOND : angle 2.12406 ( 10) covalent geometry : bond 0.00398 (13545) covalent geometry : angle 0.67955 (18435) Misc. bond : bond 0.00085 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 141 time to evaluate : 1.369 Fit side-chains REVERT: A 48 TYR cc_start: -0.0146 (OUTLIER) cc_final: -0.1987 (m-80) REVERT: A 102 ASN cc_start: 0.6233 (p0) cc_final: 0.5697 (p0) REVERT: A 234 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8048 (tp) REVERT: A 318 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7306 (p90) REVERT: B 48 TYR cc_start: -0.0306 (OUTLIER) cc_final: -0.1816 (m-80) REVERT: B 102 ASN cc_start: 0.6232 (p0) cc_final: 0.5718 (p0) REVERT: B 110 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7239 (mtm180) REVERT: C 48 TYR cc_start: 0.0097 (OUTLIER) cc_final: -0.2353 (m-80) REVERT: C 102 ASN cc_start: 0.6050 (p0) cc_final: 0.5604 (p0) REVERT: C 110 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7455 (mtm180) REVERT: C 255 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5072 (m-80) REVERT: D 48 TYR cc_start: -0.0176 (OUTLIER) cc_final: -0.1597 (m-80) REVERT: D 110 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7253 (mtm180) REVERT: D 248 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: D 255 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5611 (m-80) REVERT: D 318 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7377 (p90) REVERT: E 48 TYR cc_start: -0.0021 (OUTLIER) cc_final: -0.1663 (m-80) REVERT: E 102 ASN cc_start: 0.6231 (p0) cc_final: 0.5709 (p0) REVERT: E 110 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7292 (mtt180) REVERT: E 255 PHE cc_start: 0.5876 (OUTLIER) cc_final: 0.5184 (m-80) REVERT: E 304 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7200 (mtmt) outliers start: 63 outliers final: 44 residues processed: 190 average time/residue: 0.2379 time to fit residues: 66.7210 Evaluate side-chains 200 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 181 TRP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 TRP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 181 TRP Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 432 PHE Chi-restraints excluded: chain D residue 48 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 181 TRP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 181 TRP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 316 PHE Chi-restraints excluded: chain E residue 432 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 124 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 28 optimal weight: 40.0000 chunk 39 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.234956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.200943 restraints weight = 13299.991| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 1.16 r_work: 0.3800 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13580 Z= 0.274 Angle : 0.789 10.976 18520 Z= 0.377 Chirality : 0.050 0.253 2185 Planarity : 0.004 0.035 2235 Dihedral : 8.088 48.945 2270 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.29 % Favored : 95.38 % Rotamer: Outliers : 4.62 % Allowed : 31.82 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1560 helix: 2.57 (0.24), residues: 500 sheet: -0.83 (0.24), residues: 310 loop : -1.92 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 261 HIS 0.005 0.001 HIS A 131 PHE 0.026 0.002 PHE C 99 TYR 0.012 0.002 TYR B 309 ARG 0.004 0.001 ARG B 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 10) link_NAG-ASN : angle 1.82797 ( 30) link_ALPHA1-4 : bond 0.00739 ( 5) link_ALPHA1-4 : angle 3.60969 ( 15) link_BETA1-4 : bond 0.00490 ( 10) link_BETA1-4 : angle 2.58149 ( 30) hydrogen bonds : bond 0.03866 ( 625) hydrogen bonds : angle 4.31231 ( 2220) SS BOND : bond 0.00966 ( 5) SS BOND : angle 2.75124 ( 10) covalent geometry : bond 0.00645 (13545) covalent geometry : angle 0.77054 (18435) Misc. bond : bond 0.00120 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7590.29 seconds wall clock time: 135 minutes 42.03 seconds (8142.03 seconds total)