Starting phenix.real_space_refine on Thu Jun 12 13:07:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bl8_16103/06_2025/8bl8_16103.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bl8_16103/06_2025/8bl8_16103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bl8_16103/06_2025/8bl8_16103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bl8_16103/06_2025/8bl8_16103.map" model { file = "/net/cci-nas-00/data/ceres_data/8bl8_16103/06_2025/8bl8_16103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bl8_16103/06_2025/8bl8_16103.cif" } resolution = 3.21 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= 0.000 sd= 0.043 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 50 5.16 5 C 9279 2.51 5 N 2181 2.21 5 O 2509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14019 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2768 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2761 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 1 Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2697 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2756 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 18, 'TRANS': 315} Chain breaks: 1 Chain: "E" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2687 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Time building chain proxies: 9.33, per 1000 atoms: 0.67 Number of scatterers: 14019 At special positions: 0 Unit cell: (96.18, 96.18, 121.37, 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 50 16.00 O 2509 8.00 N 2181 7.00 C 9279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 104 " " NAG B 501 " - " ASN B 104 " " NAG C 501 " - " ASN C 104 " " NAG D 501 " - " ASN D 104 " " NAG E 501 " - " ASN E 104 " " NAG F 1 " - " ASN A 186 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 186 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN C 186 " " NAG K 1 " - " ASN C 170 " " NAG L 1 " - " ASN D 186 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 186 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 42.1% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 98 through 103 removed outlier: 4.190A pdb=" N ASP A 103 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 242 through 264 removed outlier: 4.407A pdb=" N LEU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.516A pdb=" N PHE A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 292 Processing helix chain 'A' and resid 303 through 330 Processing helix chain 'A' and resid 444 through 477 removed outlier: 3.649A pdb=" N TYR A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 45 removed outlier: 4.342A pdb=" N ASN B 44 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 4.221A pdb=" N ASP B 103 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 163 through 166 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 270 through 295 Processing helix chain 'B' and resid 303 through 329 removed outlier: 3.504A pdb=" N ILE B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 477 removed outlier: 3.725A pdb=" N TYR B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.240A pdb=" N ASP C 103 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 163 through 166 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 249 through 264 removed outlier: 3.736A pdb=" N PHE C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 removed outlier: 3.850A pdb=" N VAL C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 327 Processing helix chain 'C' and resid 447 through 476 removed outlier: 4.329A pdb=" N LYS C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 removed outlier: 4.210A pdb=" N ASN D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.245A pdb=" N ASP D 103 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 163 through 166 Processing helix chain 'D' and resid 192 through 199 Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 249 through 262 removed outlier: 3.601A pdb=" N ILE D 261 " --> pdb=" O MET D 257 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 270 through 295 removed outlier: 3.547A pdb=" N ILE D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 330 Processing helix chain 'D' and resid 444 through 476 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 98 through 103 removed outlier: 4.190A pdb=" N ASP E 103 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 192 through 199 Processing helix chain 'E' and resid 242 through 249 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 293 removed outlier: 3.606A pdb=" N VAL E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE E 289 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 316 removed outlier: 3.566A pdb=" N VAL E 307 " --> pdb=" O PRO E 303 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR E 308 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 310 " --> pdb=" O GLY E 306 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 316 " --> pdb=" O CYS E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 477 removed outlier: 4.002A pdb=" N VAL E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.013A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 154 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.013A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A 83 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE A 70 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TRP A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR A 68 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ARG A 87 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE A 66 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR A 89 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP A 64 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR A 91 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N SER A 62 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 4.118A pdb=" N SER A 177 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 213 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A 239 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU A 211 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.945A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL B 154 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.945A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 83 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE B 70 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TRP B 85 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR B 68 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ARG B 87 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 66 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR B 89 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP B 64 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 91 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N SER B 62 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.931A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.931A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 213 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG B 239 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU B 211 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.028A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL C 154 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.028A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL C 79 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL C 73 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 81 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TRP C 85 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL C 67 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG C 87 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL C 65 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TYR C 89 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE C 63 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR C 91 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL C 61 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.843A pdb=" N SER C 177 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASN C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N MET C 223 " --> pdb=" O ASN C 227 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 213 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG C 239 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU C 211 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.905A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL D 154 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.905A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 79 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL D 73 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 81 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TRP D 85 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL D 67 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG D 87 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL D 65 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR D 89 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE D 63 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR D 91 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL D 61 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 120 through 122 removed outlier: 4.004A pdb=" N SER D 177 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY D 213 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG D 239 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU D 211 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.036A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL E 154 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.036A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL E 79 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL E 73 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR E 81 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TRP E 85 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL E 67 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG E 87 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL E 65 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR E 89 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE E 63 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR E 91 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL E 61 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 120 through 122 removed outlier: 4.058A pdb=" N SER E 177 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN E 227 " --> pdb=" O MET E 223 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET E 223 " --> pdb=" O ASN E 227 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 213 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG E 239 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU E 211 " --> pdb=" O ARG E 239 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2208 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: 4.22 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4169 1.35 - 1.48: 4046 1.48 - 1.61: 6105 1.61 - 1.74: 1 1.74 - 1.87: 85 Bond restraints: 14406 Sorted by residual: bond pdb=" CB PRO E 268 " pdb=" CG PRO E 268 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" CB CYS A 171 " pdb=" SG CYS A 171 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.10e+00 bond pdb=" N ARG E 31 " pdb=" CA ARG E 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ARG A 31 " pdb=" CA ARG A 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ARG B 31 " pdb=" CA ARG B 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 14401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 19160 1.67 - 3.34: 443 3.34 - 5.01: 84 5.01 - 6.68: 6 6.68 - 8.35: 1 Bond angle restraints: 19694 Sorted by residual: angle pdb=" CA PRO E 268 " pdb=" N PRO E 268 " pdb=" CD PRO E 268 " ideal model delta sigma weight residual 112.00 103.65 8.35 1.40e+00 5.10e-01 3.56e+01 angle pdb=" N VAL B 126 " pdb=" CA VAL B 126 " pdb=" C VAL B 126 " ideal model delta sigma weight residual 113.42 108.16 5.26 1.17e+00 7.31e-01 2.02e+01 angle pdb=" N PRO E 268 " pdb=" CD PRO E 268 " pdb=" CG PRO E 268 " ideal model delta sigma weight residual 103.20 97.70 5.50 1.50e+00 4.44e-01 1.34e+01 angle pdb=" N PRO E 268 " pdb=" CA PRO E 268 " pdb=" CB PRO E 268 " ideal model delta sigma weight residual 103.51 100.94 2.57 9.60e-01 1.09e+00 7.14e+00 angle pdb=" N GLY D 263 " pdb=" CA GLY D 263 " pdb=" C GLY D 263 " ideal model delta sigma weight residual 114.67 111.76 2.91 1.10e+00 8.26e-01 6.99e+00 ... (remaining 19689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7989 17.96 - 35.93: 637 35.93 - 53.89: 123 53.89 - 71.85: 19 71.85 - 89.81: 12 Dihedral angle restraints: 8780 sinusoidal: 3829 harmonic: 4951 Sorted by residual: dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual 93.00 163.24 -70.24 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CA ASN D 163 " pdb=" C ASN D 163 " pdb=" N PHE D 164 " pdb=" CA PHE D 164 " ideal model delta harmonic sigma weight residual 180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N PHE C 164 " pdb=" CA PHE C 164 " ideal model delta harmonic sigma weight residual -180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 8777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2050 0.071 - 0.142: 297 0.142 - 0.213: 2 0.213 - 0.284: 4 0.284 - 0.355: 2 Chirality restraints: 2355 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 170 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ILE B 254 " pdb=" N ILE B 254 " pdb=" C ILE B 254 " pdb=" CB ILE B 254 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA ILE E 254 " pdb=" N ILE E 254 " pdb=" C ILE E 254 " pdb=" CB ILE E 254 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2352 not shown) Planarity restraints: 2383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 267 " 0.069 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO E 268 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO E 268 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 268 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 267 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 268 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 200 " -0.143 9.50e-02 1.11e+02 6.45e-02 3.35e+00 pdb=" NE ARG C 200 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 200 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 200 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 200 " 0.000 2.00e-02 2.50e+03 ... (remaining 2380 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2554 2.77 - 3.30: 13850 3.30 - 3.84: 23296 3.84 - 4.37: 27058 4.37 - 4.90: 47787 Nonbonded interactions: 114545 Sorted by model distance: nonbonded pdb=" OD2 ASP A 167 " pdb=" NE2 GLN A 169 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG A 273 " pdb=" OD1 ASP A 450 " model vdw 2.246 3.120 nonbonded pdb=" OD1 ASP D 64 " pdb=" N VAL D 65 " model vdw 2.307 3.120 nonbonded pdb=" O ASP B 160 " pdb=" OD1 ASP B 160 " model vdw 2.313 3.040 nonbonded pdb=" OD2 ASP C 260 " pdb=" OH TYR C 457 " model vdw 2.316 3.040 ... (remaining 114540 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 320 or resid 44 \ 6 through 476 or resid 501)) selection = (chain 'B' and (resid 31 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 320 or resid 44 \ 6 through 476 or resid 501)) selection = (chain 'C' and (resid 31 through 320 or resid 446 through 476 or resid 501)) selection = (chain 'D' and (resid 31 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 320 or resid 44 \ 6 through 476 or resid 501)) selection = (chain 'E' and (resid 31 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB )) or resid 128 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 320 or resid 44 \ 6 through 476 or resid 501)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.370 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 14436 Z= 0.179 Angle : 0.635 8.350 19779 Z= 0.331 Chirality : 0.046 0.355 2355 Planarity : 0.005 0.100 2368 Dihedral : 13.409 89.814 5563 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.06 % Allowed : 11.55 % Favored : 88.39 % Cbeta Deviations : 0.06 % 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: 0.16 (0.21), residues: 1636 helix: 1.91 (0.21), residues: 593 sheet: -0.87 (0.23), residues: 451 loop : -0.87 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 475 HIS 0.002 0.001 HIS D 455 PHE 0.014 0.001 PHE D 264 TYR 0.012 0.001 TYR E 138 ARG 0.016 0.001 ARG C 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 15) link_NAG-ASN : angle 2.05614 ( 45) link_BETA1-4 : bond 0.00309 ( 10) link_BETA1-4 : angle 1.91616 ( 30) hydrogen bonds : bond 0.14012 ( 707) hydrogen bonds : angle 6.89431 ( 2208) SS BOND : bond 0.00223 ( 5) SS BOND : angle 1.72062 ( 10) covalent geometry : bond 0.00411 (14406) covalent geometry : angle 0.62274 (19694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.9110 (tptt) cc_final: 0.8606 (mmmm) REVERT: A 457 TYR cc_start: 0.8464 (t80) cc_final: 0.8249 (t80) REVERT: B 78 GLN cc_start: 0.9060 (mm110) cc_final: 0.8857 (mm-40) REVERT: B 89 TYR cc_start: 0.7667 (p90) cc_final: 0.7137 (p90) REVERT: D 152 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 184 ASP cc_start: 0.8367 (m-30) cc_final: 0.8124 (m-30) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.2370 time to fit residues: 82.7751 Evaluate side-chains 196 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 154 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 68 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 152 GLN C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107620 restraints weight = 18407.214| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.79 r_work: 0.3112 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14436 Z= 0.146 Angle : 0.621 7.286 19779 Z= 0.320 Chirality : 0.046 0.212 2355 Planarity : 0.004 0.049 2368 Dihedral : 6.160 57.715 2357 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.00 % Allowed : 12.52 % Favored : 85.48 % 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: 0.39 (0.21), residues: 1636 helix: 2.20 (0.20), residues: 596 sheet: -0.89 (0.23), residues: 442 loop : -0.75 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 190 HIS 0.002 0.000 HIS B 455 PHE 0.026 0.002 PHE B 264 TYR 0.014 0.001 TYR D 235 ARG 0.006 0.001 ARG E 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 15) link_NAG-ASN : angle 1.93396 ( 45) link_BETA1-4 : bond 0.00392 ( 10) link_BETA1-4 : angle 1.23991 ( 30) hydrogen bonds : bond 0.04280 ( 707) hydrogen bonds : angle 5.08586 ( 2208) SS BOND : bond 0.00139 ( 5) SS BOND : angle 1.59494 ( 10) covalent geometry : bond 0.00337 (14406) covalent geometry : angle 0.61289 (19694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.9008 (tptt) cc_final: 0.8535 (mmmm) REVERT: B 78 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8865 (mm-40) REVERT: B 80 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7908 (pt) REVERT: B 89 TYR cc_start: 0.7537 (p90) cc_final: 0.6968 (p90) REVERT: B 158 SER cc_start: 0.8786 (p) cc_final: 0.8553 (t) REVERT: C 80 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8338 (pt) REVERT: D 80 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8212 (pt) REVERT: D 152 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8524 (tm-30) REVERT: D 169 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8323 (mm110) REVERT: D 444 ARG cc_start: 0.4099 (mpp-170) cc_final: 0.3713 (mpt180) REVERT: E 75 GLU cc_start: 0.7835 (mp0) cc_final: 0.7495 (mp0) REVERT: E 89 TYR cc_start: 0.7851 (p90) cc_final: 0.7429 (p90) REVERT: E 124 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: E 272 GLU cc_start: 0.7900 (mp0) cc_final: 0.7544 (mt-10) outliers start: 31 outliers final: 16 residues processed: 238 average time/residue: 0.2297 time to fit residues: 83.1203 Evaluate side-chains 218 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 124 optimal weight: 0.0470 chunk 161 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108659 restraints weight = 18449.581| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.83 r_work: 0.3129 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14436 Z= 0.122 Angle : 0.563 6.609 19779 Z= 0.288 Chirality : 0.044 0.153 2355 Planarity : 0.004 0.051 2368 Dihedral : 5.873 57.585 2357 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.39 % Allowed : 13.16 % Favored : 84.45 % 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: 0.51 (0.21), residues: 1636 helix: 2.34 (0.20), residues: 595 sheet: -0.97 (0.23), residues: 438 loop : -0.60 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 475 HIS 0.001 0.000 HIS D 141 PHE 0.019 0.001 PHE E 244 TYR 0.015 0.001 TYR E 89 ARG 0.004 0.000 ARG A 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 15) link_NAG-ASN : angle 1.41867 ( 45) link_BETA1-4 : bond 0.00328 ( 10) link_BETA1-4 : angle 1.20903 ( 30) hydrogen bonds : bond 0.03765 ( 707) hydrogen bonds : angle 4.72464 ( 2208) SS BOND : bond 0.00271 ( 5) SS BOND : angle 1.13274 ( 10) covalent geometry : bond 0.00279 (14406) covalent geometry : angle 0.55798 (19694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.8022 (p90) cc_final: 0.7803 (p90) REVERT: A 195 LYS cc_start: 0.9087 (tptt) cc_final: 0.8598 (mmmm) REVERT: A 282 LEU cc_start: 0.8256 (tt) cc_final: 0.8043 (tp) REVERT: B 78 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8867 (mm-40) REVERT: B 80 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7805 (pt) REVERT: B 158 SER cc_start: 0.8711 (p) cc_final: 0.8412 (t) REVERT: C 204 MET cc_start: 0.8192 (ttp) cc_final: 0.7741 (ttm) REVERT: D 80 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8138 (pt) REVERT: D 152 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8542 (tm-30) REVERT: D 444 ARG cc_start: 0.4244 (mpp-170) cc_final: 0.3962 (mpt180) REVERT: E 75 GLU cc_start: 0.7849 (mp0) cc_final: 0.7504 (mp0) REVERT: E 89 TYR cc_start: 0.7975 (p90) cc_final: 0.7597 (p90) REVERT: E 124 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: E 272 GLU cc_start: 0.7911 (mp0) cc_final: 0.7604 (mt-10) outliers start: 37 outliers final: 20 residues processed: 255 average time/residue: 0.2278 time to fit residues: 88.7410 Evaluate side-chains 225 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN C 78 GLN C 476 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107561 restraints weight = 18429.519| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.84 r_work: 0.3091 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14436 Z= 0.139 Angle : 0.564 7.204 19779 Z= 0.286 Chirality : 0.044 0.237 2355 Planarity : 0.004 0.052 2368 Dihedral : 5.774 57.461 2357 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.16 % Allowed : 14.45 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1636 helix: 2.46 (0.20), residues: 597 sheet: -1.03 (0.23), residues: 446 loop : -0.57 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 472 HIS 0.002 0.000 HIS B 455 PHE 0.024 0.001 PHE B 264 TYR 0.014 0.001 TYR E 89 ARG 0.006 0.000 ARG A 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 15) link_NAG-ASN : angle 1.47306 ( 45) link_BETA1-4 : bond 0.00300 ( 10) link_BETA1-4 : angle 1.20818 ( 30) hydrogen bonds : bond 0.03554 ( 707) hydrogen bonds : angle 4.58415 ( 2208) SS BOND : bond 0.00178 ( 5) SS BOND : angle 1.29280 ( 10) covalent geometry : bond 0.00331 (14406) covalent geometry : angle 0.55770 (19694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.8089 (p90) cc_final: 0.7877 (p90) REVERT: B 77 ASN cc_start: 0.9024 (m-40) cc_final: 0.8586 (m110) REVERT: B 78 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8877 (mm-40) REVERT: B 80 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7864 (pt) REVERT: B 152 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7445 (tp-100) REVERT: B 158 SER cc_start: 0.8717 (p) cc_final: 0.8445 (t) REVERT: C 204 MET cc_start: 0.8128 (ttp) cc_final: 0.7677 (ttm) REVERT: D 80 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8167 (pt) REVERT: D 152 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8532 (tm-30) REVERT: D 313 MET cc_start: 0.8275 (tpp) cc_final: 0.7990 (tpp) REVERT: D 444 ARG cc_start: 0.4670 (mpp-170) cc_final: 0.4365 (mpt180) REVERT: E 75 GLU cc_start: 0.7917 (mp0) cc_final: 0.7678 (mp0) REVERT: E 124 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: E 221 PHE cc_start: 0.8337 (t80) cc_final: 0.8091 (t80) outliers start: 49 outliers final: 30 residues processed: 243 average time/residue: 0.3941 time to fit residues: 146.9573 Evaluate side-chains 225 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 61 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107103 restraints weight = 18540.666| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.81 r_work: 0.3085 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14436 Z= 0.151 Angle : 0.560 6.831 19779 Z= 0.285 Chirality : 0.044 0.167 2355 Planarity : 0.004 0.052 2368 Dihedral : 5.769 57.827 2357 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.35 % Allowed : 14.58 % Favored : 82.06 % 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: 0.59 (0.21), residues: 1636 helix: 2.51 (0.20), residues: 597 sheet: -1.03 (0.23), residues: 450 loop : -0.57 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 475 HIS 0.001 0.000 HIS D 141 PHE 0.013 0.001 PHE B 264 TYR 0.022 0.001 TYR B 83 ARG 0.004 0.000 ARG A 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 15) link_NAG-ASN : angle 1.39815 ( 45) link_BETA1-4 : bond 0.00228 ( 10) link_BETA1-4 : angle 1.21775 ( 30) hydrogen bonds : bond 0.03520 ( 707) hydrogen bonds : angle 4.54175 ( 2208) SS BOND : bond 0.00173 ( 5) SS BOND : angle 1.16297 ( 10) covalent geometry : bond 0.00363 (14406) covalent geometry : angle 0.55425 (19694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 2.153 Fit side-chains REVERT: A 124 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: B 77 ASN cc_start: 0.8995 (m-40) cc_final: 0.8566 (m110) REVERT: B 78 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8880 (mm-40) REVERT: B 80 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7885 (pt) REVERT: B 158 SER cc_start: 0.8727 (p) cc_final: 0.8464 (t) REVERT: C 204 MET cc_start: 0.8094 (ttp) cc_final: 0.7673 (ttm) REVERT: D 80 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8192 (pt) REVERT: D 152 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8542 (tm-30) REVERT: D 444 ARG cc_start: 0.4787 (mpp-170) cc_final: 0.4505 (mpt180) REVERT: E 89 TYR cc_start: 0.8139 (p90) cc_final: 0.7704 (p90) REVERT: E 124 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: E 152 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8492 (tm-30) REVERT: E 221 PHE cc_start: 0.8334 (t80) cc_final: 0.8083 (t80) REVERT: E 257 MET cc_start: 0.7179 (mtp) cc_final: 0.6978 (mmm) outliers start: 52 outliers final: 34 residues processed: 237 average time/residue: 0.2522 time to fit residues: 92.3463 Evaluate side-chains 230 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.0570 chunk 136 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 GLN C 476 GLN E 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107860 restraints weight = 18623.817| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.81 r_work: 0.3098 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14436 Z= 0.131 Angle : 0.552 7.115 19779 Z= 0.279 Chirality : 0.044 0.261 2355 Planarity : 0.004 0.053 2368 Dihedral : 5.664 57.549 2357 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.35 % Allowed : 15.74 % Favored : 80.90 % 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: 0.63 (0.21), residues: 1636 helix: 2.56 (0.20), residues: 596 sheet: -1.06 (0.23), residues: 454 loop : -0.51 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 472 HIS 0.002 0.000 HIS B 455 PHE 0.011 0.001 PHE C 221 TYR 0.013 0.001 TYR A 89 ARG 0.004 0.000 ARG A 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 15) link_NAG-ASN : angle 1.35551 ( 45) link_BETA1-4 : bond 0.00270 ( 10) link_BETA1-4 : angle 1.17416 ( 30) hydrogen bonds : bond 0.03401 ( 707) hydrogen bonds : angle 4.49701 ( 2208) SS BOND : bond 0.00251 ( 5) SS BOND : angle 1.23801 ( 10) covalent geometry : bond 0.00314 (14406) covalent geometry : angle 0.54632 (19694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 2.064 Fit side-chains REVERT: A 124 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: A 208 GLU cc_start: 0.7771 (tt0) cc_final: 0.6965 (tp30) REVERT: B 77 ASN cc_start: 0.9010 (m-40) cc_final: 0.8593 (m110) REVERT: B 78 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8825 (mm-40) REVERT: B 80 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7830 (pt) REVERT: B 152 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7958 (mp-120) REVERT: B 158 SER cc_start: 0.8717 (p) cc_final: 0.8462 (t) REVERT: B 257 MET cc_start: 0.8023 (mtp) cc_final: 0.7675 (mtp) REVERT: C 204 MET cc_start: 0.8147 (ttp) cc_final: 0.7698 (ttm) REVERT: D 76 LYS cc_start: 0.8941 (tptm) cc_final: 0.8735 (tptm) REVERT: D 80 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8121 (pt) REVERT: D 152 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8453 (tm-30) REVERT: D 313 MET cc_start: 0.8346 (tpp) cc_final: 0.7961 (tpp) REVERT: D 444 ARG cc_start: 0.4583 (mpp-170) cc_final: 0.4346 (mpt180) REVERT: E 89 TYR cc_start: 0.8101 (p90) cc_final: 0.7608 (p90) REVERT: E 124 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: E 152 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8484 (tm-30) REVERT: E 221 PHE cc_start: 0.8308 (t80) cc_final: 0.8079 (t80) outliers start: 52 outliers final: 35 residues processed: 249 average time/residue: 0.2350 time to fit residues: 92.3398 Evaluate side-chains 235 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 150 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106310 restraints weight = 18589.674| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.81 r_work: 0.3075 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14436 Z= 0.168 Angle : 0.575 6.734 19779 Z= 0.291 Chirality : 0.045 0.233 2355 Planarity : 0.004 0.055 2368 Dihedral : 5.742 58.344 2357 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.55 % Allowed : 15.94 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1636 helix: 2.61 (0.20), residues: 596 sheet: -1.07 (0.23), residues: 454 loop : -0.56 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 472 HIS 0.002 0.000 HIS D 141 PHE 0.021 0.001 PHE C 221 TYR 0.015 0.001 TYR E 89 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 15) link_NAG-ASN : angle 1.39823 ( 45) link_BETA1-4 : bond 0.00229 ( 10) link_BETA1-4 : angle 1.23792 ( 30) hydrogen bonds : bond 0.03525 ( 707) hydrogen bonds : angle 4.50202 ( 2208) SS BOND : bond 0.00165 ( 5) SS BOND : angle 1.50215 ( 10) covalent geometry : bond 0.00409 (14406) covalent geometry : angle 0.56975 (19694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 1.698 Fit side-chains REVERT: A 124 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: A 280 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (tt) REVERT: B 77 ASN cc_start: 0.9034 (m-40) cc_final: 0.8701 (m110) REVERT: B 78 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8842 (mm-40) REVERT: B 80 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7835 (pt) REVERT: B 152 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7883 (mp-120) REVERT: B 158 SER cc_start: 0.8729 (p) cc_final: 0.8485 (t) REVERT: B 257 MET cc_start: 0.8010 (mtp) cc_final: 0.7637 (mtp) REVERT: C 204 MET cc_start: 0.7955 (ttp) cc_final: 0.7553 (ttm) REVERT: D 76 LYS cc_start: 0.8946 (tptm) cc_final: 0.8728 (tptm) REVERT: D 80 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8198 (pt) REVERT: D 152 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8466 (tm-30) REVERT: D 313 MET cc_start: 0.8312 (tpp) cc_final: 0.7912 (tpp) REVERT: D 444 ARG cc_start: 0.4559 (mpp-170) cc_final: 0.4336 (mpt180) REVERT: E 89 TYR cc_start: 0.8163 (p90) cc_final: 0.7600 (p90) REVERT: E 124 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: E 138 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: E 152 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8523 (tm-30) REVERT: E 221 PHE cc_start: 0.8309 (t80) cc_final: 0.8073 (t80) outliers start: 55 outliers final: 39 residues processed: 242 average time/residue: 0.2271 time to fit residues: 84.7416 Evaluate side-chains 239 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 148 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108958 restraints weight = 18427.058| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.78 r_work: 0.3115 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14436 Z= 0.113 Angle : 0.545 8.291 19779 Z= 0.275 Chirality : 0.043 0.201 2355 Planarity : 0.004 0.051 2368 Dihedral : 5.506 57.347 2357 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.90 % Allowed : 16.71 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1636 helix: 2.68 (0.20), residues: 596 sheet: -1.06 (0.23), residues: 454 loop : -0.45 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 472 HIS 0.001 0.000 HIS C 141 PHE 0.021 0.001 PHE C 221 TYR 0.011 0.001 TYR C 86 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 15) link_NAG-ASN : angle 1.30125 ( 45) link_BETA1-4 : bond 0.00346 ( 10) link_BETA1-4 : angle 1.08015 ( 30) hydrogen bonds : bond 0.03226 ( 707) hydrogen bonds : angle 4.40065 ( 2208) SS BOND : bond 0.00119 ( 5) SS BOND : angle 0.94385 ( 10) covalent geometry : bond 0.00264 (14406) covalent geometry : angle 0.54074 (19694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: A 208 GLU cc_start: 0.7884 (tt0) cc_final: 0.7054 (tp30) REVERT: A 329 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7366 (tt) REVERT: B 77 ASN cc_start: 0.9035 (m-40) cc_final: 0.8625 (m110) REVERT: B 78 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8857 (mm-40) REVERT: B 80 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7785 (pt) REVERT: B 108 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8960 (pt) REVERT: B 152 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7795 (mp-120) REVERT: B 257 MET cc_start: 0.7972 (mtp) cc_final: 0.7540 (mtp) REVERT: B 288 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7242 (mp) REVERT: C 204 MET cc_start: 0.7936 (ttp) cc_final: 0.7500 (ttm) REVERT: D 152 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8471 (tm-30) REVERT: D 444 ARG cc_start: 0.4579 (mpp-170) cc_final: 0.4326 (mpt180) REVERT: D 451 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7374 (tttm) REVERT: E 89 TYR cc_start: 0.8207 (p90) cc_final: 0.7670 (p90) REVERT: E 124 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: E 152 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8260 (tm-30) REVERT: E 221 PHE cc_start: 0.8261 (t80) cc_final: 0.8029 (t80) outliers start: 45 outliers final: 30 residues processed: 241 average time/residue: 0.2265 time to fit residues: 84.1420 Evaluate side-chains 233 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 19 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 139 optimal weight: 0.0980 chunk 88 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 52 optimal weight: 0.0020 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 56 optimal weight: 0.0870 overall best weight: 0.2766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110865 restraints weight = 18233.095| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.82 r_work: 0.3142 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14436 Z= 0.098 Angle : 0.537 8.021 19779 Z= 0.269 Chirality : 0.043 0.171 2355 Planarity : 0.004 0.048 2368 Dihedral : 5.309 57.493 2357 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.39 % Allowed : 17.29 % Favored : 80.32 % 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: 0.83 (0.22), residues: 1636 helix: 2.76 (0.20), residues: 595 sheet: -1.00 (0.23), residues: 454 loop : -0.39 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 472 HIS 0.001 0.000 HIS C 141 PHE 0.021 0.001 PHE C 221 TYR 0.011 0.001 TYR E 245 ARG 0.004 0.000 ARG A 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 15) link_NAG-ASN : angle 1.23771 ( 45) link_BETA1-4 : bond 0.00320 ( 10) link_BETA1-4 : angle 1.08131 ( 30) hydrogen bonds : bond 0.03055 ( 707) hydrogen bonds : angle 4.30473 ( 2208) SS BOND : bond 0.00105 ( 5) SS BOND : angle 0.87326 ( 10) covalent geometry : bond 0.00220 (14406) covalent geometry : angle 0.53245 (19694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8668 (t0) cc_final: 0.8176 (t0) REVERT: A 76 LYS cc_start: 0.8780 (tptp) cc_final: 0.8574 (tptp) REVERT: A 124 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: A 208 GLU cc_start: 0.7890 (tt0) cc_final: 0.7198 (tp30) REVERT: A 329 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7406 (tt) REVERT: B 77 ASN cc_start: 0.9042 (m-40) cc_final: 0.8641 (m110) REVERT: B 78 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8926 (mm-40) REVERT: B 80 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7749 (pt) REVERT: B 108 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8940 (pt) REVERT: B 139 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.9006 (mm) REVERT: B 152 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7751 (mp-120) REVERT: B 257 MET cc_start: 0.7602 (mtp) cc_final: 0.7124 (mtp) REVERT: B 288 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7264 (mp) REVERT: C 103 ASP cc_start: 0.8460 (t0) cc_final: 0.7899 (t0) REVERT: C 204 MET cc_start: 0.8016 (ttp) cc_final: 0.7573 (mtp) REVERT: D 81 THR cc_start: 0.8939 (m) cc_final: 0.8706 (p) REVERT: D 113 ASP cc_start: 0.8531 (p0) cc_final: 0.8310 (p0) REVERT: D 152 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8526 (tm-30) REVERT: D 444 ARG cc_start: 0.4479 (mpp-170) cc_final: 0.4246 (mpt180) REVERT: D 451 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7394 (tttm) REVERT: E 89 TYR cc_start: 0.8134 (p90) cc_final: 0.7664 (p90) REVERT: E 152 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8361 (tm-30) REVERT: E 221 PHE cc_start: 0.8150 (t80) cc_final: 0.7918 (t80) outliers start: 37 outliers final: 25 residues processed: 253 average time/residue: 0.2197 time to fit residues: 85.3257 Evaluate side-chains 233 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107720 restraints weight = 18458.448| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.86 r_work: 0.3098 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14436 Z= 0.142 Angle : 0.566 8.332 19779 Z= 0.284 Chirality : 0.044 0.193 2355 Planarity : 0.004 0.050 2368 Dihedral : 5.453 57.790 2357 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.19 % Allowed : 17.55 % Favored : 80.26 % 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: 0.82 (0.22), residues: 1636 helix: 2.75 (0.20), residues: 596 sheet: -0.97 (0.23), residues: 454 loop : -0.43 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 472 HIS 0.001 0.000 HIS A 141 PHE 0.022 0.001 PHE C 221 TYR 0.014 0.001 TYR E 86 ARG 0.003 0.000 ARG C 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 15) link_NAG-ASN : angle 1.32133 ( 45) link_BETA1-4 : bond 0.00215 ( 10) link_BETA1-4 : angle 1.18175 ( 30) hydrogen bonds : bond 0.03278 ( 707) hydrogen bonds : angle 4.33513 ( 2208) SS BOND : bond 0.00110 ( 5) SS BOND : angle 1.27399 ( 10) covalent geometry : bond 0.00343 (14406) covalent geometry : angle 0.56129 (19694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3272 Ramachandran restraints generated. 1636 Oldfield, 0 Emsley, 1636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: A 208 GLU cc_start: 0.7897 (tt0) cc_final: 0.7288 (tp30) REVERT: A 329 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7493 (tt) REVERT: B 78 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8996 (mm-40) REVERT: B 108 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.9007 (pt) REVERT: B 152 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7786 (mp-120) REVERT: B 257 MET cc_start: 0.7976 (mtp) cc_final: 0.7540 (mtp) REVERT: B 288 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7318 (mp) REVERT: D 72 ASN cc_start: 0.8529 (t0) cc_final: 0.8246 (t0) REVERT: D 152 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8451 (tm-30) REVERT: D 444 ARG cc_start: 0.4462 (mpp-170) cc_final: 0.4240 (mpt180) REVERT: D 451 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7476 (tttm) REVERT: E 89 TYR cc_start: 0.8208 (p90) cc_final: 0.7825 (p90) REVERT: E 138 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: E 152 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8385 (tm-30) REVERT: E 221 PHE cc_start: 0.8213 (t80) cc_final: 0.7997 (t80) outliers start: 34 outliers final: 27 residues processed: 227 average time/residue: 0.2297 time to fit residues: 79.4548 Evaluate side-chains 226 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 149 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 121 optimal weight: 0.0470 chunk 136 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110281 restraints weight = 18482.803| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.79 r_work: 0.3135 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14436 Z= 0.105 Angle : 0.545 8.331 19779 Z= 0.272 Chirality : 0.043 0.180 2355 Planarity : 0.004 0.048 2368 Dihedral : 5.294 57.245 2357 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.32 % Allowed : 17.48 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.22), residues: 1636 helix: 2.83 (0.20), residues: 595 sheet: -0.97 (0.23), residues: 454 loop : -0.37 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 472 HIS 0.001 0.000 HIS D 141 PHE 0.022 0.001 PHE C 221 TYR 0.011 0.001 TYR E 245 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.20826 ( 45) link_BETA1-4 : bond 0.00303 ( 10) link_BETA1-4 : angle 1.06302 ( 30) hydrogen bonds : bond 0.03053 ( 707) hydrogen bonds : angle 4.26784 ( 2208) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.96562 ( 10) covalent geometry : bond 0.00244 (14406) covalent geometry : angle 0.54093 (19694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7664.20 seconds wall clock time: 135 minutes 13.19 seconds (8113.19 seconds total)