Starting phenix.real_space_refine on Tue May 20 03:29:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3z_29711/05_2025/8g3z_29711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3z_29711/05_2025/8g3z_29711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3z_29711/05_2025/8g3z_29711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3z_29711/05_2025/8g3z_29711.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3z_29711/05_2025/8g3z_29711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3z_29711/05_2025/8g3z_29711.cif" } resolution = 2.3 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= 0.002 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 144 5.16 5 C 12244 2.51 5 N 3360 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19485 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "I" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "K" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "B" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "C" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "D" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 370} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.65, per 1000 atoms: 0.60 Number of scatterers: 19485 At special positions: 0 Unit cell: (170.56, 168.92, 94.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 144 16.00 O 3732 8.00 N 3360 7.00 C 12244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.01 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.01 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.00 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 420 " distance=2.05 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 127 " distance=2.04 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 236 " distance=2.04 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 447 " distance=2.05 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 420 " distance=2.04 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 127 " distance=2.04 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 229 " distance=2.05 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 420 " distance=2.04 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 229 " distance=2.04 Simple disulfide: pdb=" SG CYS C 231 " - pdb=" SG CYS C 236 " distance=2.05 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.04 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 420 " distance=2.04 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 127 " distance=2.04 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 229 " distance=2.04 Simple disulfide: pdb=" SG CYS D 231 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.04 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 447 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 503 " - " ASN A 144 " " NAG B 502 " - " ASN B 284 " " NAG B 503 " - " ASN B 144 " " NAG C 502 " - " ASN C 284 " " NAG C 503 " - " ASN C 144 " " NAG D 502 " - " ASN D 284 " " NAG D 503 " - " ASN D 144 " Time building additional restraints: 4.56 Conformation dependent library (CDL) restraints added in 2.3 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 49 sheets defined 3.0% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.551A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.552A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.553A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 196 through 199 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.529A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.522A pdb=" N ASN H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.992A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.572A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.522A pdb=" N ASN E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.515A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.888A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.530A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.523A pdb=" N ASN G 117 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.953A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.551A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.512A pdb=" N ASN J 117 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.522A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 92 through 98 removed outlier: 5.376A pdb=" N LYS A 94 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS A 447 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 113 through 122 removed outlier: 4.715A pdb=" N LEU A 113 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA A 136 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 115 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS A 134 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 132 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 156 " --> pdb=" O HIS A 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 178 through 183 removed outlier: 6.714A pdb=" N LEU A 202 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 213 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 204 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 230 through 232 removed outlier: 3.587A pdb=" N LYS A 263 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A 257 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 267 through 269 removed outlier: 6.189A pdb=" N THR A 268 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU A 316 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ARG A 292 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU A 276 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 352 through 357 removed outlier: 3.580A pdb=" N LYS A 360 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET A 375 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 401 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET A 377 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL A 399 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 379 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 92 through 98 removed outlier: 5.374A pdb=" N LYS B 94 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS B 447 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR B 409 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 430 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY B 407 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 113 through 122 removed outlier: 4.725A pdb=" N LEU B 113 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 136 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 115 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS B 134 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU B 117 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 132 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 156 " --> pdb=" O HIS B 173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 178 through 183 removed outlier: 6.698A pdb=" N LEU B 202 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 213 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 204 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 230 through 232 removed outlier: 3.594A pdb=" N LYS B 263 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG B 257 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 267 through 269 removed outlier: 6.134A pdb=" N THR B 268 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG B 292 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU B 276 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 352 through 357 removed outlier: 3.577A pdb=" N LYS B 360 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET B 377 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL B 399 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 379 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 92 through 98 removed outlier: 5.372A pdb=" N LYS C 94 " --> pdb=" O CYS C 447 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS C 447 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 122 removed outlier: 4.731A pdb=" N LEU C 113 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA C 136 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE C 115 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS C 134 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 132 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 156 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 178 through 183 removed outlier: 6.700A pdb=" N LEU C 202 " --> pdb=" O THR C 213 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR C 213 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 204 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 230 through 232 removed outlier: 3.590A pdb=" N LYS C 263 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG C 257 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 267 through 269 removed outlier: 6.147A pdb=" N THR C 268 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LEU C 316 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG C 292 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU C 276 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 352 through 357 removed outlier: 3.580A pdb=" N LYS C 360 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N MET C 375 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL C 401 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N MET C 377 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL C 399 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU C 379 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AE8, first strand: chain 'D' and resid 92 through 98 removed outlier: 5.376A pdb=" N LYS D 94 " --> pdb=" O CYS D 447 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS D 447 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 113 through 122 removed outlier: 4.731A pdb=" N LEU D 113 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA D 136 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE D 115 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS D 134 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLU D 117 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 132 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU D 156 " --> pdb=" O HIS D 173 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 178 through 183 removed outlier: 6.705A pdb=" N LEU D 202 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR D 213 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE D 204 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 230 through 232 removed outlier: 3.587A pdb=" N LYS D 263 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG D 257 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 267 through 269 removed outlier: 6.151A pdb=" N THR D 268 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU D 316 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG D 292 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU D 276 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 352 through 357 removed outlier: 3.582A pdb=" N LYS D 360 " --> pdb=" O MET D 357 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N MET D 375 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL D 401 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET D 377 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL D 399 " --> pdb=" O MET D 377 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU D 379 " --> pdb=" O SER D 397 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1650 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: 8.48 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3169 1.31 - 1.44: 5590 1.44 - 1.57: 10989 1.57 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 19952 Sorted by residual: bond pdb=" N GLU D 117 " pdb=" CA GLU D 117 " ideal model delta sigma weight residual 1.460 1.498 -0.038 7.10e-03 1.98e+04 2.79e+01 bond pdb=" C PHE K 83 " pdb=" O PHE K 83 " ideal model delta sigma weight residual 1.235 1.292 -0.057 1.15e-02 7.56e+03 2.42e+01 bond pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.10e-03 1.98e+04 2.40e+01 bond pdb=" C ILE L 48 " pdb=" O ILE L 48 " ideal model delta sigma weight residual 1.236 1.186 0.051 1.04e-02 9.25e+03 2.36e+01 bond pdb=" C PRO B 406 " pdb=" O PRO B 406 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.30e-02 5.92e+03 2.29e+01 ... (remaining 19947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 24171 2.59 - 5.18: 2641 5.18 - 7.77: 186 7.77 - 10.37: 12 10.37 - 12.96: 10 Bond angle restraints: 27020 Sorted by residual: angle pdb=" CA ILE D 120 " pdb=" CB ILE D 120 " pdb=" CG1 ILE D 120 " ideal model delta sigma weight residual 110.40 121.76 -11.36 1.70e+00 3.46e-01 4.46e+01 angle pdb=" CA ASP J 107 " pdb=" CB ASP J 107 " pdb=" CG ASP J 107 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" CB GLU J 89 " pdb=" CG GLU J 89 " pdb=" CD GLU J 89 " ideal model delta sigma weight residual 112.60 122.99 -10.39 1.70e+00 3.46e-01 3.74e+01 angle pdb=" C THR C 368 " pdb=" CA THR C 368 " pdb=" CB THR C 368 " ideal model delta sigma weight residual 109.65 119.64 -9.99 1.71e+00 3.42e-01 3.41e+01 angle pdb=" C ILE I 107 " pdb=" CA ILE I 107 " pdb=" CB ILE I 107 " ideal model delta sigma weight residual 111.23 117.41 -6.18 1.08e+00 8.57e-01 3.28e+01 ... (remaining 27015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10924 17.93 - 35.87: 811 35.87 - 53.80: 201 53.80 - 71.73: 45 71.73 - 89.67: 15 Dihedral angle restraints: 11996 sinusoidal: 4872 harmonic: 7124 Sorted by residual: dihedral pdb=" CA ALA B 441 " pdb=" C ALA B 441 " pdb=" N ALA B 442 " pdb=" CA ALA B 442 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CA ALA A 441 " pdb=" C ALA A 441 " pdb=" N ALA A 442 " pdb=" CA ALA A 442 " ideal model delta harmonic sigma weight residual 180.00 142.31 37.69 0 5.00e+00 4.00e-02 5.68e+01 dihedral pdb=" CA ALA D 441 " pdb=" C ALA D 441 " pdb=" N ALA D 442 " pdb=" CA ALA D 442 " ideal model delta harmonic sigma weight residual 180.00 142.45 37.55 0 5.00e+00 4.00e-02 5.64e+01 ... (remaining 11993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 2528 0.140 - 0.280: 372 0.280 - 0.420: 6 0.420 - 0.560: 0 0.560 - 0.701: 1 Chirality restraints: 2907 Sorted by residual: chirality pdb=" CB ILE D 120 " pdb=" CA ILE D 120 " pdb=" CG1 ILE D 120 " pdb=" CG2 ILE D 120 " both_signs ideal model delta sigma weight residual False 2.64 1.94 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA ASN B 199 " pdb=" N ASN B 199 " pdb=" C ASN B 199 " pdb=" CB ASN B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ASP C 184 " pdb=" N ASP C 184 " pdb=" C ASP C 184 " pdb=" CB ASP C 184 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2904 not shown) Planarity restraints: 3471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 503 " -0.114 2.00e-02 2.50e+03 9.42e-02 1.11e+02 pdb=" C7 NAG D 503 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 503 " -0.092 2.00e-02 2.50e+03 pdb=" N2 NAG D 503 " 0.141 2.00e-02 2.50e+03 pdb=" O7 NAG D 503 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 503 " -0.099 2.00e-02 2.50e+03 8.18e-02 8.37e+01 pdb=" C7 NAG A 503 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG A 503 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG A 503 " 0.122 2.00e-02 2.50e+03 pdb=" O7 NAG A 503 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 503 " -0.089 2.00e-02 2.50e+03 7.37e-02 6.79e+01 pdb=" C7 NAG B 503 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B 503 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG B 503 " 0.109 2.00e-02 2.50e+03 pdb=" O7 NAG B 503 " 0.009 2.00e-02 2.50e+03 ... (remaining 3468 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 6941 2.89 - 3.39: 17440 3.39 - 3.89: 36680 3.89 - 4.40: 42530 4.40 - 4.90: 71053 Nonbonded interactions: 174644 Sorted by model distance: nonbonded pdb=" O GLU B 168 " pdb=" NZ LYS C 163 " model vdw 2.386 3.120 nonbonded pdb=" O ASP C 293 " pdb="CA CA C 501 " model vdw 2.449 2.510 nonbonded pdb=" O ASP A 293 " pdb="CA CA A 501 " model vdw 2.463 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D 501 " model vdw 2.467 2.510 nonbonded pdb=" OE2 GLU B 276 " pdb=" OH TYR B 409 " model vdw 2.469 3.040 ... (remaining 174639 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 77 through 466 or resid 501 through 503)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' } 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 46.420 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 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 : 0.013 0.101 19999 Z= 0.978 Angle : 1.655 12.957 27121 Z= 1.083 Chirality : 0.093 0.701 2907 Planarity : 0.010 0.094 3464 Dihedral : 14.361 89.667 7364 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.70 % Favored : 95.10 % Rotamer: Outliers : 2.16 % Allowed : 6.49 % Favored : 91.35 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.34 (0.14), residues: 2488 helix: None (None), residues: 0 sheet: -1.45 (0.16), residues: 820 loop : -1.67 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.010 TRP J 47 HIS 0.043 0.006 HIS D 129 PHE 0.031 0.007 PHE E 64 TYR 0.081 0.011 TYR C 409 ARG 0.050 0.005 ARG D 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 7) link_NAG-ASN : angle 1.51062 ( 21) hydrogen bonds : bond 0.13281 ( 650) hydrogen bonds : angle 9.35997 ( 1650) SS BOND : bond 0.01229 ( 40) SS BOND : angle 1.36820 ( 80) covalent geometry : bond 0.01345 (19952) covalent geometry : angle 1.65563 (27020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 467 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8314 (mtm-85) REVERT: L 82 ASP cc_start: 0.8602 (m-30) cc_final: 0.8065 (m-30) REVERT: L 93 ASN cc_start: 0.8789 (m110) cc_final: 0.8550 (m110) REVERT: L 109 ARG cc_start: 0.8374 (ptm160) cc_final: 0.7505 (pmt170) REVERT: F 92 ASN cc_start: 0.8669 (t0) cc_final: 0.8460 (m-40) REVERT: F 109 ARG cc_start: 0.8170 (ptm160) cc_final: 0.7303 (pmt170) REVERT: G 43 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7726 (tt0) REVERT: I 61 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: I 82 ASP cc_start: 0.8641 (m-30) cc_final: 0.8007 (m-30) REVERT: I 93 ASN cc_start: 0.8781 (m110) cc_final: 0.8545 (m-40) REVERT: I 109 ARG cc_start: 0.8417 (ptm160) cc_final: 0.7454 (pmt170) REVERT: J 43 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7718 (tt0) REVERT: K 14 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8973 (m) REVERT: K 109 ARG cc_start: 0.8325 (ptm160) cc_final: 0.7620 (pmt170) REVERT: A 285 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8428 (ttmm) REVERT: A 369 MET cc_start: 0.9003 (mmp) cc_final: 0.8795 (mmm) REVERT: C 409 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7109 (t80) outliers start: 45 outliers final: 11 residues processed: 506 average time/residue: 1.4762 time to fit residues: 828.2664 Evaluate side-chains 344 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 331 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 92 ASN F 27 GLN G 117 ASN I 27 GLN I 37 GLN I 92 ASN K 27 GLN K 92 ASN A 134 HIS A 306 ASN C 169 ASN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.056614 restraints weight = 38953.842| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.14 r_work: 0.2715 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19999 Z= 0.149 Angle : 0.660 6.931 27121 Z= 0.358 Chirality : 0.047 0.188 2907 Planarity : 0.004 0.036 3464 Dihedral : 7.426 58.767 2940 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.59 % Rotamer: Outliers : 3.08 % Allowed : 12.88 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.50 (0.15), residues: 2488 helix: None (None), residues: 0 sheet: -0.99 (0.15), residues: 976 loop : -0.96 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 177 HIS 0.008 0.002 HIS A 101 PHE 0.011 0.002 PHE K 83 TYR 0.023 0.002 TYR K 91 ARG 0.007 0.001 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 7) link_NAG-ASN : angle 0.93671 ( 21) hydrogen bonds : bond 0.04403 ( 650) hydrogen bonds : angle 6.86679 ( 1650) SS BOND : bond 0.00262 ( 40) SS BOND : angle 0.79002 ( 80) covalent geometry : bond 0.00331 (19952) covalent geometry : angle 0.65968 (27020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 346 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 LYS cc_start: 0.9247 (ptmm) cc_final: 0.8958 (ptmt) REVERT: L 11 LEU cc_start: 0.8744 (tp) cc_final: 0.8361 (tt) REVERT: L 61 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8182 (mtm-85) REVERT: L 93 ASN cc_start: 0.9007 (m110) cc_final: 0.8588 (m-40) REVERT: L 109 ARG cc_start: 0.8461 (ptm160) cc_final: 0.7437 (pmt170) REVERT: E 13 ARG cc_start: 0.8752 (mtp85) cc_final: 0.8121 (mtp85) REVERT: E 84 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8794 (p) REVERT: F 92 ASN cc_start: 0.8577 (t0) cc_final: 0.8167 (m-40) REVERT: F 108 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8818 (ttmm) REVERT: F 109 ARG cc_start: 0.8333 (ptm160) cc_final: 0.7353 (pmt170) REVERT: G 13 ARG cc_start: 0.8695 (mtp85) cc_final: 0.8053 (mtp85) REVERT: G 43 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7882 (mp10) REVERT: G 46 GLU cc_start: 0.8777 (tt0) cc_final: 0.8428 (tt0) REVERT: G 63 LYS cc_start: 0.9391 (tttm) cc_final: 0.9084 (tttt) REVERT: G 98 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8325 (ttp-110) REVERT: I 61 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8354 (mtm-85) REVERT: I 81 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (pm20) REVERT: I 82 ASP cc_start: 0.8626 (m-30) cc_final: 0.8265 (m-30) REVERT: I 93 ASN cc_start: 0.9029 (m110) cc_final: 0.8660 (m-40) REVERT: I 109 ARG cc_start: 0.8519 (ptm160) cc_final: 0.7495 (pmt170) REVERT: J 13 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8141 (mtp85) REVERT: J 43 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7862 (mp10) REVERT: K 61 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8339 (mtm-85) REVERT: K 82 ASP cc_start: 0.8217 (m-30) cc_final: 0.7931 (m-30) REVERT: K 92 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8501 (m-40) REVERT: K 104 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8302 (tttt) REVERT: K 109 ARG cc_start: 0.8380 (ptm160) cc_final: 0.7628 (pmt170) REVERT: A 270 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8491 (tmt170) REVERT: A 285 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8247 (ttmm) REVERT: A 292 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.7014 (ttm170) REVERT: A 369 MET cc_start: 0.9274 (mmp) cc_final: 0.8959 (mmm) REVERT: B 403 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8697 (tpp) REVERT: C 270 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8670 (tpt90) REVERT: C 409 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.5749 (t80) REVERT: D 239 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8817 (tmt) outliers start: 64 outliers final: 22 residues processed: 383 average time/residue: 1.5922 time to fit residues: 674.4339 Evaluate side-chains 362 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 330 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 221 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN F 93 ASN I 27 GLN K 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.063634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.048256 restraints weight = 38910.108| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 2.15 r_work: 0.2507 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 19999 Z= 0.355 Angle : 0.714 8.571 27121 Z= 0.382 Chirality : 0.049 0.173 2907 Planarity : 0.005 0.048 3464 Dihedral : 7.153 58.950 2939 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.57 % Favored : 97.27 % Rotamer: Outliers : 3.70 % Allowed : 14.04 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.19 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.68 (0.16), residues: 976 loop : -0.82 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 177 HIS 0.013 0.002 HIS A 101 PHE 0.018 0.002 PHE E 104 TYR 0.020 0.002 TYR C 409 ARG 0.007 0.001 ARG E 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 7) link_NAG-ASN : angle 1.00477 ( 21) hydrogen bonds : bond 0.04986 ( 650) hydrogen bonds : angle 6.57428 ( 1650) SS BOND : bond 0.00488 ( 40) SS BOND : angle 0.88771 ( 80) covalent geometry : bond 0.00799 (19952) covalent geometry : angle 0.71353 (27020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 310 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: H 13 ARG cc_start: 0.8823 (mtp85) cc_final: 0.8003 (mtp85) REVERT: H 76 THR cc_start: 0.9153 (p) cc_final: 0.8852 (t) REVERT: L 61 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8481 (mtm-85) REVERT: L 81 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: L 93 ASN cc_start: 0.9006 (m110) cc_final: 0.8553 (m-40) REVERT: L 109 ARG cc_start: 0.8614 (ptm160) cc_final: 0.7416 (pmt170) REVERT: E 13 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8177 (mtp85) REVERT: E 76 THR cc_start: 0.9170 (p) cc_final: 0.8891 (t) REVERT: E 84 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8837 (p) REVERT: F 92 ASN cc_start: 0.8610 (t0) cc_final: 0.8254 (m-40) REVERT: F 109 ARG cc_start: 0.8491 (ptm160) cc_final: 0.7347 (pmt170) REVERT: G 13 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8206 (mtp85) REVERT: G 43 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8065 (mp10) REVERT: G 46 GLU cc_start: 0.8804 (tt0) cc_final: 0.8460 (tt0) REVERT: G 63 LYS cc_start: 0.9343 (tttm) cc_final: 0.9102 (tttt) REVERT: G 76 THR cc_start: 0.9149 (p) cc_final: 0.8874 (t) REVERT: I 61 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8469 (mtm-85) REVERT: I 93 ASN cc_start: 0.9062 (m110) cc_final: 0.8629 (m-40) REVERT: I 109 ARG cc_start: 0.8596 (ptm160) cc_final: 0.7358 (pmt170) REVERT: J 43 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8022 (mp10) REVERT: J 76 THR cc_start: 0.9155 (p) cc_final: 0.8898 (t) REVERT: K 81 GLU cc_start: 0.8843 (pm20) cc_final: 0.8186 (pm20) REVERT: K 104 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8385 (tttt) REVERT: K 109 ARG cc_start: 0.8539 (ptm160) cc_final: 0.7480 (pmt170) REVERT: A 239 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8742 (tmt) REVERT: A 268 THR cc_start: 0.9054 (m) cc_final: 0.8753 (p) REVERT: A 292 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.6520 (ttm170) REVERT: B 239 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8751 (tmt) REVERT: C 239 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8696 (tmt) REVERT: C 268 THR cc_start: 0.8955 (m) cc_final: 0.8558 (p) REVERT: C 337 CYS cc_start: 0.8210 (m) cc_final: 0.7649 (m) REVERT: D 239 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8705 (tmt) outliers start: 77 outliers final: 27 residues processed: 357 average time/residue: 1.6202 time to fit residues: 636.9005 Evaluate side-chains 330 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 295 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN I 27 GLN K 27 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.066493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.051374 restraints weight = 38753.208| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.15 r_work: 0.2591 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19999 Z= 0.145 Angle : 0.584 5.793 27121 Z= 0.314 Chirality : 0.045 0.153 2907 Planarity : 0.004 0.033 3464 Dihedral : 6.611 59.657 2936 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.49 % Favored : 97.35 % Rotamer: Outliers : 2.26 % Allowed : 16.15 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.08 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.61 (0.16), residues: 960 loop : -0.74 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 177 HIS 0.008 0.001 HIS A 101 PHE 0.010 0.001 PHE D 119 TYR 0.020 0.001 TYR K 91 ARG 0.007 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 7) link_NAG-ASN : angle 0.92260 ( 21) hydrogen bonds : bond 0.03839 ( 650) hydrogen bonds : angle 6.27127 ( 1650) SS BOND : bond 0.00284 ( 40) SS BOND : angle 0.62033 ( 80) covalent geometry : bond 0.00319 (19952) covalent geometry : angle 0.58401 (27020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8038 (mtp85) REVERT: H 62 GLN cc_start: 0.8838 (tt0) cc_final: 0.8565 (tp-100) REVERT: H 76 THR cc_start: 0.9175 (p) cc_final: 0.8892 (t) REVERT: L 11 LEU cc_start: 0.8694 (tp) cc_final: 0.8308 (tt) REVERT: L 61 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8463 (mtm-85) REVERT: L 93 ASN cc_start: 0.8963 (m110) cc_final: 0.8480 (m-40) REVERT: L 109 ARG cc_start: 0.8590 (ptm160) cc_final: 0.7405 (pmt170) REVERT: E 13 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8638 (mtp85) REVERT: E 43 GLN cc_start: 0.7929 (tt0) cc_final: 0.7566 (mp10) REVERT: E 62 GLN cc_start: 0.8952 (tt0) cc_final: 0.8662 (tp-100) REVERT: E 76 THR cc_start: 0.9169 (p) cc_final: 0.8905 (t) REVERT: E 84 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8890 (p) REVERT: F 81 GLU cc_start: 0.8907 (pm20) cc_final: 0.8280 (pm20) REVERT: F 82 ASP cc_start: 0.8847 (m-30) cc_final: 0.8599 (m-30) REVERT: F 92 ASN cc_start: 0.8605 (t0) cc_final: 0.8309 (m-40) REVERT: F 93 ASN cc_start: 0.9050 (m110) cc_final: 0.8684 (m-40) REVERT: F 108 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8857 (ttmm) REVERT: F 109 ARG cc_start: 0.8497 (ptm160) cc_final: 0.7357 (pmt170) REVERT: G 13 ARG cc_start: 0.8920 (mtp85) cc_final: 0.8207 (mtp85) REVERT: G 46 GLU cc_start: 0.8824 (tt0) cc_final: 0.8515 (tt0) REVERT: G 63 LYS cc_start: 0.9343 (tttm) cc_final: 0.9126 (tttt) REVERT: G 76 THR cc_start: 0.9171 (p) cc_final: 0.8909 (t) REVERT: G 84 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8979 (p) REVERT: I 93 ASN cc_start: 0.8982 (m110) cc_final: 0.8512 (m-40) REVERT: I 109 ARG cc_start: 0.8568 (ptm160) cc_final: 0.7427 (pmt170) REVERT: J 13 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8094 (mtp85) REVERT: J 62 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8641 (tp-100) REVERT: J 76 THR cc_start: 0.9160 (p) cc_final: 0.8914 (t) REVERT: K 81 GLU cc_start: 0.8883 (pm20) cc_final: 0.8368 (pm20) REVERT: K 82 ASP cc_start: 0.8310 (m-30) cc_final: 0.8005 (m-30) REVERT: K 104 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8394 (tttt) REVERT: K 109 ARG cc_start: 0.8559 (ptm160) cc_final: 0.7468 (pmt170) REVERT: A 268 THR cc_start: 0.9082 (m) cc_final: 0.8722 (p) REVERT: A 270 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8862 (tpt90) REVERT: A 285 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8053 (mttm) REVERT: B 239 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8632 (tmt) REVERT: C 239 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8546 (tmt) REVERT: C 268 THR cc_start: 0.9068 (m) cc_final: 0.8748 (p) REVERT: D 239 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8604 (tmt) REVERT: D 268 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8822 (p) REVERT: D 342 ASP cc_start: 0.8707 (m-30) cc_final: 0.8265 (p0) outliers start: 47 outliers final: 22 residues processed: 354 average time/residue: 1.6535 time to fit residues: 643.9954 Evaluate side-chains 326 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 78 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 229 optimal weight: 0.0170 chunk 185 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN I 27 GLN K 27 GLN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.062390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.047090 restraints weight = 39116.517| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 2.14 r_work: 0.2478 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2364 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 19999 Z= 0.416 Angle : 0.706 8.598 27121 Z= 0.375 Chirality : 0.050 0.156 2907 Planarity : 0.005 0.053 3464 Dihedral : 6.771 58.585 2932 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 4.13 % Allowed : 15.72 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.09 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.54 (0.16), residues: 976 loop : -0.81 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 177 HIS 0.012 0.002 HIS A 101 PHE 0.018 0.003 PHE J 104 TYR 0.019 0.002 TYR L 49 ARG 0.007 0.001 ARG C 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 7) link_NAG-ASN : angle 1.14487 ( 21) hydrogen bonds : bond 0.04916 ( 650) hydrogen bonds : angle 6.42838 ( 1650) SS BOND : bond 0.00504 ( 40) SS BOND : angle 0.84300 ( 80) covalent geometry : bond 0.00935 (19952) covalent geometry : angle 0.70545 (27020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 299 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.8856 (mtp85) cc_final: 0.7993 (mtp85) REVERT: H 43 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: H 76 THR cc_start: 0.9107 (p) cc_final: 0.8860 (t) REVERT: L 11 LEU cc_start: 0.8627 (tp) cc_final: 0.8397 (tp) REVERT: L 93 ASN cc_start: 0.9046 (m110) cc_final: 0.8573 (m-40) REVERT: L 109 ARG cc_start: 0.8622 (ptm160) cc_final: 0.7354 (pmt170) REVERT: E 13 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8092 (mtp85) REVERT: E 43 GLN cc_start: 0.7988 (tt0) cc_final: 0.7783 (mp10) REVERT: E 76 THR cc_start: 0.9096 (p) cc_final: 0.8849 (t) REVERT: E 84 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8855 (p) REVERT: F 80 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.9083 (p) REVERT: F 81 GLU cc_start: 0.8919 (pm20) cc_final: 0.8242 (pm20) REVERT: F 82 ASP cc_start: 0.8894 (m-30) cc_final: 0.8564 (m-30) REVERT: F 92 ASN cc_start: 0.8600 (t0) cc_final: 0.8292 (m-40) REVERT: F 93 ASN cc_start: 0.9086 (m110) cc_final: 0.8751 (m-40) REVERT: F 109 ARG cc_start: 0.8556 (ptm160) cc_final: 0.7291 (pmt170) REVERT: G 13 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8129 (mtp85) REVERT: G 46 GLU cc_start: 0.8854 (tt0) cc_final: 0.8528 (tt0) REVERT: G 63 LYS cc_start: 0.9344 (tttm) cc_final: 0.9136 (tttt) REVERT: G 76 THR cc_start: 0.9081 (p) cc_final: 0.8844 (t) REVERT: G 84 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8920 (p) REVERT: G 98 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7987 (ttp-110) REVERT: I 82 ASP cc_start: 0.8812 (m-30) cc_final: 0.8471 (m-30) REVERT: I 93 ASN cc_start: 0.9045 (m110) cc_final: 0.8707 (m-40) REVERT: I 109 ARG cc_start: 0.8626 (ptm160) cc_final: 0.7340 (pmt170) REVERT: J 13 ARG cc_start: 0.8818 (mtp85) cc_final: 0.7997 (mtp85) REVERT: J 43 GLN cc_start: 0.7964 (mp10) cc_final: 0.7712 (mp10) REVERT: J 76 THR cc_start: 0.9070 (p) cc_final: 0.8831 (t) REVERT: K 81 GLU cc_start: 0.8866 (pm20) cc_final: 0.8332 (pm20) REVERT: K 82 ASP cc_start: 0.8550 (m-30) cc_final: 0.8116 (m-30) REVERT: K 104 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8437 (tttt) REVERT: K 109 ARG cc_start: 0.8653 (ptm160) cc_final: 0.7375 (pmt170) REVERT: A 268 THR cc_start: 0.9056 (m) cc_final: 0.8715 (p) REVERT: A 285 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8106 (mttp) REVERT: A 292 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.6568 (ttm170) REVERT: B 239 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8773 (tmt) REVERT: B 285 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8324 (mttp) REVERT: B 292 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: B 375 MET cc_start: 0.9225 (mmp) cc_final: 0.8996 (mmm) REVERT: C 239 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8766 (tmt) REVERT: C 268 THR cc_start: 0.9111 (m) cc_final: 0.8836 (p) REVERT: C 285 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8170 (mttm) REVERT: D 239 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8753 (tmt) REVERT: D 268 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8942 (p) REVERT: D 285 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8149 (mttm) REVERT: D 342 ASP cc_start: 0.8729 (m-30) cc_final: 0.8266 (p0) outliers start: 86 outliers final: 41 residues processed: 360 average time/residue: 1.6411 time to fit residues: 652.8240 Evaluate side-chains 347 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 50 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 227 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN G 3 GLN K 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.065332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.050024 restraints weight = 38574.270| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.20 r_work: 0.2557 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19999 Z= 0.165 Angle : 0.591 6.036 27121 Z= 0.316 Chirality : 0.045 0.188 2907 Planarity : 0.004 0.038 3464 Dihedral : 6.297 57.818 2932 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer: Outliers : 2.93 % Allowed : 17.12 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.98 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.50 (0.16), residues: 980 loop : -0.70 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 177 HIS 0.008 0.001 HIS A 101 PHE 0.010 0.001 PHE D 119 TYR 0.017 0.001 TYR K 91 ARG 0.010 0.001 ARG K 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 7) link_NAG-ASN : angle 1.06741 ( 21) hydrogen bonds : bond 0.03778 ( 650) hydrogen bonds : angle 6.12245 ( 1650) SS BOND : bond 0.00270 ( 40) SS BOND : angle 0.54495 ( 80) covalent geometry : bond 0.00361 (19952) covalent geometry : angle 0.59023 (27020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 318 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8017 (mtp85) REVERT: H 43 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7686 (mp10) REVERT: H 62 GLN cc_start: 0.8794 (tt0) cc_final: 0.8458 (tp-100) REVERT: H 76 THR cc_start: 0.9085 (p) cc_final: 0.8856 (t) REVERT: L 17 GLU cc_start: 0.7614 (mp0) cc_final: 0.7288 (mp0) REVERT: L 61 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8410 (mtm-85) REVERT: L 82 ASP cc_start: 0.8858 (m-30) cc_final: 0.8366 (m-30) REVERT: L 93 ASN cc_start: 0.8939 (m110) cc_final: 0.8439 (m-40) REVERT: L 109 ARG cc_start: 0.8619 (ptm160) cc_final: 0.7352 (pmt170) REVERT: E 13 ARG cc_start: 0.8897 (mtp85) cc_final: 0.8622 (mtp85) REVERT: E 43 GLN cc_start: 0.7926 (tt0) cc_final: 0.7644 (mp10) REVERT: E 62 GLN cc_start: 0.8853 (tt0) cc_final: 0.8479 (tp-100) REVERT: E 76 THR cc_start: 0.9049 (p) cc_final: 0.8836 (t) REVERT: E 84 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8856 (p) REVERT: F 81 GLU cc_start: 0.8954 (pm20) cc_final: 0.8356 (pm20) REVERT: F 92 ASN cc_start: 0.8575 (t0) cc_final: 0.8281 (m-40) REVERT: F 93 ASN cc_start: 0.9035 (m110) cc_final: 0.8617 (m-40) REVERT: F 108 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8878 (ttmm) REVERT: F 109 ARG cc_start: 0.8537 (ptm160) cc_final: 0.7266 (pmt170) REVERT: G 13 ARG cc_start: 0.8926 (mtp85) cc_final: 0.8130 (mtp85) REVERT: G 46 GLU cc_start: 0.8845 (tt0) cc_final: 0.8530 (tt0) REVERT: G 76 THR cc_start: 0.9044 (p) cc_final: 0.8830 (t) REVERT: I 93 ASN cc_start: 0.8946 (m110) cc_final: 0.8429 (m-40) REVERT: I 107 ILE cc_start: 0.8393 (pp) cc_final: 0.8173 (mp) REVERT: I 109 ARG cc_start: 0.8577 (ptm160) cc_final: 0.7400 (pmt170) REVERT: J 13 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8019 (mtp85) REVERT: J 43 GLN cc_start: 0.7930 (mp10) cc_final: 0.7636 (mp10) REVERT: J 62 GLN cc_start: 0.8809 (tt0) cc_final: 0.8450 (tp-100) REVERT: J 76 THR cc_start: 0.9034 (p) cc_final: 0.8823 (t) REVERT: J 98 ARG cc_start: 0.8534 (ttt-90) cc_final: 0.8193 (ttt-90) REVERT: K 11 LEU cc_start: 0.8618 (tp) cc_final: 0.8329 (tt) REVERT: K 81 GLU cc_start: 0.8899 (pm20) cc_final: 0.8363 (pm20) REVERT: K 82 ASP cc_start: 0.8524 (m-30) cc_final: 0.8103 (m-30) REVERT: K 104 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8395 (tttt) REVERT: K 109 ARG cc_start: 0.8651 (ptm160) cc_final: 0.7320 (pmt170) REVERT: A 263 LYS cc_start: 0.9001 (tttp) cc_final: 0.8724 (ttpt) REVERT: A 268 THR cc_start: 0.9033 (m) cc_final: 0.8774 (p) REVERT: A 285 LYS cc_start: 0.8565 (mtpp) cc_final: 0.7970 (mttm) REVERT: A 453 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: B 239 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8565 (tmt) REVERT: B 285 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8178 (mttm) REVERT: B 292 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.7161 (ttm170) REVERT: B 375 MET cc_start: 0.9207 (mmp) cc_final: 0.8987 (mmm) REVERT: C 239 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8547 (tmt) REVERT: C 285 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8131 (mttm) REVERT: D 239 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8560 (tmt) REVERT: D 285 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8099 (mttm) REVERT: D 342 ASP cc_start: 0.8718 (m-30) cc_final: 0.8261 (p0) outliers start: 61 outliers final: 32 residues processed: 366 average time/residue: 1.6407 time to fit residues: 661.0622 Evaluate side-chains 346 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 306 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 118 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.0070 chunk 232 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN E 3 GLN F 27 GLN G 3 GLN I 27 GLN K 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.065191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.049723 restraints weight = 38412.586| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.21 r_work: 0.2547 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19999 Z= 0.193 Angle : 0.597 6.219 27121 Z= 0.318 Chirality : 0.045 0.179 2907 Planarity : 0.004 0.055 3464 Dihedral : 6.170 59.491 2931 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.11 % Rotamer: Outliers : 3.08 % Allowed : 17.40 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.41 (0.16), residues: 980 loop : -0.67 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 94 HIS 0.009 0.001 HIS A 101 PHE 0.010 0.002 PHE E 115 TYR 0.018 0.001 TYR K 91 ARG 0.012 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 7) link_NAG-ASN : angle 1.05474 ( 21) hydrogen bonds : bond 0.03804 ( 650) hydrogen bonds : angle 6.01739 ( 1650) SS BOND : bond 0.00291 ( 40) SS BOND : angle 0.58625 ( 80) covalent geometry : bond 0.00434 (19952) covalent geometry : angle 0.59700 (27020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 315 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8056 (mtp85) REVERT: H 43 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: H 62 GLN cc_start: 0.8806 (tt0) cc_final: 0.8459 (tp-100) REVERT: L 17 GLU cc_start: 0.7748 (mp0) cc_final: 0.7465 (mp0) REVERT: L 93 ASN cc_start: 0.8972 (m110) cc_final: 0.8437 (m-40) REVERT: L 109 ARG cc_start: 0.8632 (ptm160) cc_final: 0.7345 (pmt170) REVERT: E 13 ARG cc_start: 0.8912 (mtp85) cc_final: 0.8636 (mtp85) REVERT: E 43 GLN cc_start: 0.8046 (tt0) cc_final: 0.7677 (mp10) REVERT: E 62 GLN cc_start: 0.8812 (tt0) cc_final: 0.8436 (tp-100) REVERT: E 76 THR cc_start: 0.9060 (p) cc_final: 0.8858 (t) REVERT: E 84 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8879 (p) REVERT: F 81 GLU cc_start: 0.8935 (pm20) cc_final: 0.8352 (pm20) REVERT: F 92 ASN cc_start: 0.8538 (t0) cc_final: 0.8270 (m-40) REVERT: F 93 ASN cc_start: 0.9073 (m110) cc_final: 0.8687 (m-40) REVERT: F 109 ARG cc_start: 0.8545 (ptm160) cc_final: 0.7252 (pmt170) REVERT: G 13 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8121 (mtp85) REVERT: G 46 GLU cc_start: 0.8801 (tt0) cc_final: 0.8537 (tt0) REVERT: G 98 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8401 (ttp-110) REVERT: I 93 ASN cc_start: 0.8959 (m110) cc_final: 0.8445 (m-40) REVERT: I 106 GLU cc_start: 0.6331 (tp30) cc_final: 0.6071 (tp30) REVERT: I 107 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8120 (mp) REVERT: I 109 ARG cc_start: 0.8550 (ptm160) cc_final: 0.7388 (pmt170) REVERT: J 13 ARG cc_start: 0.8861 (mtp85) cc_final: 0.8026 (mtp85) REVERT: J 43 GLN cc_start: 0.7985 (mp10) cc_final: 0.7643 (mp10) REVERT: J 62 GLN cc_start: 0.8802 (tt0) cc_final: 0.8429 (tp-100) REVERT: J 76 THR cc_start: 0.9027 (p) cc_final: 0.8819 (t) REVERT: K 81 GLU cc_start: 0.8871 (pm20) cc_final: 0.8359 (pm20) REVERT: K 82 ASP cc_start: 0.8525 (m-30) cc_final: 0.8003 (m-30) REVERT: K 104 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8373 (tttt) REVERT: K 109 ARG cc_start: 0.8660 (ptm160) cc_final: 0.7293 (pmt170) REVERT: A 263 LYS cc_start: 0.9027 (tttp) cc_final: 0.8726 (ttpt) REVERT: A 268 THR cc_start: 0.9040 (m) cc_final: 0.8798 (p) REVERT: A 285 LYS cc_start: 0.8577 (mtpp) cc_final: 0.7979 (mttm) REVERT: B 153 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9019 (mm) REVERT: B 239 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8565 (tmt) REVERT: B 285 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8235 (mttp) REVERT: C 153 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9029 (mm) REVERT: C 239 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8518 (tmt) REVERT: C 285 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8145 (mttm) REVERT: D 239 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8555 (tmt) REVERT: D 285 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8132 (mttm) REVERT: D 342 ASP cc_start: 0.8722 (m-30) cc_final: 0.8331 (p0) outliers start: 64 outliers final: 38 residues processed: 368 average time/residue: 1.6109 time to fit residues: 653.4519 Evaluate side-chains 355 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 109 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 61 optimal weight: 0.0000 chunk 10 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN E 3 GLN F 27 GLN G 3 GLN I 27 GLN K 27 GLN B 134 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.065140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.049586 restraints weight = 38406.368| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.21 r_work: 0.2544 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19999 Z= 0.203 Angle : 0.598 6.182 27121 Z= 0.318 Chirality : 0.045 0.137 2907 Planarity : 0.004 0.058 3464 Dihedral : 5.982 55.847 2926 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.77 % Favored : 97.07 % Rotamer: Outliers : 3.08 % Allowed : 17.64 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.33 (0.16), residues: 980 loop : -0.66 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 177 HIS 0.009 0.001 HIS A 101 PHE 0.010 0.002 PHE E 115 TYR 0.018 0.002 TYR K 91 ARG 0.012 0.001 ARG K 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 7) link_NAG-ASN : angle 1.06519 ( 21) hydrogen bonds : bond 0.03796 ( 650) hydrogen bonds : angle 5.99748 ( 1650) SS BOND : bond 0.00304 ( 40) SS BOND : angle 0.60907 ( 80) covalent geometry : bond 0.00457 (19952) covalent geometry : angle 0.59750 (27020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 313 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.8913 (mtp85) cc_final: 0.8053 (mtp85) REVERT: H 62 GLN cc_start: 0.8805 (tt0) cc_final: 0.8462 (tp-100) REVERT: H 73 ASP cc_start: 0.8174 (t0) cc_final: 0.7957 (t0) REVERT: L 17 GLU cc_start: 0.7812 (mp0) cc_final: 0.7522 (mp0) REVERT: L 48 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7733 (mm) REVERT: L 93 ASN cc_start: 0.9002 (m110) cc_final: 0.8439 (m-40) REVERT: L 109 ARG cc_start: 0.8630 (ptm160) cc_final: 0.7326 (pmt170) REVERT: E 13 ARG cc_start: 0.8920 (mtp85) cc_final: 0.8112 (mtp85) REVERT: E 43 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: E 62 GLN cc_start: 0.8789 (tt0) cc_final: 0.8419 (tp-100) REVERT: E 84 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8880 (p) REVERT: F 17 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: F 81 GLU cc_start: 0.8939 (pm20) cc_final: 0.8362 (pm20) REVERT: F 92 ASN cc_start: 0.8525 (t0) cc_final: 0.8271 (m-40) REVERT: F 93 ASN cc_start: 0.9083 (m110) cc_final: 0.8675 (m-40) REVERT: F 108 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8832 (ttmm) REVERT: F 109 ARG cc_start: 0.8543 (ptm160) cc_final: 0.7238 (pmt170) REVERT: G 13 ARG cc_start: 0.8925 (mtp85) cc_final: 0.8103 (mtp85) REVERT: G 46 GLU cc_start: 0.8816 (tt0) cc_final: 0.8503 (tt0) REVERT: I 17 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: I 81 GLU cc_start: 0.8926 (pm20) cc_final: 0.8193 (pm20) REVERT: I 93 ASN cc_start: 0.9004 (m110) cc_final: 0.8498 (m-40) REVERT: I 104 LYS cc_start: 0.8636 (tttt) cc_final: 0.8339 (tttp) REVERT: I 106 GLU cc_start: 0.6366 (tp30) cc_final: 0.6165 (tp30) REVERT: I 107 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8100 (mp) REVERT: I 109 ARG cc_start: 0.8604 (ptm160) cc_final: 0.7446 (pmt170) REVERT: J 13 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8052 (mtp85) REVERT: J 43 GLN cc_start: 0.8087 (mp10) cc_final: 0.7700 (mp10) REVERT: J 62 GLN cc_start: 0.8791 (tt0) cc_final: 0.8428 (tp-100) REVERT: K 17 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: K 81 GLU cc_start: 0.8897 (pm20) cc_final: 0.8378 (pm20) REVERT: K 82 ASP cc_start: 0.8585 (m-30) cc_final: 0.8044 (m-30) REVERT: K 109 ARG cc_start: 0.8665 (ptm160) cc_final: 0.7270 (pmt170) REVERT: A 153 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9014 (mm) REVERT: A 263 LYS cc_start: 0.9046 (tttp) cc_final: 0.8726 (ttpt) REVERT: A 268 THR cc_start: 0.9063 (m) cc_final: 0.8830 (p) REVERT: A 285 LYS cc_start: 0.8577 (mtpp) cc_final: 0.7999 (mttm) REVERT: B 239 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8573 (tmt) REVERT: B 285 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8183 (mttm) REVERT: B 373 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8364 (mtpp) REVERT: C 239 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8540 (tmt) REVERT: C 285 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8155 (mttm) REVERT: D 239 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8589 (tmt) REVERT: D 285 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8145 (mttm) REVERT: D 342 ASP cc_start: 0.8723 (m-30) cc_final: 0.8363 (p0) outliers start: 64 outliers final: 39 residues processed: 361 average time/residue: 1.6040 time to fit residues: 641.6335 Evaluate side-chains 362 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN F 27 GLN G 3 GLN I 27 GLN K 27 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.063553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.047894 restraints weight = 38589.968| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.21 r_work: 0.2499 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 19999 Z= 0.299 Angle : 0.651 6.909 27121 Z= 0.346 Chirality : 0.048 0.241 2907 Planarity : 0.005 0.065 3464 Dihedral : 6.191 55.952 2926 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.91 % Rotamer: Outliers : 3.03 % Allowed : 17.79 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.87 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.29 (0.16), residues: 960 loop : -0.74 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 177 HIS 0.011 0.002 HIS A 101 PHE 0.015 0.002 PHE J 104 TYR 0.018 0.002 TYR K 91 ARG 0.014 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 7) link_NAG-ASN : angle 1.14625 ( 21) hydrogen bonds : bond 0.04234 ( 650) hydrogen bonds : angle 6.15253 ( 1650) SS BOND : bond 0.00398 ( 40) SS BOND : angle 0.71121 ( 80) covalent geometry : bond 0.00672 (19952) covalent geometry : angle 0.64988 (27020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.8921 (mtp85) cc_final: 0.8048 (mtp85) REVERT: H 62 GLN cc_start: 0.8840 (tt0) cc_final: 0.8474 (tp-100) REVERT: H 73 ASP cc_start: 0.8178 (t0) cc_final: 0.7925 (t0) REVERT: L 17 GLU cc_start: 0.7800 (mp0) cc_final: 0.7429 (mp0) REVERT: L 48 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7866 (mm) REVERT: L 93 ASN cc_start: 0.9028 (m110) cc_final: 0.8498 (m-40) REVERT: L 109 ARG cc_start: 0.8629 (ptm160) cc_final: 0.7262 (pmt170) REVERT: E 13 ARG cc_start: 0.8914 (mtp85) cc_final: 0.8100 (mtp85) REVERT: E 43 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: E 62 GLN cc_start: 0.8850 (tt0) cc_final: 0.8472 (tp-100) REVERT: E 84 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8840 (p) REVERT: F 17 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: F 81 GLU cc_start: 0.8914 (pm20) cc_final: 0.8398 (pm20) REVERT: F 92 ASN cc_start: 0.8533 (t0) cc_final: 0.8267 (m-40) REVERT: F 93 ASN cc_start: 0.9111 (m110) cc_final: 0.8711 (m-40) REVERT: F 104 LYS cc_start: 0.8608 (tttt) cc_final: 0.8345 (tttp) REVERT: F 109 ARG cc_start: 0.8576 (ptm160) cc_final: 0.7222 (pmt170) REVERT: G 13 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8084 (mtp85) REVERT: G 46 GLU cc_start: 0.8860 (tt0) cc_final: 0.8585 (tt0) REVERT: I 17 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: I 81 GLU cc_start: 0.8922 (pm20) cc_final: 0.8326 (pm20) REVERT: I 93 ASN cc_start: 0.8997 (m110) cc_final: 0.8514 (m-40) REVERT: I 109 ARG cc_start: 0.8619 (ptm160) cc_final: 0.7427 (pmt170) REVERT: J 13 ARG cc_start: 0.8849 (mtp85) cc_final: 0.7997 (mtp85) REVERT: J 43 GLN cc_start: 0.8105 (mp10) cc_final: 0.7672 (mp10) REVERT: J 62 GLN cc_start: 0.8838 (tt0) cc_final: 0.8470 (tp-100) REVERT: K 17 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: K 81 GLU cc_start: 0.8868 (pm20) cc_final: 0.8362 (pm20) REVERT: K 82 ASP cc_start: 0.8638 (m-30) cc_final: 0.8269 (m-30) REVERT: K 109 ARG cc_start: 0.8688 (ptm160) cc_final: 0.7215 (pmt170) REVERT: A 84 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.7496 (mtp180) REVERT: A 153 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9082 (mm) REVERT: A 263 LYS cc_start: 0.9030 (tttp) cc_final: 0.8700 (ttpt) REVERT: A 268 THR cc_start: 0.9069 (m) cc_final: 0.8809 (p) REVERT: A 285 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8037 (mttm) REVERT: B 239 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8673 (tmt) REVERT: B 285 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8185 (mttm) REVERT: B 373 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8346 (mtpp) REVERT: C 239 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8646 (tmt) REVERT: C 285 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8166 (mttm) REVERT: D 239 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8659 (tmt) REVERT: D 285 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8131 (mttm) REVERT: D 342 ASP cc_start: 0.8735 (m-30) cc_final: 0.8323 (p0) outliers start: 63 outliers final: 41 residues processed: 355 average time/residue: 1.6392 time to fit residues: 641.5084 Evaluate side-chains 360 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN K 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.051536 restraints weight = 38265.296| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.16 r_work: 0.2596 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19999 Z= 0.135 Angle : 0.577 6.116 27121 Z= 0.307 Chirality : 0.045 0.188 2907 Planarity : 0.004 0.052 3464 Dihedral : 5.808 56.411 2926 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 2.31 % Allowed : 18.41 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.75 (0.17), residues: 2488 helix: None (None), residues: 0 sheet: -0.28 (0.17), residues: 944 loop : -0.60 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.007 0.001 HIS A 101 PHE 0.013 0.001 PHE H 29 TYR 0.016 0.001 TYR F 91 ARG 0.017 0.001 ARG K 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 7) link_NAG-ASN : angle 1.12238 ( 21) hydrogen bonds : bond 0.03407 ( 650) hydrogen bonds : angle 5.93551 ( 1650) SS BOND : bond 0.00220 ( 40) SS BOND : angle 0.60436 ( 80) covalent geometry : bond 0.00305 (19952) covalent geometry : angle 0.57678 (27020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 316 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 GLN cc_start: 0.8768 (tt0) cc_final: 0.8437 (tp-100) REVERT: H 73 ASP cc_start: 0.8169 (t0) cc_final: 0.7925 (t0) REVERT: L 3 VAL cc_start: 0.9463 (t) cc_final: 0.9198 (p) REVERT: L 17 GLU cc_start: 0.7790 (mp0) cc_final: 0.7414 (mp0) REVERT: L 93 ASN cc_start: 0.8971 (m110) cc_final: 0.8400 (m-40) REVERT: L 109 ARG cc_start: 0.8625 (ptm160) cc_final: 0.7314 (pmt170) REVERT: E 13 ARG cc_start: 0.8936 (mtp85) cc_final: 0.8682 (mtp85) REVERT: E 62 GLN cc_start: 0.8738 (tt0) cc_final: 0.8407 (tp-100) REVERT: F 3 VAL cc_start: 0.9474 (t) cc_final: 0.9173 (p) REVERT: F 17 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: F 81 GLU cc_start: 0.8962 (pm20) cc_final: 0.8413 (pm20) REVERT: F 82 ASP cc_start: 0.8879 (m-30) cc_final: 0.8570 (m-30) REVERT: F 92 ASN cc_start: 0.8517 (t0) cc_final: 0.8279 (m-40) REVERT: F 93 ASN cc_start: 0.9035 (m110) cc_final: 0.8601 (m-40) REVERT: F 108 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8823 (ttmm) REVERT: F 109 ARG cc_start: 0.8555 (ptm160) cc_final: 0.7214 (pmt170) REVERT: G 13 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8208 (mtp85) REVERT: G 46 GLU cc_start: 0.8810 (tt0) cc_final: 0.8464 (tt0) REVERT: I 3 VAL cc_start: 0.9466 (t) cc_final: 0.9192 (p) REVERT: I 17 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: I 81 GLU cc_start: 0.8915 (pm20) cc_final: 0.8288 (pm20) REVERT: I 93 ASN cc_start: 0.8954 (m110) cc_final: 0.8381 (m-40) REVERT: I 104 LYS cc_start: 0.8647 (tttt) cc_final: 0.8425 (tttp) REVERT: I 109 ARG cc_start: 0.8576 (ptm160) cc_final: 0.7499 (pmt170) REVERT: J 13 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8060 (mtp85) REVERT: J 43 GLN cc_start: 0.8103 (mp10) cc_final: 0.7755 (mp10) REVERT: J 62 GLN cc_start: 0.8739 (tt0) cc_final: 0.8411 (tp-100) REVERT: J 116 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8722 (mt-10) REVERT: K 3 VAL cc_start: 0.9458 (t) cc_final: 0.9184 (p) REVERT: K 17 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: K 109 ARG cc_start: 0.8624 (ptm160) cc_final: 0.7194 (pmt170) REVERT: A 263 LYS cc_start: 0.9041 (tttp) cc_final: 0.8733 (ttpt) REVERT: A 285 LYS cc_start: 0.8472 (mtpp) cc_final: 0.7918 (mttm) REVERT: B 239 MET cc_start: 0.9047 (ttp) cc_final: 0.8602 (tmt) REVERT: B 285 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8152 (mttm) REVERT: B 373 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8340 (mtpp) REVERT: C 239 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8550 (tmt) REVERT: C 285 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8117 (mttm) REVERT: D 285 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8082 (mttm) REVERT: D 292 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7930 (ttm170) REVERT: D 342 ASP cc_start: 0.8687 (m-30) cc_final: 0.8367 (p0) outliers start: 48 outliers final: 29 residues processed: 358 average time/residue: 1.6344 time to fit residues: 644.8345 Evaluate side-chains 339 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 117 ASN Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 456 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 215 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 0.0020 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN F 27 GLN I 27 GLN K 27 GLN A 134 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.064818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.049190 restraints weight = 38549.526| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 2.22 r_work: 0.2534 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19999 Z= 0.236 Angle : 0.623 6.443 27121 Z= 0.331 Chirality : 0.046 0.141 2907 Planarity : 0.005 0.069 3464 Dihedral : 5.923 56.648 2926 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.19 % Rotamer: Outliers : 2.36 % Allowed : 18.46 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.80 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.29 (0.16), residues: 964 loop : -0.65 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 177 HIS 0.010 0.002 HIS A 101 PHE 0.013 0.002 PHE J 104 TYR 0.017 0.002 TYR K 49 ARG 0.014 0.001 ARG I 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 7) link_NAG-ASN : angle 1.10715 ( 21) hydrogen bonds : bond 0.03918 ( 650) hydrogen bonds : angle 5.96825 ( 1650) SS BOND : bond 0.00325 ( 40) SS BOND : angle 0.64315 ( 80) covalent geometry : bond 0.00531 (19952) covalent geometry : angle 0.62270 (27020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18029.30 seconds wall clock time: 310 minutes 5.70 seconds (18605.70 seconds total)