Starting phenix.real_space_refine on Sat Jul 4 07:51:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3z_29711/07_2026/8g3z_29711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3z_29711/07_2026/8g3z_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8g3z_29711/07_2026/8g3z_29711.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3z_29711/07_2026/8g3z_29711.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g3z_29711/07_2026/8g3z_29711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3z_29711/07_2026/8g3z_29711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3z_29711/07_2026/8g3z_29711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3z_29711/07_2026/8g3z_29711.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 chiralities: 2 Time building chain proxies: 4.50, per 1000 atoms: 0.23 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: 1.69 Conformation dependent library (CDL) restraints added in 873.1 milliseconds 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: 0.85 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: 4.28 Time building geometry restraints manager: 2.18 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: 10774 17.93 - 35.87: 795 35.87 - 53.80: 199 53.80 - 71.73: 45 71.73 - 89.67: 15 Dihedral angle restraints: 11828 sinusoidal: 4704 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 11825 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 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: 2.410 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: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.730 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 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 : 14.439 89.667 7196 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.050 0.005 ARG D 257 TYR 0.081 0.011 TYR C 409 PHE 0.031 0.007 PHE E 64 TRP 0.045 0.010 TRP J 47 HIS 0.043 0.006 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.01345 / 0.98 (19952) covalent geometry : angle 1.65563 / 1.08 (27020) SS BOND : bond 0.01229 / 0.80 ( 40) SS BOND : angle 1.36820 / 0.91 ( 80) hydrogen bonds : bond 0.13281 / 8.90 ( 650) hydrogen bonds : angle 9.35997 / 6.47 ( 1650) link_NAG-ASN : bond 0.00279 / 0.12 ( 7) link_NAG-ASN : angle 1.51062 / 0.95 ( 21) *********************** 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 : 0.752 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: 0.7031 time to fit residues: 395.2651 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 : 0.762 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN L 92 ASN F 27 GLN G 117 ASN I 27 GLN I 37 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 92 ASN A 134 HIS A 306 ASN C 169 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.056424 restraints weight = 39112.565| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.15 r_work: 0.2710 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19999 Z= 0.151 Angle : 0.665 6.611 27121 Z= 0.360 Chirality : 0.047 0.228 2907 Planarity : 0.004 0.040 3464 Dihedral : 7.336 58.317 2772 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.13 % Favored : 97.71 % Rotamer: Outliers : 2.88 % Allowed : 12.74 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.97 (0.15), residues: 976 loop : -0.94 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 295 TYR 0.023 0.002 TYR K 91 PHE 0.012 0.002 PHE K 83 TRP 0.018 0.002 TRP C 177 HIS 0.007 0.002 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (19952) covalent geometry : angle 0.66392 / 0.36 (27020) SS BOND : bond 0.00246 / 0.13 ( 40) SS BOND : angle 0.78800 / 0.52 ( 80) hydrogen bonds : bond 0.04333 / 2.93 ( 650) hydrogen bonds : angle 6.80965 / 4.74 ( 1650) link_NAG-ASN : bond 0.00228 / 0.12 ( 7) link_NAG-ASN : angle 1.10799 / 0.80 ( 21) *********************** 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 405 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 345 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 LYS cc_start: 0.9283 (ptmm) cc_final: 0.9012 (ptmt) REVERT: L 11 LEU cc_start: 0.8737 (tp) cc_final: 0.8357 (tt) REVERT: L 61 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8317 (mtm-85) REVERT: L 93 ASN cc_start: 0.9007 (m110) cc_final: 0.8558 (m-40) REVERT: L 109 ARG cc_start: 0.8498 (ptm160) cc_final: 0.7444 (pmt170) REVERT: E 13 ARG cc_start: 0.8761 (mtp85) cc_final: 0.8128 (mtp85) REVERT: E 46 GLU cc_start: 0.8736 (tt0) cc_final: 0.8492 (tt0) REVERT: E 84 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8803 (p) REVERT: E 111 GLU cc_start: 0.8145 (mp0) cc_final: 0.7940 (mp0) REVERT: F 61 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8170 (mtm-85) REVERT: F 92 ASN cc_start: 0.8577 (t0) cc_final: 0.8180 (m-40) REVERT: F 108 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8825 (ttmm) REVERT: F 109 ARG cc_start: 0.8330 (ptm160) cc_final: 0.7330 (pmt170) REVERT: G 13 ARG cc_start: 0.8714 (mtp85) cc_final: 0.8069 (mtp85) REVERT: G 43 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7910 (mp10) REVERT: G 46 GLU cc_start: 0.8790 (tt0) cc_final: 0.8446 (tt0) REVERT: G 63 LYS cc_start: 0.9392 (tttm) cc_final: 0.9083 (tttt) REVERT: G 98 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8363 (ttp-110) REVERT: I 61 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8352 (mtm-85) REVERT: I 81 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8652 (pm20) REVERT: I 93 ASN cc_start: 0.9031 (m110) cc_final: 0.8663 (m-40) REVERT: I 109 ARG cc_start: 0.8532 (ptm160) cc_final: 0.7492 (pmt170) REVERT: J 13 ARG cc_start: 0.8714 (mtp85) cc_final: 0.8152 (mtp85) REVERT: J 43 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7896 (mp10) REVERT: J 46 GLU cc_start: 0.8725 (tt0) cc_final: 0.8481 (tt0) REVERT: K 82 ASP cc_start: 0.8240 (m-30) cc_final: 0.7949 (m-30) REVERT: K 104 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8300 (tttt) REVERT: K 109 ARG cc_start: 0.8397 (ptm160) cc_final: 0.7634 (pmt170) REVERT: A 270 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8525 (tmt170) REVERT: A 285 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8273 (ttmm) REVERT: A 292 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7074 (ttm170) REVERT: A 369 MET cc_start: 0.9276 (mmp) cc_final: 0.8963 (mmm) REVERT: B 403 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8671 (tpp) REVERT: C 409 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.5753 (t80) REVERT: D 138 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8576 (tm-30) outliers start: 60 outliers final: 20 residues processed: 382 average time/residue: 0.7793 time to fit residues: 329.1972 Evaluate side-chains 356 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 329 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 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 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 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 229 CYS 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 201 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN F 27 GLN I 27 GLN K 27 GLN D 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.062129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.046706 restraints weight = 39284.617| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 2.15 r_work: 0.2465 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2351 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.075 19999 Z= 0.475 Angle : 0.780 10.027 27121 Z= 0.415 Chirality : 0.053 0.176 2907 Planarity : 0.006 0.062 3464 Dihedral : 7.191 58.984 2767 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.19 % Rotamer: Outliers : 4.47 % Allowed : 13.22 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.65 (0.16), residues: 976 loop : -0.86 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 102 TYR 0.021 0.002 TYR L 49 PHE 0.022 0.003 PHE E 104 TRP 0.015 0.002 TRP J 36 HIS 0.015 0.003 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01068 / 0.48 (19952) covalent geometry : angle 0.77941 / 0.42 (27020) SS BOND : bond 0.00727 / 0.37 ( 40) SS BOND : angle 0.94654 / 0.62 ( 80) hydrogen bonds : bond 0.05430 / 3.63 ( 650) hydrogen bonds : angle 6.71229 / 4.63 ( 1650) link_NAG-ASN : bond 0.00394 / 0.19 ( 7) link_NAG-ASN : angle 1.09686 / 0.69 ( 21) *********************** 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 391 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 298 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 ARG cc_start: 0.8803 (mtp85) cc_final: 0.7977 (mtp85) REVERT: H 46 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8651 (tt0) REVERT: H 76 THR cc_start: 0.9121 (p) cc_final: 0.8834 (t) REVERT: L 93 ASN cc_start: 0.9032 (m110) cc_final: 0.8749 (m-40) REVERT: L 109 ARG cc_start: 0.8647 (ptm160) cc_final: 0.7377 (pmt170) REVERT: E 13 ARG cc_start: 0.8845 (mtp85) cc_final: 0.8123 (mtp85) REVERT: E 46 GLU cc_start: 0.8837 (tt0) cc_final: 0.8143 (tt0) REVERT: E 63 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8633 (ttpt) REVERT: E 76 THR cc_start: 0.9113 (p) cc_final: 0.8845 (t) REVERT: E 84 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8816 (p) REVERT: F 81 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: F 92 ASN cc_start: 0.8640 (t0) cc_final: 0.8277 (m-40) REVERT: F 109 ARG cc_start: 0.8537 (ptm160) cc_final: 0.7330 (pmt170) REVERT: G 13 ARG cc_start: 0.8868 (mtp85) cc_final: 0.8136 (mtp85) REVERT: G 43 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8089 (mp10) REVERT: G 46 GLU cc_start: 0.8864 (tt0) cc_final: 0.8557 (tt0) REVERT: G 63 LYS cc_start: 0.9328 (tttm) cc_final: 0.9112 (tttt) REVERT: G 76 THR cc_start: 0.9106 (p) cc_final: 0.8842 (t) REVERT: G 84 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8887 (p) REVERT: I 61 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8463 (mtm-85) REVERT: I 93 ASN cc_start: 0.9054 (m110) cc_final: 0.8780 (m-40) REVERT: I 109 ARG cc_start: 0.8656 (ptm160) cc_final: 0.7325 (pmt170) REVERT: J 43 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8028 (mp10) REVERT: J 46 GLU cc_start: 0.8823 (tt0) cc_final: 0.8585 (tt0) REVERT: J 76 THR cc_start: 0.9105 (p) cc_final: 0.8842 (t) REVERT: K 81 GLU cc_start: 0.8816 (pm20) cc_final: 0.8216 (pm20) REVERT: K 82 ASP cc_start: 0.8534 (m-30) cc_final: 0.8069 (m-30) REVERT: K 104 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8330 (tttt) REVERT: K 109 ARG cc_start: 0.8590 (ptm160) cc_final: 0.7459 (pmt170) REVERT: A 239 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8844 (tmt) REVERT: A 268 THR cc_start: 0.9032 (m) cc_final: 0.8765 (p) REVERT: A 292 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.6489 (ttm170) REVERT: B 239 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8848 (tmt) REVERT: C 239 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8822 (tmt) REVERT: C 268 THR cc_start: 0.9043 (m) cc_final: 0.8677 (p) REVERT: D 239 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8834 (tmt) REVERT: D 268 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8701 (p) outliers start: 93 outliers final: 31 residues processed: 356 average time/residue: 0.8153 time to fit residues: 319.9318 Evaluate side-chains 332 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU 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 E residue 63 LYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain K residue 7 SER 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 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 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 307 VAL 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 409 TYR Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain D residue 81 THR 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 268 THR 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 28 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 217 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 ASN K 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.050818 restraints weight = 38683.346| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.16 r_work: 0.2574 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19999 Z= 0.147 Angle : 0.595 5.930 27121 Z= 0.318 Chirality : 0.045 0.145 2907 Planarity : 0.004 0.034 3464 Dihedral : 6.586 56.722 2764 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 2.26 % Allowed : 15.96 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.56 (0.16), residues: 976 loop : -0.79 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 54 TYR 0.016 0.001 TYR K 91 PHE 0.018 0.001 PHE I 83 TRP 0.014 0.001 TRP A 177 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (19952) covalent geometry : angle 0.59498 / 0.32 (27020) SS BOND : bond 0.00266 / 0.14 ( 40) SS BOND : angle 0.56190 / 0.37 ( 80) hydrogen bonds : bond 0.03919 / 2.62 ( 650) hydrogen bonds : angle 6.31804 / 4.37 ( 1650) link_NAG-ASN : bond 0.00169 / 0.08 ( 7) link_NAG-ASN : angle 0.96436 / 0.61 ( 21) *********************** 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 367 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 0.770 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: 0.8869 (mtp85) cc_final: 0.8054 (mtp85) REVERT: H 46 GLU cc_start: 0.8866 (tt0) cc_final: 0.8637 (tt0) REVERT: H 62 GLN cc_start: 0.8864 (tt0) cc_final: 0.8579 (tp-100) REVERT: H 76 THR cc_start: 0.9156 (p) cc_final: 0.8877 (t) REVERT: L 11 LEU cc_start: 0.8688 (tp) cc_final: 0.8316 (tt) REVERT: L 93 ASN cc_start: 0.8985 (m110) cc_final: 0.8540 (m-40) REVERT: L 109 ARG cc_start: 0.8605 (ptm160) cc_final: 0.7360 (pmt170) REVERT: E 13 ARG cc_start: 0.8911 (mtp85) cc_final: 0.8637 (mtp85) REVERT: E 43 GLN cc_start: 0.7902 (tt0) cc_final: 0.7625 (mp10) REVERT: E 46 GLU cc_start: 0.8803 (tt0) cc_final: 0.8601 (tt0) REVERT: E 76 THR cc_start: 0.9140 (p) cc_final: 0.8882 (t) REVERT: E 84 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8871 (p) REVERT: F 81 GLU cc_start: 0.8948 (pm20) cc_final: 0.8326 (pm20) REVERT: F 92 ASN cc_start: 0.8608 (t0) cc_final: 0.8325 (m-40) REVERT: F 93 ASN cc_start: 0.9041 (m110) cc_final: 0.8614 (m-40) REVERT: F 109 ARG cc_start: 0.8523 (ptm160) cc_final: 0.7314 (pmt170) REVERT: G 13 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8217 (mtp85) REVERT: G 46 GLU cc_start: 0.8820 (tt0) cc_final: 0.8514 (tt0) REVERT: G 63 LYS cc_start: 0.9330 (tttm) cc_final: 0.9118 (tttt) REVERT: G 76 THR cc_start: 0.9136 (p) cc_final: 0.8878 (t) REVERT: G 98 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7879 (ttp-110) REVERT: I 93 ASN cc_start: 0.8978 (m110) cc_final: 0.8561 (m-40) REVERT: I 109 ARG cc_start: 0.8603 (ptm160) cc_final: 0.7381 (pmt170) REVERT: J 13 ARG cc_start: 0.8861 (mtp85) cc_final: 0.8092 (mtp85) REVERT: J 76 THR cc_start: 0.9136 (p) cc_final: 0.8895 (t) REVERT: K 11 LEU cc_start: 0.8528 (tp) cc_final: 0.8318 (tp) REVERT: K 81 GLU cc_start: 0.8881 (pm20) cc_final: 0.8384 (pm20) REVERT: K 82 ASP cc_start: 0.8524 (m-30) cc_final: 0.8048 (m-30) REVERT: K 104 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8399 (tttt) REVERT: K 109 ARG cc_start: 0.8579 (ptm160) cc_final: 0.7443 (pmt170) REVERT: A 268 THR cc_start: 0.9075 (m) cc_final: 0.8760 (p) REVERT: A 285 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8049 (mttm) REVERT: B 239 MET cc_start: 0.9069 (ttp) cc_final: 0.8613 (tmt) REVERT: B 268 THR cc_start: 0.9054 (m) cc_final: 0.8677 (p) REVERT: B 285 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8364 (mttp) REVERT: C 239 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8608 (tmt) REVERT: C 268 THR cc_start: 0.9102 (m) cc_final: 0.8821 (p) REVERT: C 285 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8170 (mttp) REVERT: D 239 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8629 (tmt) REVERT: D 342 ASP cc_start: 0.8712 (m-30) cc_final: 0.8256 (p0) outliers start: 47 outliers final: 30 residues processed: 359 average time/residue: 0.7947 time to fit residues: 314.3790 Evaluate side-chains 329 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 295 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 G residue 98 ARG Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 47 LEU 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 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 171 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 32 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN G 3 GLN I 27 GLN J 3 GLN K 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.049464 restraints weight = 38791.231| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.14 r_work: 0.2541 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19999 Z= 0.219 Angle : 0.605 5.890 27121 Z= 0.322 Chirality : 0.046 0.142 2907 Planarity : 0.004 0.035 3464 Dihedral : 6.451 58.610 2764 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.19 % Rotamer: Outliers : 3.61 % Allowed : 15.91 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.53 (0.16), residues: 988 loop : -0.74 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 24 TYR 0.017 0.002 TYR K 91 PHE 0.019 0.002 PHE I 83 TRP 0.011 0.001 TRP A 177 HIS 0.009 0.002 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (19952) covalent geometry : angle 0.60446 / 0.32 (27020) SS BOND : bond 0.00326 / 0.18 ( 40) SS BOND : angle 0.62988 / 0.41 ( 80) hydrogen bonds : bond 0.04130 / 2.77 ( 650) hydrogen bonds : angle 6.20300 / 4.28 ( 1650) link_NAG-ASN : bond 0.00146 / 0.08 ( 7) link_NAG-ASN : angle 0.99335 / 0.62 ( 21) *********************** 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 383 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 308 time to evaluate : 0.796 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: 0.8876 (mtp85) cc_final: 0.8063 (mtp85) REVERT: H 46 GLU cc_start: 0.8859 (tt0) cc_final: 0.8623 (tt0) REVERT: H 62 GLN cc_start: 0.8868 (tt0) cc_final: 0.8588 (tp-100) REVERT: H 76 THR cc_start: 0.9143 (p) cc_final: 0.8891 (t) REVERT: L 93 ASN cc_start: 0.9024 (m110) cc_final: 0.8549 (m-40) REVERT: L 109 ARG cc_start: 0.8603 (ptm160) cc_final: 0.7388 (pmt170) REVERT: E 13 ARG cc_start: 0.8931 (mtp85) cc_final: 0.8674 (mtp85) REVERT: E 43 GLN cc_start: 0.7962 (tt0) cc_final: 0.7674 (mp10) REVERT: E 46 GLU cc_start: 0.8832 (tt0) cc_final: 0.8568 (tt0) REVERT: E 76 THR cc_start: 0.9124 (p) cc_final: 0.8878 (t) REVERT: E 84 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8872 (p) REVERT: F 81 GLU cc_start: 0.8982 (pm20) cc_final: 0.8376 (pm20) REVERT: F 92 ASN cc_start: 0.8586 (t0) cc_final: 0.8336 (m-40) REVERT: F 93 ASN cc_start: 0.9094 (m110) cc_final: 0.8650 (m-40) REVERT: F 108 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8886 (ttmm) REVERT: F 109 ARG cc_start: 0.8529 (ptm160) cc_final: 0.7299 (pmt170) REVERT: G 13 ARG cc_start: 0.8946 (mtp85) cc_final: 0.8192 (mtp85) REVERT: G 46 GLU cc_start: 0.8839 (tt0) cc_final: 0.8549 (tt0) REVERT: G 76 THR cc_start: 0.9112 (p) cc_final: 0.8873 (t) REVERT: G 84 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8970 (p) REVERT: I 93 ASN cc_start: 0.8996 (m110) cc_final: 0.8555 (m-40) REVERT: I 109 ARG cc_start: 0.8574 (ptm160) cc_final: 0.7362 (pmt170) REVERT: J 13 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8028 (mtp85) REVERT: J 76 THR cc_start: 0.9124 (p) cc_final: 0.8891 (t) REVERT: K 81 GLU cc_start: 0.8867 (pm20) cc_final: 0.8422 (pm20) REVERT: K 82 ASP cc_start: 0.8550 (m-30) cc_final: 0.8075 (m-30) REVERT: K 104 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8425 (tttt) REVERT: K 109 ARG cc_start: 0.8631 (ptm160) cc_final: 0.7390 (pmt170) REVERT: A 268 THR cc_start: 0.9085 (m) cc_final: 0.8818 (p) REVERT: A 285 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8092 (mttm) REVERT: B 153 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9064 (mm) REVERT: B 239 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8624 (tmt) REVERT: B 268 THR cc_start: 0.9062 (m) cc_final: 0.8790 (p) REVERT: B 285 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8276 (mttm) REVERT: B 292 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7356 (ttm170) REVERT: C 153 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9074 (mm) REVERT: C 239 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8576 (tmt) REVERT: C 268 THR cc_start: 0.9134 (m) cc_final: 0.8921 (p) REVERT: C 285 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8206 (mttp) REVERT: D 239 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8594 (tmt) REVERT: D 263 LYS cc_start: 0.9065 (tttp) cc_final: 0.8803 (ttpt) REVERT: D 285 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8257 (mttp) REVERT: D 342 ASP cc_start: 0.8729 (m-30) cc_final: 0.8306 (p0) outliers start: 75 outliers final: 36 residues processed: 360 average time/residue: 0.7376 time to fit residues: 292.8880 Evaluate side-chains 350 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 48 MET 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 74 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 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 456 TRP Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN 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 292 ARG Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 456 TRP 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 171 ILE 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 110 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 177 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN L 27 GLN G 3 GLN I 27 GLN K 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.048128 restraints weight = 38778.185| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 2.15 r_work: 0.2505 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 19999 Z= 0.296 Angle : 0.638 6.651 27121 Z= 0.341 Chirality : 0.047 0.171 2907 Planarity : 0.005 0.050 3464 Dihedral : 6.522 57.891 2764 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.85 % Favored : 96.99 % Rotamer: Outliers : 3.70 % Allowed : 15.87 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.45 (0.16), residues: 984 loop : -0.76 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 24 TYR 0.018 0.002 TYR K 91 PHE 0.017 0.002 PHE I 83 TRP 0.013 0.001 TRP A 177 HIS 0.011 0.002 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.30 (19952) covalent geometry : angle 0.63710 / 0.34 (27020) SS BOND : bond 0.00397 / 0.21 ( 40) SS BOND : angle 0.69127 / 0.46 ( 80) hydrogen bonds : bond 0.04370 / 2.94 ( 650) hydrogen bonds : angle 6.22652 / 4.29 ( 1650) link_NAG-ASN : bond 0.00245 / 0.13 ( 7) link_NAG-ASN : angle 1.05363 / 0.66 ( 21) *********************** 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 393 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 316 time to evaluate : 0.777 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: 0.8872 (mtp85) cc_final: 0.8030 (mtp85) REVERT: H 46 GLU cc_start: 0.8868 (tt0) cc_final: 0.8591 (tt0) REVERT: H 62 GLN cc_start: 0.8888 (tt0) cc_final: 0.8596 (tp-100) REVERT: H 76 THR cc_start: 0.9110 (p) cc_final: 0.8893 (t) REVERT: L 81 GLU cc_start: 0.8882 (pm20) cc_final: 0.8233 (pm20) REVERT: L 93 ASN cc_start: 0.9072 (m110) cc_final: 0.8578 (m-40) REVERT: L 109 ARG cc_start: 0.8649 (ptm160) cc_final: 0.7326 (pmt170) REVERT: E 13 ARG cc_start: 0.8932 (mtp85) cc_final: 0.8149 (mtp85) REVERT: E 43 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: E 46 GLU cc_start: 0.8827 (tt0) cc_final: 0.8598 (tt0) REVERT: E 76 THR cc_start: 0.9088 (p) cc_final: 0.8872 (t) REVERT: E 84 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8843 (p) REVERT: F 81 GLU cc_start: 0.8998 (pm20) cc_final: 0.8432 (pm20) REVERT: F 92 ASN cc_start: 0.8585 (t0) cc_final: 0.8319 (m-40) REVERT: F 93 ASN cc_start: 0.9115 (m110) cc_final: 0.8676 (m-40) REVERT: F 109 ARG cc_start: 0.8577 (ptm160) cc_final: 0.7260 (pmt170) REVERT: G 13 ARG cc_start: 0.8947 (mtp85) cc_final: 0.8161 (mtp85) REVERT: G 46 GLU cc_start: 0.8836 (tt0) cc_final: 0.8565 (tt0) REVERT: G 76 THR cc_start: 0.9091 (p) cc_final: 0.8877 (t) REVERT: G 84 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8975 (p) REVERT: I 93 ASN cc_start: 0.9015 (m110) cc_final: 0.8505 (m-40) REVERT: I 107 ILE cc_start: 0.8462 (pp) cc_final: 0.8244 (mp) REVERT: I 109 ARG cc_start: 0.8603 (ptm160) cc_final: 0.7373 (pmt170) REVERT: J 13 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8032 (mtp85) REVERT: J 76 THR cc_start: 0.9059 (p) cc_final: 0.8833 (t) REVERT: K 81 GLU cc_start: 0.8933 (pm20) cc_final: 0.8443 (pm20) REVERT: K 82 ASP cc_start: 0.8630 (m-30) cc_final: 0.8027 (m-30) REVERT: K 104 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8424 (tttt) REVERT: K 109 ARG cc_start: 0.8665 (ptm160) cc_final: 0.7330 (pmt170) REVERT: A 153 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9100 (mm) REVERT: A 263 LYS cc_start: 0.9032 (tttp) cc_final: 0.8743 (ttpt) REVERT: A 268 THR cc_start: 0.9073 (m) cc_final: 0.8809 (p) REVERT: A 285 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8133 (mttp) REVERT: A 453 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: B 153 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9109 (mm) REVERT: B 239 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8675 (tmt) REVERT: B 268 THR cc_start: 0.9100 (m) cc_final: 0.8834 (p) REVERT: B 285 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8226 (mttm) REVERT: B 292 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.7410 (ttm170) REVERT: C 153 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9116 (mm) REVERT: C 239 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8692 (tmt) REVERT: C 285 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8207 (mttp) REVERT: D 239 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8707 (tmt) REVERT: D 263 LYS cc_start: 0.9094 (tttp) cc_final: 0.8800 (ttpt) REVERT: D 285 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8193 (mttp) REVERT: D 342 ASP cc_start: 0.8743 (m-30) cc_final: 0.8310 (p0) REVERT: D 453 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8114 (mt0) outliers start: 77 outliers final: 45 residues processed: 374 average time/residue: 0.7769 time to fit residues: 320.3982 Evaluate side-chains 362 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 305 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 48 MET 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 G residue 48 MET Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 SER 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 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 135 TYR Chi-restraints excluded: chain A residue 153 LEU 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 85 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 ASN 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 264 GLU 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 85 LEU 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 171 ILE Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 264 GLU 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 85 LEU Chi-restraints excluded: chain D residue 110 SER 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 453 GLN 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 101 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 229 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN I 27 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 = 0.2998 r_free = 0.2998 target = 0.065445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.050156 restraints weight = 38693.926| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 2.20 r_work: 0.2561 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19999 Z= 0.156 Angle : 0.595 6.159 27121 Z= 0.317 Chirality : 0.045 0.204 2907 Planarity : 0.004 0.051 3464 Dihedral : 6.213 58.260 2762 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 2.98 % Allowed : 17.36 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.37 (0.16), residues: 976 loop : -0.66 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 24 TYR 0.017 0.001 TYR K 91 PHE 0.016 0.001 PHE I 83 TRP 0.014 0.001 TRP D 177 HIS 0.008 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (19952) covalent geometry : angle 0.59425 / 0.32 (27020) SS BOND : bond 0.00245 / 0.13 ( 40) SS BOND : angle 0.53569 / 0.35 ( 80) hydrogen bonds : bond 0.03627 / 2.44 ( 650) hydrogen bonds : angle 6.01554 / 4.15 ( 1650) link_NAG-ASN : bond 0.00037 / 0.02 ( 7) link_NAG-ASN : angle 1.07295 / 0.67 ( 21) *********************** 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 387 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 325 time to evaluate : 0.584 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: 0.8910 (mtp85) cc_final: 0.8096 (mtp85) REVERT: H 46 GLU cc_start: 0.8804 (tt0) cc_final: 0.8584 (tt0) REVERT: H 62 GLN cc_start: 0.8867 (tt0) cc_final: 0.8561 (tp-100) REVERT: L 48 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7719 (mm) REVERT: L 81 GLU cc_start: 0.8861 (pm20) cc_final: 0.8279 (pm20) REVERT: L 93 ASN cc_start: 0.8976 (m110) cc_final: 0.8412 (m-40) REVERT: L 109 ARG cc_start: 0.8627 (ptm160) cc_final: 0.7328 (pmt170) REVERT: E 13 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8670 (mtp85) REVERT: E 43 GLN cc_start: 0.8014 (tt0) cc_final: 0.7742 (mp10) REVERT: E 46 GLU cc_start: 0.8797 (tt0) cc_final: 0.8504 (tt0) REVERT: F 81 GLU cc_start: 0.9023 (pm20) cc_final: 0.8435 (pm20) REVERT: F 92 ASN cc_start: 0.8519 (t0) cc_final: 0.8273 (m-40) REVERT: F 93 ASN cc_start: 0.9041 (m110) cc_final: 0.8571 (m-40) REVERT: F 109 ARG cc_start: 0.8535 (ptm160) cc_final: 0.7216 (pmt170) REVERT: G 13 ARG cc_start: 0.8936 (mtp85) cc_final: 0.8138 (mtp85) REVERT: G 46 GLU cc_start: 0.8818 (tt0) cc_final: 0.8476 (tt0) REVERT: I 17 GLU cc_start: 0.7567 (mp0) cc_final: 0.7218 (mp0) REVERT: I 93 ASN cc_start: 0.8962 (m110) cc_final: 0.8433 (m-40) REVERT: I 106 GLU cc_start: 0.6345 (tp30) cc_final: 0.6095 (tp30) REVERT: I 107 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8133 (mp) REVERT: I 109 ARG cc_start: 0.8557 (ptm160) cc_final: 0.7382 (pmt170) REVERT: J 13 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8043 (mtp85) REVERT: J 62 GLN cc_start: 0.8773 (tt0) cc_final: 0.8412 (tp-100) REVERT: K 81 GLU cc_start: 0.8878 (pm20) cc_final: 0.8457 (pm20) REVERT: K 82 ASP cc_start: 0.8631 (m-30) cc_final: 0.8211 (m-30) REVERT: K 109 ARG cc_start: 0.8650 (ptm160) cc_final: 0.7300 (pmt170) REVERT: A 153 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9007 (mm) REVERT: A 263 LYS cc_start: 0.9036 (tttp) cc_final: 0.8730 (ttpt) REVERT: A 268 THR cc_start: 0.9040 (m) cc_final: 0.8816 (p) REVERT: A 270 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8615 (tmt170) REVERT: A 285 LYS cc_start: 0.8537 (mtpp) cc_final: 0.7954 (mttm) REVERT: B 239 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8618 (tmt) REVERT: B 268 THR cc_start: 0.9061 (m) cc_final: 0.8834 (p) REVERT: B 285 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8147 (mttm) REVERT: B 292 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.7136 (ttm170) REVERT: C 153 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9011 (mm) REVERT: C 239 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8592 (tmt) REVERT: C 285 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8095 (mttm) REVERT: D 239 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8592 (tmt) REVERT: D 263 LYS cc_start: 0.9061 (tttp) cc_final: 0.8735 (ttpt) REVERT: D 285 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8104 (mttm) REVERT: D 292 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7650 (ttm170) REVERT: D 342 ASP cc_start: 0.8721 (m-30) cc_final: 0.8344 (p0) outliers start: 62 outliers final: 29 residues processed: 373 average time/residue: 0.7263 time to fit residues: 298.8876 Evaluate side-chains 350 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL 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 103 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain I residue 7 SER 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 K residue 74 THR Chi-restraints excluded: chain A residue 153 LEU 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 151 ASN 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 325 THR Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 171 ILE 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 110 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 207 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN L 27 GLN E 3 GLN F 27 GLN G 3 GLN I 27 GLN K 27 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.048992 restraints weight = 38570.890| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.22 r_work: 0.2529 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19999 Z= 0.229 Angle : 0.615 5.901 27121 Z= 0.327 Chirality : 0.046 0.210 2907 Planarity : 0.004 0.034 3464 Dihedral : 6.244 59.348 2762 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.11 % Rotamer: Outliers : 2.98 % Allowed : 17.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.32 (0.16), residues: 976 loop : -0.67 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 100 TYR 0.016 0.002 TYR K 91 PHE 0.016 0.002 PHE I 83 TRP 0.015 0.001 TRP K 94 HIS 0.010 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (19952) covalent geometry : angle 0.61410 / 0.33 (27020) SS BOND : bond 0.00326 / 0.17 ( 40) SS BOND : angle 0.64411 / 0.43 ( 80) hydrogen bonds : bond 0.03936 / 2.66 ( 650) hydrogen bonds : angle 6.00028 / 4.13 ( 1650) link_NAG-ASN : bond 0.00155 / 0.08 ( 7) link_NAG-ASN : angle 1.06483 / 0.67 ( 21) *********************** 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 374 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 312 time to evaluate : 0.789 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: 0.8091 (mtp85) REVERT: H 46 GLU cc_start: 0.8823 (tt0) cc_final: 0.8536 (tt0) REVERT: H 62 GLN cc_start: 0.8883 (tt0) cc_final: 0.8573 (tp-100) REVERT: H 73 ASP cc_start: 0.8167 (t0) cc_final: 0.7927 (t0) REVERT: L 17 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: L 48 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7787 (mm) REVERT: L 81 GLU cc_start: 0.8847 (pm20) cc_final: 0.8281 (pm20) REVERT: L 93 ASN cc_start: 0.9028 (m110) cc_final: 0.8488 (m-40) REVERT: L 109 ARG cc_start: 0.8641 (ptm160) cc_final: 0.7323 (pmt170) REVERT: E 13 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8669 (mtp85) REVERT: E 43 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: E 46 GLU cc_start: 0.8805 (tt0) cc_final: 0.8548 (tt0) REVERT: F 17 GLU cc_start: 0.8732 (pt0) cc_final: 0.8277 (pm20) REVERT: F 81 GLU cc_start: 0.9013 (pm20) cc_final: 0.8428 (pm20) REVERT: F 92 ASN cc_start: 0.8525 (t0) cc_final: 0.8256 (m-40) REVERT: F 93 ASN cc_start: 0.9091 (m110) cc_final: 0.8643 (m-40) REVERT: F 109 ARG cc_start: 0.8550 (ptm160) cc_final: 0.7207 (pmt170) REVERT: G 13 ARG cc_start: 0.8939 (mtp85) cc_final: 0.8115 (mtp85) REVERT: G 46 GLU cc_start: 0.8815 (tt0) cc_final: 0.8552 (tt0) REVERT: I 17 GLU cc_start: 0.7699 (mp0) cc_final: 0.7341 (mp0) REVERT: I 81 GLU cc_start: 0.8908 (pm20) cc_final: 0.8218 (pm20) REVERT: I 93 ASN cc_start: 0.8986 (m110) cc_final: 0.8451 (m-40) REVERT: I 106 GLU cc_start: 0.6385 (tp30) cc_final: 0.6170 (tp30) REVERT: I 107 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8133 (mp) REVERT: I 109 ARG cc_start: 0.8580 (ptm160) cc_final: 0.7386 (pmt170) REVERT: J 13 ARG cc_start: 0.8864 (mtp85) cc_final: 0.8040 (mtp85) REVERT: J 62 GLN cc_start: 0.8789 (tt0) cc_final: 0.8434 (tp-100) REVERT: K 17 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: K 81 GLU cc_start: 0.8878 (pm20) cc_final: 0.8470 (pm20) REVERT: K 82 ASP cc_start: 0.8551 (m-30) cc_final: 0.8134 (m-30) REVERT: K 109 ARG cc_start: 0.8672 (ptm160) cc_final: 0.7296 (pmt170) REVERT: A 153 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9046 (mm) REVERT: A 263 LYS cc_start: 0.9052 (tttp) cc_final: 0.8720 (ttpt) REVERT: A 268 THR cc_start: 0.9039 (m) cc_final: 0.8795 (p) REVERT: A 285 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8024 (mttm) REVERT: B 239 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8611 (tmt) REVERT: B 268 THR cc_start: 0.9058 (m) cc_final: 0.8846 (p) REVERT: B 285 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8184 (mttm) REVERT: C 239 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8543 (tmt) REVERT: C 285 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8192 (mttp) REVERT: D 239 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8586 (tmt) REVERT: D 263 LYS cc_start: 0.9054 (tttp) cc_final: 0.8728 (ttpt) REVERT: D 285 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8175 (mttp) REVERT: D 342 ASP cc_start: 0.8732 (m-30) cc_final: 0.8365 (p0) outliers start: 62 outliers final: 37 residues processed: 361 average time/residue: 0.7244 time to fit residues: 288.4214 Evaluate side-chains 355 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 309 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 17 GLU 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 103 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain I residue 7 SER 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 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 153 LEU 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 85 LEU Chi-restraints excluded: chain B residue 151 ASN 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 110 SER Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 171 ILE 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 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 126 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2983 r_free = 0.2983 target = 0.064749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.049164 restraints weight = 38187.438| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.21 r_work: 0.2534 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 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 : 0.005 0.039 19999 Z= 0.219 Angle : 0.611 5.753 27121 Z= 0.325 Chirality : 0.046 0.145 2907 Planarity : 0.005 0.062 3464 Dihedral : 6.234 59.346 2762 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 2.60 % Allowed : 18.41 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.32 (0.16), residues: 976 loop : -0.66 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 24 TYR 0.017 0.002 TYR K 91 PHE 0.015 0.002 PHE I 83 TRP 0.013 0.001 TRP K 94 HIS 0.009 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (19952) covalent geometry : angle 0.61033 / 0.32 (27020) SS BOND : bond 0.00322 / 0.17 ( 40) SS BOND : angle 0.62251 / 0.41 ( 80) hydrogen bonds : bond 0.03857 / 2.61 ( 650) hydrogen bonds : angle 6.00758 / 4.13 ( 1650) link_NAG-ASN : bond 0.00117 / 0.06 ( 7) link_NAG-ASN : angle 1.08487 / 0.69 ( 21) *********************** 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 365 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.806 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: H 46 GLU cc_start: 0.8810 (tt0) cc_final: 0.8512 (tt0) REVERT: H 62 GLN cc_start: 0.8878 (tt0) cc_final: 0.8569 (tp-100) REVERT: H 73 ASP cc_start: 0.8172 (t0) cc_final: 0.7929 (t0) REVERT: L 3 VAL cc_start: 0.9515 (t) cc_final: 0.9225 (p) REVERT: L 17 GLU cc_start: 0.8747 (pt0) cc_final: 0.8301 (pm20) REVERT: L 48 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7802 (mm) REVERT: L 93 ASN cc_start: 0.9022 (m110) cc_final: 0.8499 (m-40) REVERT: L 109 ARG cc_start: 0.8644 (ptm160) cc_final: 0.7325 (pmt170) REVERT: E 13 ARG cc_start: 0.8928 (mtp85) cc_final: 0.8672 (mtp85) REVERT: E 43 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: E 46 GLU cc_start: 0.8826 (tt0) cc_final: 0.8599 (tt0) REVERT: F 17 GLU cc_start: 0.8764 (pt0) cc_final: 0.8358 (pm20) REVERT: F 81 GLU cc_start: 0.9024 (pm20) cc_final: 0.8450 (pm20) REVERT: F 92 ASN cc_start: 0.8527 (t0) cc_final: 0.8261 (m-40) REVERT: F 93 ASN cc_start: 0.9064 (m110) cc_final: 0.8618 (m-40) REVERT: F 109 ARG cc_start: 0.8565 (ptm160) cc_final: 0.7211 (pmt170) REVERT: G 13 ARG cc_start: 0.8943 (mtp85) cc_final: 0.8126 (mtp85) REVERT: G 46 GLU cc_start: 0.8845 (tt0) cc_final: 0.8587 (tt0) REVERT: I 3 VAL cc_start: 0.9489 (t) cc_final: 0.9188 (p) REVERT: I 17 GLU cc_start: 0.7727 (mp0) cc_final: 0.7356 (mp0) REVERT: I 81 GLU cc_start: 0.8878 (pm20) cc_final: 0.8253 (pm20) REVERT: I 82 ASP cc_start: 0.8860 (m-30) cc_final: 0.8489 (m-30) REVERT: I 93 ASN cc_start: 0.8996 (m110) cc_final: 0.8432 (m-40) REVERT: I 104 LYS cc_start: 0.8735 (tttp) cc_final: 0.8526 (tttp) REVERT: I 106 GLU cc_start: 0.6382 (tp30) cc_final: 0.6180 (tp30) REVERT: I 107 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8137 (mp) REVERT: I 109 ARG cc_start: 0.8591 (ptm160) cc_final: 0.7393 (pmt170) REVERT: J 62 GLN cc_start: 0.8783 (tt0) cc_final: 0.8402 (tp-100) REVERT: K 17 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8241 (pm20) REVERT: K 81 GLU cc_start: 0.8867 (pm20) cc_final: 0.8353 (pm20) REVERT: K 109 ARG cc_start: 0.8685 (ptm160) cc_final: 0.7241 (pmt170) REVERT: A 263 LYS cc_start: 0.9040 (tttp) cc_final: 0.8712 (ttpt) REVERT: A 268 THR cc_start: 0.9036 (m) cc_final: 0.8798 (p) REVERT: A 285 LYS cc_start: 0.8554 (mtpp) cc_final: 0.7985 (mttm) REVERT: B 268 THR cc_start: 0.9054 (m) cc_final: 0.8852 (p) REVERT: B 285 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8240 (mttp) REVERT: B 373 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8353 (mtpp) REVERT: C 239 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8594 (tmt) REVERT: C 285 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8184 (mttp) REVERT: D 239 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8571 (tmt) REVERT: D 263 LYS cc_start: 0.9053 (tttp) cc_final: 0.8720 (ttpt) REVERT: D 285 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8163 (mttp) REVERT: D 342 ASP cc_start: 0.8749 (m-30) cc_final: 0.8388 (p0) outliers start: 54 outliers final: 38 residues processed: 354 average time/residue: 0.7662 time to fit residues: 299.2177 Evaluate side-chains 354 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL 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 103 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR 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 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 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 81 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 171 ILE 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 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 89 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN F 27 GLN 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 = 0.3019 r_free = 0.3019 target = 0.066347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.051110 restraints weight = 38244.341| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.19 r_work: 0.2587 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19999 Z= 0.145 Angle : 0.583 6.184 27121 Z= 0.310 Chirality : 0.045 0.202 2907 Planarity : 0.004 0.032 3464 Dihedral : 6.035 59.282 2762 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.77 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 18.99 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2488 helix: None (None), residues: 0 sheet: -0.25 (0.17), residues: 944 loop : -0.59 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 54 TYR 0.016 0.001 TYR K 91 PHE 0.015 0.001 PHE I 83 TRP 0.014 0.001 TRP K 94 HIS 0.008 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (19952) covalent geometry : angle 0.58178 / 0.31 (27020) SS BOND : bond 0.00266 / 0.17 ( 40) SS BOND : angle 0.83511 / 0.56 ( 80) hydrogen bonds : bond 0.03442 / 2.32 ( 650) hydrogen bonds : angle 5.89884 / 4.06 ( 1650) link_NAG-ASN : bond 0.00058 / 0.02 ( 7) link_NAG-ASN : angle 1.12887 / 0.72 ( 21) ********************** 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 366 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 319 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8800 (tt0) cc_final: 0.8489 (tt0) REVERT: H 62 GLN cc_start: 0.8837 (tt0) cc_final: 0.8554 (tp-100) REVERT: H 73 ASP cc_start: 0.8167 (t0) cc_final: 0.7922 (t0) REVERT: H 116 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8793 (mt-10) REVERT: L 3 VAL cc_start: 0.9489 (t) cc_final: 0.9222 (p) REVERT: L 17 GLU cc_start: 0.8789 (pt0) cc_final: 0.8424 (pm20) REVERT: L 48 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7639 (mm) REVERT: L 93 ASN cc_start: 0.8995 (m110) cc_final: 0.8399 (m-40) REVERT: L 109 ARG cc_start: 0.8632 (ptm160) cc_final: 0.7359 (pmt170) REVERT: E 13 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8177 (mtp85) REVERT: E 43 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: E 46 GLU cc_start: 0.8802 (tt0) cc_final: 0.8562 (tt0) REVERT: F 3 VAL cc_start: 0.9492 (t) cc_final: 0.9202 (p) REVERT: F 17 GLU cc_start: 0.8785 (pt0) cc_final: 0.8425 (pm20) REVERT: F 81 GLU cc_start: 0.8997 (pm20) cc_final: 0.8455 (pm20) REVERT: F 92 ASN cc_start: 0.8519 (t0) cc_final: 0.8282 (m-40) REVERT: F 93 ASN cc_start: 0.9045 (m110) cc_final: 0.8548 (m-40) REVERT: F 109 ARG cc_start: 0.8551 (ptm160) cc_final: 0.7198 (pmt170) REVERT: G 12 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8599 (mmtp) REVERT: G 13 ARG cc_start: 0.8962 (mtp85) cc_final: 0.8250 (mtp85) REVERT: G 46 GLU cc_start: 0.8791 (tt0) cc_final: 0.8485 (tt0) REVERT: I 3 VAL cc_start: 0.9467 (t) cc_final: 0.9192 (p) REVERT: I 17 GLU cc_start: 0.7779 (mp0) cc_final: 0.7408 (mp0) REVERT: I 81 GLU cc_start: 0.8863 (pm20) cc_final: 0.8240 (pm20) REVERT: I 82 ASP cc_start: 0.8871 (m-30) cc_final: 0.8507 (m-30) REVERT: I 93 ASN cc_start: 0.8950 (m110) cc_final: 0.8364 (m-40) REVERT: I 104 LYS cc_start: 0.8714 (tttp) cc_final: 0.8509 (tttp) REVERT: I 107 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8194 (mp) REVERT: I 109 ARG cc_start: 0.8559 (ptm160) cc_final: 0.7462 (pmt170) REVERT: J 12 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8610 (mmtp) REVERT: J 62 GLN cc_start: 0.8732 (tt0) cc_final: 0.8383 (tp-100) REVERT: K 3 VAL cc_start: 0.9472 (t) cc_final: 0.9207 (p) REVERT: K 17 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: K 109 ARG cc_start: 0.8635 (ptm160) cc_final: 0.7196 (pmt170) REVERT: A 263 LYS cc_start: 0.9049 (tttp) cc_final: 0.8730 (ttpt) REVERT: A 285 LYS cc_start: 0.8471 (mtpp) cc_final: 0.7916 (mttm) REVERT: B 239 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8599 (tmt) REVERT: B 285 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8250 (mttp) REVERT: B 373 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8362 (mtpp) REVERT: C 239 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8587 (tmt) REVERT: C 285 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8155 (mttm) REVERT: D 239 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8636 (tmt) REVERT: D 263 LYS cc_start: 0.9066 (tttp) cc_final: 0.8730 (ttpt) REVERT: D 285 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8082 (mttm) REVERT: D 292 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7980 (ttm170) REVERT: D 342 ASP cc_start: 0.8704 (m-30) cc_final: 0.8387 (p0) outliers start: 47 outliers final: 29 residues processed: 358 average time/residue: 0.7904 time to fit residues: 312.0327 Evaluate side-chains 344 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 74 THR 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 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 229 CYS Chi-restraints excluded: chain A residue 292 ARG 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 239 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 171 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 47 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN F 27 GLN 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 = 0.2988 r_free = 0.2988 target = 0.064930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.049377 restraints weight = 38509.317| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.21 r_work: 0.2539 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19999 Z= 0.226 Angle : 0.616 6.158 27121 Z= 0.327 Chirality : 0.046 0.227 2907 Planarity : 0.004 0.035 3464 Dihedral : 6.078 56.753 2758 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.85 % Favored : 96.99 % Rotamer: Outliers : 2.16 % Allowed : 19.18 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2488 helix: None (None), residues: 0 sheet: -0.29 (0.16), residues: 960 loop : -0.64 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 61 TYR 0.017 0.002 TYR K 49 PHE 0.017 0.002 PHE I 83 TRP 0.011 0.001 TRP C 177 HIS 0.009 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (19952) covalent geometry : angle 0.61483 / 0.33 (27020) SS BOND : bond 0.00355 / 0.20 ( 40) SS BOND : angle 0.91323 / 0.60 ( 80) hydrogen bonds : bond 0.03841 / 2.60 ( 650) hydrogen bonds : angle 5.95513 / 4.09 ( 1650) link_NAG-ASN : bond 0.00147 / 0.08 ( 7) link_NAG-ASN : angle 1.09269 / 0.70 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8861.28 seconds wall clock time: 151 minutes 38.94 seconds (9098.94 seconds total)