Starting phenix.real_space_refine on Tue Oct 27 14:06:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqu_74582/10_2026/9zqu_74582.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqu_74582/10_2026/9zqu_74582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zqu_74582/10_2026/9zqu_74582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqu_74582/10_2026/9zqu_74582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zqu_74582/10_2026/9zqu_74582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqu_74582/10_2026/9zqu_74582.map" } resolution = 2.18 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= 0.000 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 P 42 5.49 5 S 114 5.16 5 C 14922 2.51 5 N 4164 2.21 5 O 5374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24616 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 469} Chain: "B" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 469} Chain: "C" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 469} Chain: "D" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 469} Chain: "E" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 469} Chain: "F" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3844 Classifications: {'peptide': 491} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 469} Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'GTP': 1, 'NAI': 2} Inner-chain residues flagged as termini: ['pdbres="GGL A 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'GTP': 1, 'NAI': 2} Inner-chain residues flagged as termini: ['pdbres="GGL B 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'GTP': 1, 'NAI': 2} Inner-chain residues flagged as termini: ['pdbres="GGL C 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'GTP': 1, 'NAI': 2} Inner-chain residues flagged as termini: ['pdbres="GGL D 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'GTP': 1, 'NAI': 2} Inner-chain residues flagged as termini: ['pdbres="GGL E 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 130 Unusual residues: {'GTP': 1, 'NAI': 2} Inner-chain residues flagged as termini: ['pdbres="GGL F 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "C" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Classifications: {'water': 133} Link IDs: {None: 132} Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "F" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Time building chain proxies: 4.85, per 1000 atoms: 0.20 Number of scatterers: 24616 At special positions: 0 Unit cell: (122.478, 114.258, 161.934, 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) S 114 16.00 P 42 15.00 O 5374 8.00 N 4164 7.00 C 14922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 969.2 milliseconds 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 9 sheets defined 57.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 removed outlier: 4.950A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 157 through 175 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.599A pdb=" N VAL A 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 420 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 479 Processing helix chain 'A' and resid 490 through 496 removed outlier: 3.667A pdb=" N ARG A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 528 Processing helix chain 'A' and resid 533 through 553 Processing helix chain 'B' and resid 65 through 89 removed outlier: 4.924A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 344 through 356 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.602A pdb=" N VAL B 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 479 Processing helix chain 'B' and resid 490 through 496 removed outlier: 3.666A pdb=" N ARG B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 528 Processing helix chain 'B' and resid 533 through 553 Processing helix chain 'C' and resid 65 through 89 removed outlier: 4.942A pdb=" N ASP C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 110 Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 194 through 212 Processing helix chain 'C' and resid 229 through 244 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.601A pdb=" N VAL C 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 420 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 479 Processing helix chain 'C' and resid 490 through 496 removed outlier: 3.656A pdb=" N ARG C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 528 Processing helix chain 'C' and resid 533 through 553 Processing helix chain 'D' and resid 65 through 89 removed outlier: 4.943A pdb=" N ASP D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 110 Processing helix chain 'D' and resid 157 through 175 Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 194 through 212 Processing helix chain 'D' and resid 229 through 244 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 344 through 356 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.603A pdb=" N VAL D 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 420 Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 479 Processing helix chain 'D' and resid 490 through 496 removed outlier: 3.667A pdb=" N ARG D 496 " --> pdb=" O GLU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 528 Processing helix chain 'D' and resid 533 through 553 Processing helix chain 'E' and resid 65 through 89 removed outlier: 4.925A pdb=" N ASP E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 157 through 175 Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'E' and resid 194 through 212 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 370 through 374 removed outlier: 3.598A pdb=" N VAL E 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 420 Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 479 Processing helix chain 'E' and resid 490 through 496 removed outlier: 3.667A pdb=" N ARG E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 528 Processing helix chain 'E' and resid 533 through 553 Processing helix chain 'F' and resid 65 through 89 removed outlier: 4.941A pdb=" N ASP F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 110 Processing helix chain 'F' and resid 157 through 175 Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 194 through 212 Processing helix chain 'F' and resid 229 through 244 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 286 through 294 Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 370 through 374 removed outlier: 3.591A pdb=" N VAL F 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 420 Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 479 Processing helix chain 'F' and resid 490 through 496 removed outlier: 3.656A pdb=" N ARG F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 528 Processing helix chain 'F' and resid 533 through 553 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224 removed outlier: 6.579A pdb=" N CYS A 146 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA A 223 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY A 148 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY A 149 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY C 149 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS C 146 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA C 223 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY C 148 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 367 removed outlier: 4.205A pdb=" N SER A 336 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 306 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A 330 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR A 303 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 380 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 305 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 401 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 220 through 224 removed outlier: 6.615A pdb=" N CYS B 146 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA B 223 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY B 148 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY B 149 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY E 149 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS E 146 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA E 223 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY E 148 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 367 removed outlier: 4.156A pdb=" N SER B 336 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE B 304 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLY B 331 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 306 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR B 303 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 380 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 305 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 401 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 365 through 367 removed outlier: 4.119A pdb=" N SER C 336 " --> pdb=" O TYR C 367 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE C 304 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLY C 331 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL C 306 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 303 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE C 380 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 305 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU C 379 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 401 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 220 through 224 removed outlier: 6.597A pdb=" N CYS D 146 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA D 223 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY D 148 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY D 149 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY F 149 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS F 146 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ALA F 223 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY F 148 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 365 through 367 removed outlier: 4.140A pdb=" N SER D 336 " --> pdb=" O TYR D 367 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE D 304 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N GLY D 331 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL D 306 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR D 303 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE D 380 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL D 305 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE D 401 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 365 through 367 removed outlier: 4.140A pdb=" N SER E 336 " --> pdb=" O TYR E 367 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE E 304 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N GLY E 331 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 306 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR E 303 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE E 380 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 305 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE E 401 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 365 through 367 removed outlier: 4.120A pdb=" N SER F 336 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE F 304 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLY F 331 " --> pdb=" O PHE F 304 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F 306 " --> pdb=" O GLY F 331 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR F 303 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE F 380 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL F 305 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE F 401 " --> pdb=" O ILE F 425 " (cutoff:3.500A) 1370 hydrogen bonds defined for protein. 3948 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: 4.80 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7787 1.34 - 1.47: 5831 1.47 - 1.59: 10538 1.59 - 1.71: 30 1.71 - 1.83: 204 Bond restraints: 24390 Sorted by residual: bond pdb=" O5' GTP E 601 " pdb=" PA GTP E 601 " ideal model delta sigma weight residual 1.610 1.833 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" O5' GTP B 601 " pdb=" PA GTP B 601 " ideal model delta sigma weight residual 1.610 1.833 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" O5' GTP A 601 " pdb=" PA GTP A 601 " ideal model delta sigma weight residual 1.610 1.832 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" O5' GTP D 601 " pdb=" PA GTP D 601 " ideal model delta sigma weight residual 1.610 1.832 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" O5' GTP C 601 " pdb=" PA GTP C 601 " ideal model delta sigma weight residual 1.610 1.830 -0.220 2.00e-02 2.50e+03 1.22e+02 ... (remaining 24385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 32578 3.20 - 6.40: 321 6.40 - 9.61: 101 9.61 - 12.81: 42 12.81 - 16.01: 24 Bond angle restraints: 33066 Sorted by residual: angle pdb=" O2B GTP F 601 " pdb=" PB GTP F 601 " pdb=" O3A GTP F 601 " ideal model delta sigma weight residual 109.50 93.49 16.01 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O2B GTP C 601 " pdb=" PB GTP C 601 " pdb=" O3A GTP C 601 " ideal model delta sigma weight residual 109.50 93.50 16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O2B GTP D 601 " pdb=" PB GTP D 601 " pdb=" O3A GTP D 601 " ideal model delta sigma weight residual 109.50 93.65 15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O2B GTP B 601 " pdb=" PB GTP B 601 " pdb=" O3A GTP B 601 " ideal model delta sigma weight residual 109.50 93.69 15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O2B GTP E 601 " pdb=" PB GTP E 601 " pdb=" O3A GTP E 601 " ideal model delta sigma weight residual 109.50 93.71 15.79 3.00e+00 1.11e-01 2.77e+01 ... (remaining 33061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 14545 35.89 - 71.79: 433 71.79 - 107.68: 16 107.68 - 143.58: 12 143.58 - 179.47: 6 Dihedral angle restraints: 15012 sinusoidal: 6600 harmonic: 8412 Sorted by residual: dihedral pdb=" C8 GTP C 601 " pdb=" C1' GTP C 601 " pdb=" N9 GTP C 601 " pdb=" O4' GTP C 601 " ideal model delta sinusoidal sigma weight residual 104.59 -75.94 -179.47 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP F 601 " pdb=" C1' GTP F 601 " pdb=" N9 GTP F 601 " pdb=" O4' GTP F 601 " ideal model delta sinusoidal sigma weight residual 104.59 -75.98 -179.42 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -74.49 179.08 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 15009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3133 0.074 - 0.148: 384 0.148 - 0.222: 47 0.222 - 0.296: 6 0.296 - 0.370: 6 Chirality restraints: 3576 Sorted by residual: chirality pdb=" C3' GTP D 601 " pdb=" C2' GTP D 601 " pdb=" C4' GTP D 601 " pdb=" O3' GTP D 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.84 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C3' GTP B 601 " pdb=" C2' GTP B 601 " pdb=" C4' GTP B 601 " pdb=" O3' GTP B 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.84 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C3' GTP A 601 " pdb=" C2' GTP A 601 " pdb=" C4' GTP A 601 " pdb=" O3' GTP A 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.84 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 3573 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 221 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 222 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 222 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 222 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 221 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO C 222 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 222 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 222 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 223 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO C 224 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 224 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 224 " 0.021 5.00e-02 4.00e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 177 2.46 - 3.07: 17509 3.07 - 3.68: 41839 3.68 - 4.29: 66791 4.29 - 4.90: 105081 Nonbonded interactions: 231397 Sorted by model distance: nonbonded pdb=" OH TYR F 451 " pdb=" O HOH F 701 " model vdw 1.848 3.040 nonbonded pdb=" O PHE F 440 " pdb=" O HOH F 701 " model vdw 1.993 3.040 nonbonded pdb=" OG1 THR E 94 " pdb=" OE1 GLN E 97 " model vdw 2.035 3.040 nonbonded pdb=" OE2 GLU C 133 " pdb=" O HOH C 701 " model vdw 2.144 3.040 nonbonded pdb=" NZ LYS A 200 " pdb=" O HOH A 701 " model vdw 2.148 3.120 ... (remaining 231392 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 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 : 0.007 0.223 24390 Z= 0.361 Angle : 0.970 16.012 33066 Z= 0.382 Chirality : 0.053 0.370 3576 Planarity : 0.004 0.044 4200 Dihedral : 16.194 179.470 9648 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 0.61 % Allowed : 9.06 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.53 (0.15), residues: 2934 helix: 2.01 (0.12), residues: 1500 sheet: 0.10 (0.27), residues: 414 loop : -0.02 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 420 TYR 0.009 0.001 TYR A 170 PHE 0.015 0.002 PHE C 205 TRP 0.016 0.002 TRP B 442 HIS 0.006 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.36 (24390) covalent geometry : angle 0.96990 / 0.38 (33066) hydrogen bonds : bond 0.18678 / 12.65 ( 1370) hydrogen bonds : angle 5.78509 / 4.17 ( 3948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 367 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: B 391 SER cc_start: 0.8414 (m) cc_final: 0.8078 (p) REVERT: C 526 MET cc_start: 0.8014 (mmt) cc_final: 0.7769 (mmm) REVERT: D 544 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8178 (mt-10) REVERT: E 97 GLN cc_start: 0.7090 (mt0) cc_final: 0.6722 (mt0) REVERT: F 515 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8323 (tm-30) REVERT: F 526 MET cc_start: 0.8013 (mmt) cc_final: 0.7767 (mmm) outliers start: 15 outliers final: 11 residues processed: 381 average time/residue: 0.6877 time to fit residues: 297.6421 Evaluate side-chains 353 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 342 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 365 LYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 365 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 285 ASN B 387 GLN C 387 GLN C 471 GLN D 471 GLN E 285 ASN E 387 GLN F 246 HIS F 311 ASN F 387 GLN F 471 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115169 restraints weight = 22408.330| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.13 r_work: 0.3138 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24390 Z= 0.136 Angle : 0.526 6.582 33066 Z= 0.271 Chirality : 0.043 0.145 3576 Planarity : 0.004 0.038 4200 Dihedral : 14.773 178.338 4112 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.42 % Allowed : 7.97 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.26 (0.15), residues: 2934 helix: 2.79 (0.12), residues: 1524 sheet: 0.15 (0.28), residues: 402 loop : 0.09 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 123 TYR 0.009 0.001 TYR F 451 PHE 0.015 0.002 PHE F 67 TRP 0.013 0.001 TRP B 442 HIS 0.004 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (24390) covalent geometry : angle 0.52639 / 0.27 (33066) hydrogen bonds : bond 0.05073 / 3.46 ( 1370) hydrogen bonds : angle 4.38993 / 3.18 ( 3948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 382 time to evaluate : 0.872 Fit side-chains REVERT: A 444 ASN cc_start: 0.8611 (t0) cc_final: 0.8328 (t0) REVERT: B 76 ARG cc_start: 0.8348 (ttt90) cc_final: 0.8110 (tpp80) REVERT: B 391 SER cc_start: 0.8332 (m) cc_final: 0.7892 (p) REVERT: B 444 ASN cc_start: 0.8576 (t0) cc_final: 0.8132 (t0) REVERT: B 504 ASP cc_start: 0.8473 (m-30) cc_final: 0.8241 (m-30) REVERT: C 226 MET cc_start: 0.8965 (mtp) cc_final: 0.8759 (mtp) REVERT: C 444 ASN cc_start: 0.8631 (t0) cc_final: 0.8155 (t0) REVERT: C 526 MET cc_start: 0.8416 (mmt) cc_final: 0.8142 (mmm) REVERT: D 444 ASN cc_start: 0.8626 (t0) cc_final: 0.8343 (t0) REVERT: E 444 ASN cc_start: 0.8577 (t0) cc_final: 0.8119 (t0) REVERT: E 504 ASP cc_start: 0.8485 (m-30) cc_final: 0.8254 (m-30) REVERT: F 373 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7800 (mt-10) REVERT: F 397 LYS cc_start: 0.7676 (mptt) cc_final: 0.7370 (mppt) REVERT: F 444 ASN cc_start: 0.8602 (t0) cc_final: 0.8144 (t0) REVERT: F 515 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8199 (tm-30) REVERT: F 526 MET cc_start: 0.8403 (mmt) cc_final: 0.8126 (mmm) outliers start: 35 outliers final: 22 residues processed: 401 average time/residue: 0.6679 time to fit residues: 305.6235 Evaluate side-chains 364 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 342 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [215, 190, 178, 5, 207, 47, 147, 213, 67, 144, 206] chunk 215 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 178 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 213 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN C 246 HIS C 285 ASN C 471 GLN D 285 ASN D 471 GLN E 471 GLN F 471 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113516 restraints weight = 22449.786| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.13 r_work: 0.3115 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24390 Z= 0.155 Angle : 0.536 6.279 33066 Z= 0.275 Chirality : 0.044 0.144 3576 Planarity : 0.004 0.038 4200 Dihedral : 14.691 178.348 4094 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.27 % Allowed : 8.50 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.32 (0.15), residues: 2934 helix: 2.85 (0.12), residues: 1530 sheet: 0.08 (0.27), residues: 396 loop : 0.11 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 101 TYR 0.009 0.002 TYR B 458 PHE 0.019 0.002 PHE E 67 TRP 0.012 0.001 TRP B 442 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (24390) covalent geometry : angle 0.53570 / 0.28 (33066) hydrogen bonds : bond 0.05092 / 3.47 ( 1370) hydrogen bonds : angle 4.32341 / 3.14 ( 3948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 352 time to evaluate : 0.747 Fit side-chains REVERT: A 395 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7967 (mtm-85) REVERT: A 444 ASN cc_start: 0.8650 (t0) cc_final: 0.8186 (t0) REVERT: A 552 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: B 391 SER cc_start: 0.8306 (m) cc_final: 0.7821 (p) REVERT: B 444 ASN cc_start: 0.8593 (t0) cc_final: 0.8156 (t0) REVERT: B 504 ASP cc_start: 0.8477 (m-30) cc_final: 0.8222 (m-30) REVERT: C 101 ARG cc_start: 0.8072 (ttt90) cc_final: 0.7824 (ttt90) REVERT: C 444 ASN cc_start: 0.8661 (t0) cc_final: 0.8223 (t0) REVERT: C 526 MET cc_start: 0.8428 (mmt) cc_final: 0.8147 (mmm) REVERT: D 444 ASN cc_start: 0.8655 (t0) cc_final: 0.8198 (t0) REVERT: D 552 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: E 76 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7640 (ttp-170) REVERT: E 97 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6511 (mt0) REVERT: E 444 ASN cc_start: 0.8595 (t0) cc_final: 0.8145 (t0) REVERT: E 504 ASP cc_start: 0.8489 (m-30) cc_final: 0.8233 (m-30) REVERT: F 101 ARG cc_start: 0.8069 (ttt90) cc_final: 0.7820 (ttt90) REVERT: F 397 LYS cc_start: 0.7670 (mptt) cc_final: 0.7374 (mppt) REVERT: F 444 ASN cc_start: 0.8661 (t0) cc_final: 0.8216 (t0) REVERT: F 526 MET cc_start: 0.8409 (mmt) cc_final: 0.8127 (mmm) outliers start: 56 outliers final: 31 residues processed: 389 average time/residue: 0.7185 time to fit residues: 318.3729 Evaluate side-chains 372 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 337 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [78, 96, 9, 88, 263, 128, 236, 159, 115, 211, 17] chunk 78 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 9 optimal weight: 0.0270 chunk 88 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 211 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 285 ASN A 471 GLN B 471 GLN C 471 GLN D 471 GLN F 471 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115328 restraints weight = 22336.841| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.10 r_work: 0.3129 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24390 Z= 0.128 Angle : 0.502 6.423 33066 Z= 0.258 Chirality : 0.042 0.138 3576 Planarity : 0.004 0.037 4200 Dihedral : 14.422 177.362 4092 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.22 % Allowed : 9.34 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.40 (0.15), residues: 2934 helix: 2.96 (0.12), residues: 1530 sheet: -0.07 (0.27), residues: 408 loop : 0.17 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 123 TYR 0.007 0.001 TYR B 458 PHE 0.012 0.002 PHE C 277 TRP 0.012 0.001 TRP B 442 HIS 0.004 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (24390) covalent geometry : angle 0.50203 / 0.26 (33066) hydrogen bonds : bond 0.04537 / 3.09 ( 1370) hydrogen bonds : angle 4.23497 / 3.07 ( 3948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 0.832 Fit side-chains REVERT: A 395 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7933 (mtm-85) REVERT: A 444 ASN cc_start: 0.8599 (t0) cc_final: 0.8281 (t0) REVERT: A 552 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: B 76 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7670 (ttp-170) REVERT: B 391 SER cc_start: 0.8273 (m) cc_final: 0.7800 (p) REVERT: B 444 ASN cc_start: 0.8568 (t0) cc_final: 0.8286 (t0) REVERT: B 504 ASP cc_start: 0.8484 (m-30) cc_final: 0.8218 (m-30) REVERT: C 101 ARG cc_start: 0.8032 (ttt90) cc_final: 0.7826 (ttt90) REVERT: C 226 MET cc_start: 0.9017 (mtp) cc_final: 0.8742 (mtp) REVERT: C 444 ASN cc_start: 0.8611 (t0) cc_final: 0.8335 (t0) REVERT: C 526 MET cc_start: 0.8434 (mmt) cc_final: 0.8192 (mmm) REVERT: D 444 ASN cc_start: 0.8600 (t0) cc_final: 0.8306 (t0) REVERT: D 552 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: E 76 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7730 (ttp-170) REVERT: E 444 ASN cc_start: 0.8569 (t0) cc_final: 0.8279 (t0) REVERT: E 504 ASP cc_start: 0.8489 (m-30) cc_final: 0.8249 (m-30) REVERT: F 101 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7831 (ttt90) REVERT: F 226 MET cc_start: 0.8950 (mtp) cc_final: 0.8737 (mtp) REVERT: F 397 LYS cc_start: 0.7672 (mptt) cc_final: 0.7420 (mppt) REVERT: F 444 ASN cc_start: 0.8623 (t0) cc_final: 0.8346 (t0) REVERT: F 526 MET cc_start: 0.8445 (mmt) cc_final: 0.8167 (mmm) REVERT: F 552 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7053 (mp0) outliers start: 55 outliers final: 29 residues processed: 393 average time/residue: 0.7241 time to fit residues: 323.6172 Evaluate side-chains 373 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 339 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 552 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [244, 53, 240, 6, 187, 51, 265, 126, 209, 55, 164] chunk 244 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 187 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 209 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN C 246 HIS C 285 ASN C 471 GLN D 471 GLN F 246 HIS F 471 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117428 restraints weight = 22361.197| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.10 r_work: 0.3170 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24390 Z= 0.112 Angle : 0.478 6.411 33066 Z= 0.245 Chirality : 0.042 0.142 3576 Planarity : 0.004 0.038 4200 Dihedral : 14.148 176.221 4092 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.18 % Allowed : 10.28 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.45 (0.16), residues: 2934 helix: 3.04 (0.12), residues: 1536 sheet: -0.05 (0.27), residues: 402 loop : 0.10 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 123 TYR 0.006 0.001 TYR E 458 PHE 0.024 0.002 PHE E 67 TRP 0.011 0.001 TRP E 442 HIS 0.003 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (24390) covalent geometry : angle 0.47829 / 0.25 (33066) hydrogen bonds : bond 0.04172 / 2.84 ( 1370) hydrogen bonds : angle 4.15918 / 3.02 ( 3948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 360 time to evaluate : 0.783 Fit side-chains REVERT: A 444 ASN cc_start: 0.8550 (t0) cc_final: 0.8215 (t0) REVERT: B 71 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: B 76 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7735 (ttp-170) REVERT: B 390 LYS cc_start: 0.8477 (tttm) cc_final: 0.8183 (ttmm) REVERT: B 391 SER cc_start: 0.8292 (m) cc_final: 0.7815 (p) REVERT: B 444 ASN cc_start: 0.8553 (t0) cc_final: 0.8250 (t0) REVERT: B 504 ASP cc_start: 0.8408 (m-30) cc_final: 0.8183 (m-30) REVERT: C 101 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7793 (ttt90) REVERT: C 226 MET cc_start: 0.8999 (mtp) cc_final: 0.8754 (mtp) REVERT: C 444 ASN cc_start: 0.8575 (t0) cc_final: 0.8276 (t0) REVERT: D 444 ASN cc_start: 0.8559 (t0) cc_final: 0.8235 (t0) REVERT: D 552 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6473 (mp0) REVERT: E 76 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7707 (ttp-170) REVERT: E 97 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6351 (mt0) REVERT: E 444 ASN cc_start: 0.8558 (t0) cc_final: 0.8243 (t0) REVERT: E 504 ASP cc_start: 0.8412 (m-30) cc_final: 0.8182 (m-30) REVERT: F 101 ARG cc_start: 0.8017 (ttt90) cc_final: 0.7812 (ttt90) REVERT: F 397 LYS cc_start: 0.7661 (mptt) cc_final: 0.7413 (mppt) REVERT: F 444 ASN cc_start: 0.8594 (t0) cc_final: 0.8284 (t0) outliers start: 54 outliers final: 25 residues processed: 398 average time/residue: 0.7184 time to fit residues: 325.1014 Evaluate side-chains 364 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 334 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [105, 88, 188, 225, 170, 257, 6, 114, 191, 199, 255] chunk 105 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 199 optimal weight: 0.5980 chunk 255 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 387 GLN C 246 HIS C 471 GLN D 471 GLN F 246 HIS F 471 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115198 restraints weight = 22270.227| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.10 r_work: 0.3123 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24390 Z= 0.150 Angle : 0.526 6.614 33066 Z= 0.269 Chirality : 0.043 0.136 3576 Planarity : 0.004 0.042 4200 Dihedral : 14.437 178.750 4092 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.43 % Allowed : 10.80 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.44 (0.16), residues: 2934 helix: 2.99 (0.12), residues: 1530 sheet: 0.03 (0.27), residues: 402 loop : 0.15 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 123 TYR 0.009 0.002 TYR B 458 PHE 0.014 0.002 PHE C 277 TRP 0.010 0.001 TRP B 442 HIS 0.005 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (24390) covalent geometry : angle 0.52591 / 0.27 (33066) hydrogen bonds : bond 0.04755 / 3.24 ( 1370) hydrogen bonds : angle 4.22873 / 3.07 ( 3948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 347 time to evaluate : 0.977 Fit side-chains REVERT: A 395 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7991 (mtp180) REVERT: A 444 ASN cc_start: 0.8636 (t0) cc_final: 0.8380 (t0) REVERT: A 552 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: B 76 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7678 (ttp-170) REVERT: B 390 LYS cc_start: 0.8498 (tttm) cc_final: 0.8217 (ttmm) REVERT: B 391 SER cc_start: 0.8279 (m) cc_final: 0.7794 (p) REVERT: B 504 ASP cc_start: 0.8463 (m-30) cc_final: 0.8198 (m-30) REVERT: C 101 ARG cc_start: 0.8023 (ttt90) cc_final: 0.7804 (ttt90) REVERT: C 123 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7910 (ttp-110) REVERT: C 459 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: C 552 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: D 444 ASN cc_start: 0.8648 (t0) cc_final: 0.8185 (t0) REVERT: E 76 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7652 (ttp-170) REVERT: E 97 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6364 (mt0) REVERT: E 373 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7713 (mt-10) REVERT: E 504 ASP cc_start: 0.8464 (m-30) cc_final: 0.8192 (m-30) REVERT: F 101 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7810 (ttt90) REVERT: F 123 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7882 (ttp-110) REVERT: F 226 MET cc_start: 0.9022 (mtp) cc_final: 0.8784 (mtp) REVERT: F 397 LYS cc_start: 0.7656 (mptt) cc_final: 0.7424 (mppt) REVERT: F 459 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8155 (tp30) REVERT: F 552 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7026 (mp0) outliers start: 60 outliers final: 30 residues processed: 383 average time/residue: 0.7299 time to fit residues: 317.0737 Evaluate side-chains 374 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 336 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 552 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [15, 82, 136, 149, 225, 103, 251, 71, 214, 23, 27] chunk 15 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 136 optimal weight: 0.0020 chunk 149 optimal weight: 0.0980 chunk 225 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN C 246 HIS C 471 GLN D 471 GLN F 246 HIS F 471 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115275 restraints weight = 22232.406| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.15 r_work: 0.3136 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24390 Z= 0.131 Angle : 0.507 6.587 33066 Z= 0.260 Chirality : 0.043 0.150 3576 Planarity : 0.004 0.042 4200 Dihedral : 14.317 178.020 4092 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.14 % Allowed : 11.57 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.44 (0.16), residues: 2934 helix: 3.00 (0.12), residues: 1536 sheet: -0.09 (0.26), residues: 408 loop : 0.16 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 123 TYR 0.007 0.001 TYR B 458 PHE 0.013 0.002 PHE D 323 TRP 0.011 0.001 TRP B 442 HIS 0.004 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (24390) covalent geometry : angle 0.50736 / 0.26 (33066) hydrogen bonds : bond 0.04467 / 3.04 ( 1370) hydrogen bonds : angle 4.20206 / 3.05 ( 3948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 346 time to evaluate : 0.981 Fit side-chains REVERT: A 444 ASN cc_start: 0.8590 (t0) cc_final: 0.8298 (t0) REVERT: B 76 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7726 (ttp-170) REVERT: B 390 LYS cc_start: 0.8483 (tttm) cc_final: 0.8207 (ttmm) REVERT: B 391 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7784 (p) REVERT: B 504 ASP cc_start: 0.8439 (m-30) cc_final: 0.8230 (m-30) REVERT: C 101 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7779 (ttt90) REVERT: C 123 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7864 (ttp-110) REVERT: C 226 MET cc_start: 0.8985 (mtp) cc_final: 0.8694 (mtp) REVERT: C 444 ASN cc_start: 0.8609 (t0) cc_final: 0.8271 (t0) REVERT: C 552 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: D 444 ASN cc_start: 0.8597 (t0) cc_final: 0.8313 (t0) REVERT: E 76 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7605 (ttp-170) REVERT: E 97 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6375 (mt0) REVERT: E 373 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7658 (mt-10) REVERT: E 504 ASP cc_start: 0.8444 (m-30) cc_final: 0.8232 (m-30) REVERT: F 101 ARG cc_start: 0.8007 (ttt90) cc_final: 0.7781 (ttt90) REVERT: F 123 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7841 (ttp-110) REVERT: F 397 LYS cc_start: 0.7661 (mptt) cc_final: 0.7413 (mppt) REVERT: F 552 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6940 (mp0) outliers start: 53 outliers final: 31 residues processed: 376 average time/residue: 0.7296 time to fit residues: 311.5729 Evaluate side-chains 370 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 333 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 552 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [147, 170, 4, 69, 237, 98, 131, 233, 29, 261, 209] chunk 147 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 237 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 209 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN C 471 GLN D 471 GLN F 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114539 restraints weight = 22163.676| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.11 r_work: 0.3128 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24390 Z= 0.155 Angle : 0.540 6.714 33066 Z= 0.276 Chirality : 0.044 0.142 3576 Planarity : 0.004 0.043 4200 Dihedral : 14.470 179.007 4092 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.18 % Allowed : 11.37 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.41 (0.16), residues: 2934 helix: 3.00 (0.12), residues: 1524 sheet: 0.02 (0.27), residues: 396 loop : 0.08 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 123 TYR 0.009 0.002 TYR E 458 PHE 0.024 0.002 PHE E 67 TRP 0.010 0.001 TRP B 442 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (24390) covalent geometry : angle 0.53987 / 0.28 (33066) hydrogen bonds : bond 0.04794 / 3.27 ( 1370) hydrogen bonds : angle 4.24324 / 3.08 ( 3948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 338 time to evaluate : 0.887 Fit side-chains REVERT: A 444 ASN cc_start: 0.8634 (t0) cc_final: 0.8399 (t0) REVERT: A 552 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: B 76 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7672 (ttp-170) REVERT: B 390 LYS cc_start: 0.8515 (tttm) cc_final: 0.8240 (ttmm) REVERT: B 391 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7824 (p) REVERT: B 504 ASP cc_start: 0.8456 (m-30) cc_final: 0.8201 (m-30) REVERT: C 101 ARG cc_start: 0.8021 (ttt90) cc_final: 0.7796 (ttt90) REVERT: C 123 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7883 (ttp-110) REVERT: C 459 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8165 (tp30) REVERT: C 552 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: D 444 ASN cc_start: 0.8641 (t0) cc_final: 0.8188 (t0) REVERT: D 552 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: E 71 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: E 76 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7655 (ttp-170) REVERT: E 97 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6449 (mt0) REVERT: E 373 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7654 (mt-10) REVERT: E 504 ASP cc_start: 0.8453 (m-30) cc_final: 0.8190 (m-30) REVERT: F 101 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7787 (ttt90) REVERT: F 123 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7870 (ttp-110) REVERT: F 397 LYS cc_start: 0.7653 (mptt) cc_final: 0.7420 (mppt) REVERT: F 459 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8136 (tp30) REVERT: F 552 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6936 (mp0) outliers start: 54 outliers final: 30 residues processed: 370 average time/residue: 0.7188 time to fit residues: 302.3948 Evaluate side-chains 371 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 330 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 552 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [81, 35, 63, 181, 6, 289, 85, 49, 19, 225, 27] chunk 81 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN C 471 GLN D 471 GLN F 246 HIS F 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113416 restraints weight = 22125.147| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.12 r_work: 0.3112 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24390 Z= 0.180 Angle : 0.573 8.255 33066 Z= 0.293 Chirality : 0.045 0.146 3576 Planarity : 0.004 0.044 4200 Dihedral : 14.608 179.004 4092 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.02 % Allowed : 11.77 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.33 (0.16), residues: 2934 helix: 2.93 (0.12), residues: 1524 sheet: -0.03 (0.26), residues: 402 loop : 0.05 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 395 TYR 0.010 0.002 TYR E 458 PHE 0.015 0.002 PHE F 277 TRP 0.010 0.001 TRP B 442 HIS 0.006 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (24390) covalent geometry : angle 0.57273 / 0.29 (33066) hydrogen bonds : bond 0.05097 / 3.47 ( 1370) hydrogen bonds : angle 4.29366 / 3.12 ( 3948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 344 time to evaluate : 0.888 Fit side-chains REVERT: A 552 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: B 71 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: B 76 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7670 (ttp-170) REVERT: B 390 LYS cc_start: 0.8503 (tttm) cc_final: 0.8229 (ttmm) REVERT: B 391 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.7762 (p) REVERT: B 414 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: B 504 ASP cc_start: 0.8458 (m-30) cc_final: 0.8195 (m-30) REVERT: C 123 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7900 (ttp-110) REVERT: C 459 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: C 552 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: D 552 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: E 76 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7645 (ttp-170) REVERT: E 97 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6427 (mt0) REVERT: E 373 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7656 (mt-10) REVERT: E 504 ASP cc_start: 0.8460 (m-30) cc_final: 0.8189 (m-30) REVERT: F 101 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7777 (ttt90) REVERT: F 123 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7855 (ttp-110) REVERT: F 397 LYS cc_start: 0.7678 (mptt) cc_final: 0.7447 (mppt) REVERT: F 459 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: F 552 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7004 (mp0) outliers start: 50 outliers final: 30 residues processed: 372 average time/residue: 0.7328 time to fit residues: 309.3025 Evaluate side-chains 376 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 552 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 552 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [215, 201, 122, 146, 242, 65, 136, 22, 80, 113, 108] chunk 215 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 122 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN C 471 GLN D 471 GLN F 246 HIS F 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115167 restraints weight = 22156.296| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.15 r_work: 0.3136 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24390 Z= 0.136 Angle : 0.532 8.175 33066 Z= 0.272 Chirality : 0.043 0.143 3576 Planarity : 0.004 0.044 4200 Dihedral : 14.283 178.064 4092 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.74 % Allowed : 12.22 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.35 (0.16), residues: 2934 helix: 2.97 (0.12), residues: 1530 sheet: -0.13 (0.26), residues: 408 loop : 0.06 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 123 TYR 0.008 0.001 TYR E 458 PHE 0.029 0.002 PHE E 67 TRP 0.012 0.001 TRP E 442 HIS 0.004 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (24390) covalent geometry : angle 0.53231 / 0.27 (33066) hydrogen bonds : bond 0.04524 / 3.08 ( 1370) hydrogen bonds : angle 4.23700 / 3.08 ( 3948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5868 Ramachandran restraints generated. 2934 Oldfield, 0 Emsley, 2934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 341 time to evaluate : 1.025 Fit side-chains REVERT: A 444 ASN cc_start: 0.8611 (t0) cc_final: 0.8278 (t0) REVERT: B 76 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7755 (ttp-170) REVERT: B 390 LYS cc_start: 0.8507 (tttm) cc_final: 0.8228 (ttmm) REVERT: B 391 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7723 (p) REVERT: B 414 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: B 504 ASP cc_start: 0.8441 (m-30) cc_final: 0.8226 (m-30) REVERT: C 552 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: D 444 ASN cc_start: 0.8619 (t0) cc_final: 0.8284 (t0) REVERT: E 76 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7721 (ttp-170) REVERT: E 97 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6398 (mt0) REVERT: E 373 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7629 (mt-10) REVERT: E 504 ASP cc_start: 0.8443 (m-30) cc_final: 0.8193 (m-30) REVERT: F 101 ARG cc_start: 0.7997 (ttt90) cc_final: 0.7768 (ttt90) REVERT: F 397 LYS cc_start: 0.7646 (mptt) cc_final: 0.7409 (mppt) REVERT: F 552 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6910 (mp0) outliers start: 43 outliers final: 29 residues processed: 367 average time/residue: 0.7284 time to fit residues: 303.5748 Evaluate side-chains 369 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 333 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 552 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [136, 263, 172, 134, 78, 279, 69, 285, 154, 290, 62] chunk 136 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 134 optimal weight: 0.0970 chunk 78 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN C 471 GLN D 471 GLN F 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113360 restraints weight = 22140.934| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.11 r_work: 0.3112 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24390 Z= 0.180 Angle : 0.583 8.463 33066 Z= 0.296 Chirality : 0.045 0.146 3576 Planarity : 0.004 0.046 4200 Dihedral : 14.469 179.094 4092 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.78 % Allowed : 12.42 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.29 (0.16), residues: 2934 helix: 2.90 (0.12), residues: 1524 sheet: -0.05 (0.26), residues: 402 loop : 0.03 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 123 TYR 0.011 0.002 TYR B 458 PHE 0.035 0.002 PHE C 67 TRP 0.010 0.001 TRP B 442 HIS 0.006 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (24390) covalent geometry : angle 0.58263 / 0.30 (33066) hydrogen bonds : bond 0.05084 / 3.46 ( 1370) hydrogen bonds : angle 4.30218 / 3.12 ( 3948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11513.42 seconds wall clock time: 196 minutes 31.09 seconds (11791.09 seconds total)