Starting phenix.real_space_refine on Sat Dec 28 06:03:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rgl_24451/12_2024/7rgl_24451_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rgl_24451/12_2024/7rgl_24451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rgl_24451/12_2024/7rgl_24451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rgl_24451/12_2024/7rgl_24451.map" model { file = "/net/cci-nas-00/data/ceres_data/7rgl_24451/12_2024/7rgl_24451_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rgl_24451/12_2024/7rgl_24451_trim.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.239 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 168 5.16 5 C 16112 2.51 5 N 4328 2.21 5 O 4896 1.98 5 H 25408 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 202 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 50936 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "B" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "C" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "D" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "E" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "F" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "G" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "H" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 19.66, per 1000 atoms: 0.39 Number of scatterers: 50936 At special positions: 0 Unit cell: (143.31, 142.467, 122.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 P 24 15.00 O 4896 8.00 N 4328 7.00 C 16112 6.00 H 25408 1.00 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.41 Conformation dependent library (CDL) restraints added in 3.3 seconds 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 35 sheets defined 42.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.568A pdb=" N VAL A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.521A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 356 removed outlier: 4.040A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.544A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.526A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 356 removed outlier: 4.013A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.526A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.636A pdb=" N ALA C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.537A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 356 removed outlier: 4.022A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.550A pdb=" N VAL D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 193 through 198 Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.649A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.520A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 356 removed outlier: 4.022A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.522A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 193 through 198 Processing helix chain 'E' and resid 223 through 229 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.523A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 356 removed outlier: 4.024A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 2 through 7 removed outlier: 4.343A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.552A pdb=" N VAL F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 193 through 198 Processing helix chain 'F' and resid 223 through 229 Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.532A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 356 removed outlier: 4.036A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.551A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 193 through 198 Processing helix chain 'G' and resid 223 through 229 removed outlier: 3.589A pdb=" N LEU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.521A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 356 removed outlier: 4.034A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 2 through 7 removed outlier: 4.408A pdb=" N ILE H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 removed outlier: 3.545A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 193 through 198 removed outlier: 3.591A pdb=" N ALA H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.520A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 356 removed outlier: 4.040A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 416 through 421 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.530A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 299 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 4.120A pdb=" N SER A 444 " --> pdb=" O THR D 510 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.805A pdb=" N SER A 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B 444 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.531A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 299 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.806A pdb=" N SER B 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 444 " --> pdb=" O THR B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.530A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 299 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.824A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER D 444 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.529A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL D 299 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 211 Processing sheet with id=AB9, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.530A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL E 299 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 400 through 403 removed outlier: 4.108A pdb=" N SER E 444 " --> pdb=" O THR H 510 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.812A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER F 444 " --> pdb=" O THR E 510 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.530A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL F 299 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.821A pdb=" N SER F 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER G 444 " --> pdb=" O THR F 510 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AD1, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.529A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL G 299 " --> pdb=" O GLY G 320 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 209 through 211 Processing sheet with id=AD4, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.810A pdb=" N SER G 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER H 444 " --> pdb=" O THR G 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.529A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL H 299 " --> pdb=" O GLY H 320 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 209 through 211 removed outlier: 3.681A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2778 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: 17.84 Time building geometry restraints manager: 12.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 25360 1.12 - 1.29: 4261 1.29 - 1.47: 9807 1.47 - 1.64: 11647 1.64 - 1.82: 293 Bond restraints: 51368 Sorted by residual: bond pdb=" C3B NAD A 602 " pdb=" C4B NAD A 602 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3B NAD H 602 " pdb=" C4B NAD H 602 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.303 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3D NAD D 602 " pdb=" C4D NAD D 602 " ideal model delta sigma weight residual 1.531 1.303 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3B NAD D 602 " pdb=" C4B NAD D 602 " ideal model delta sigma weight residual 1.523 1.295 0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 51363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 86423 3.97 - 7.94: 6326 7.94 - 11.91: 72 11.91 - 15.88: 27 15.88 - 19.86: 24 Bond angle restraints: 92872 Sorted by residual: angle pdb=" C1' IMP C 601 " pdb=" N9 IMP C 601 " pdb=" C4 IMP C 601 " ideal model delta sigma weight residual 126.00 106.14 19.86 3.00e+00 1.11e-01 4.38e+01 angle pdb=" C1' IMP E 601 " pdb=" N9 IMP E 601 " pdb=" C4 IMP E 601 " ideal model delta sigma weight residual 126.00 106.15 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" C1' IMP B 601 " pdb=" N9 IMP B 601 " pdb=" C4 IMP B 601 " ideal model delta sigma weight residual 126.00 106.15 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" C1' IMP F 601 " pdb=" N9 IMP F 601 " pdb=" C4 IMP F 601 " ideal model delta sigma weight residual 126.00 106.16 19.84 3.00e+00 1.11e-01 4.37e+01 angle pdb=" C1' IMP G 601 " pdb=" N9 IMP G 601 " pdb=" C4 IMP G 601 " ideal model delta sigma weight residual 126.00 106.18 19.82 3.00e+00 1.11e-01 4.36e+01 ... (remaining 92867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 22769 33.19 - 66.39: 1396 66.39 - 99.58: 111 99.58 - 132.78: 0 132.78 - 165.97: 4 Dihedral angle restraints: 24280 sinusoidal: 13648 harmonic: 10632 Sorted by residual: dihedral pdb=" C5' IMP E 601 " pdb=" O5' IMP E 601 " pdb=" P IMP E 601 " pdb=" O2P IMP E 601 " ideal model delta sinusoidal sigma weight residual -168.07 -2.10 -165.97 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual -168.07 -2.11 -165.96 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' IMP F 601 " pdb=" O5' IMP F 601 " pdb=" P IMP F 601 " pdb=" O2P IMP F 601 " ideal model delta sinusoidal sigma weight residual -168.07 -2.17 -165.90 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 24277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3039 0.067 - 0.135: 921 0.135 - 0.202: 81 0.202 - 0.270: 4 0.270 - 0.337: 19 Chirality restraints: 4064 Sorted by residual: chirality pdb=" CA ARG A 474 " pdb=" N ARG A 474 " pdb=" C ARG A 474 " pdb=" CB ARG A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ARG C 474 " pdb=" N ARG C 474 " pdb=" C ARG C 474 " pdb=" CB ARG C 474 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ARG B 474 " pdb=" N ARG B 474 " pdb=" C ARG B 474 " pdb=" CB ARG B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 4061 not shown) Planarity restraints: 7592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 353 " 0.125 2.00e-02 2.50e+03 5.18e-02 8.06e+01 pdb=" CG TYR A 353 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 353 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR A 353 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 353 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 353 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 353 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 353 " 0.100 2.00e-02 2.50e+03 pdb=" HD1 TYR A 353 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 TYR A 353 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 353 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 353 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 353 " -0.120 2.00e-02 2.50e+03 4.96e-02 7.38e+01 pdb=" CG TYR B 353 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 353 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR B 353 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR B 353 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 353 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 353 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 353 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR B 353 " 0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR B 353 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR B 353 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR B 353 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 353 " -0.117 2.00e-02 2.50e+03 4.87e-02 7.10e+01 pdb=" CG TYR C 353 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 353 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR C 353 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR C 353 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR C 353 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR C 353 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 353 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR C 353 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR C 353 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 TYR C 353 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 353 " -0.005 2.00e-02 2.50e+03 ... (remaining 7589 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 2588 2.10 - 2.73: 82775 2.73 - 3.35: 149642 3.35 - 3.98: 208883 3.98 - 4.60: 307386 Nonbonded interactions: 751274 Sorted by model distance: nonbonded pdb=" HA LYS A 228 " pdb=" HD3 LYS A 228 " model vdw 1.481 2.440 nonbonded pdb=" HB2 GLN D 283 " pdb="HE21 GLN D 283 " model vdw 1.542 2.270 nonbonded pdb=" HB2 GLN F 283 " pdb="HE21 GLN F 283 " model vdw 1.543 2.270 nonbonded pdb=" HB2 GLN C 283 " pdb="HE21 GLN C 283 " model vdw 1.543 2.270 nonbonded pdb=" HB2 GLN E 283 " pdb="HE21 GLN E 283 " model vdw 1.543 2.270 ... (remaining 751269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.670 Extract box with map and model: 1.450 Check model and map are aligned: 0.300 Set scattering table: 0.350 Process input model: 84.430 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.230 25960 Z= 0.878 Angle : 1.204 19.856 35128 Z= 0.620 Chirality : 0.063 0.337 4064 Planarity : 0.008 0.093 4424 Dihedral : 16.031 165.972 9808 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 3.66 % Allowed : 9.86 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3248 helix: -0.72 (0.13), residues: 1320 sheet: -0.15 (0.27), residues: 288 loop : -1.18 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 466 PHE 0.077 0.004 PHE B 357 TYR 0.112 0.006 TYR A 353 ARG 0.010 0.001 ARG H 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 526 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.5661 (m-30) REVERT: A 243 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7640 (mm-40) REVERT: A 292 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7968 (tm130) REVERT: A 330 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9070 (pp) REVERT: A 441 GLN cc_start: 0.8466 (mt0) cc_final: 0.8119 (mt0) REVERT: B 211 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 243 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7690 (mm-40) REVERT: B 292 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7971 (tm130) REVERT: B 330 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9056 (pp) REVERT: C 243 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7683 (mm-40) REVERT: C 292 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7935 (tm130) REVERT: C 330 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9070 (pp) REVERT: C 441 GLN cc_start: 0.8414 (mt0) cc_final: 0.8164 (mt0) REVERT: D 224 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7474 (ptp-170) REVERT: D 243 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7673 (mm-40) REVERT: D 292 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7956 (tm130) REVERT: D 330 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9064 (pp) REVERT: D 441 GLN cc_start: 0.8437 (mt0) cc_final: 0.8119 (mt0) REVERT: E 243 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7661 (mm-40) REVERT: E 292 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7965 (tm130) REVERT: E 330 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9079 (pp) REVERT: F 243 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7713 (mm-40) REVERT: F 292 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7958 (tm130) REVERT: F 441 GLN cc_start: 0.8401 (mt0) cc_final: 0.8179 (mt0) REVERT: G 243 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7675 (mm-40) REVERT: G 292 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7939 (tm130) REVERT: G 330 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9068 (pp) REVERT: G 441 GLN cc_start: 0.8484 (mt0) cc_final: 0.8151 (mt0) REVERT: H 243 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7640 (mm-40) REVERT: H 292 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7973 (tm130) REVERT: H 330 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9064 (pp) REVERT: H 441 GLN cc_start: 0.8428 (mt0) cc_final: 0.8145 (mt0) outliers start: 97 outliers final: 37 residues processed: 603 average time/residue: 2.2712 time to fit residues: 1602.5693 Evaluate side-chains 513 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 466 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 336 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 296 HIS A 454 GLN B 277 GLN B 296 HIS C 277 GLN C 296 HIS C 454 GLN D 21 GLN D 277 GLN D 296 HIS D 454 GLN E 21 GLN E 277 GLN E 296 HIS E 454 GLN F 277 GLN F 296 HIS F 454 GLN G 21 GLN G 277 GLN G 296 HIS G 454 GLN H 21 GLN H 277 GLN H 296 HIS H 454 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 25960 Z= 0.194 Angle : 0.550 4.149 35128 Z= 0.292 Chirality : 0.042 0.155 4064 Planarity : 0.004 0.044 4424 Dihedral : 10.591 159.666 4131 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.13 % Allowed : 15.90 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3248 helix: 0.59 (0.14), residues: 1320 sheet: 0.04 (0.28), residues: 288 loop : -0.87 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 92 PHE 0.011 0.001 PHE C 357 TYR 0.009 0.001 TYR D 348 ARG 0.004 0.001 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 483 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9379 (tpp) cc_final: 0.9146 (tpp) REVERT: A 109 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7444 (mmtm) REVERT: A 243 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7636 (mm-40) REVERT: A 292 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7942 (tm130) REVERT: A 441 GLN cc_start: 0.8501 (mt0) cc_final: 0.8095 (mt0) REVERT: B 78 MET cc_start: 0.9375 (tpp) cc_final: 0.9126 (tpp) REVERT: B 109 LYS cc_start: 0.7740 (mmtp) cc_final: 0.7427 (mmtm) REVERT: B 243 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7617 (mm-40) REVERT: B 292 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7929 (tm130) REVERT: C 78 MET cc_start: 0.9379 (tpp) cc_final: 0.9130 (tpp) REVERT: C 109 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7402 (mmtm) REVERT: C 243 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7597 (mm-40) REVERT: C 292 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7921 (tm130) REVERT: C 441 GLN cc_start: 0.8406 (mt0) cc_final: 0.8070 (mt0) REVERT: D 78 MET cc_start: 0.9377 (tpp) cc_final: 0.9145 (tpp) REVERT: D 111 GLU cc_start: 0.7083 (tp30) cc_final: 0.6869 (tp30) REVERT: D 224 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7462 (ptp-170) REVERT: D 243 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7605 (mm-40) REVERT: D 292 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7918 (tm130) REVERT: D 441 GLN cc_start: 0.8506 (mt0) cc_final: 0.8133 (mt0) REVERT: D 495 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6630 (tpt) REVERT: E 78 MET cc_start: 0.9379 (tpp) cc_final: 0.9143 (tpp) REVERT: E 109 LYS cc_start: 0.7802 (mmtp) cc_final: 0.7466 (mmtm) REVERT: E 243 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7613 (mm-40) REVERT: E 292 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7916 (tm130) REVERT: F 78 MET cc_start: 0.9376 (tpp) cc_final: 0.9144 (tpp) REVERT: F 109 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7414 (mmtm) REVERT: F 243 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7636 (mm-40) REVERT: F 292 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7926 (tm130) REVERT: F 441 GLN cc_start: 0.8466 (mt0) cc_final: 0.8117 (mt0) REVERT: G 78 MET cc_start: 0.9376 (tpp) cc_final: 0.9145 (tpp) REVERT: G 109 LYS cc_start: 0.7745 (mmtp) cc_final: 0.7406 (mmtm) REVERT: G 243 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7593 (mm-40) REVERT: G 292 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7924 (tm130) REVERT: G 441 GLN cc_start: 0.8493 (mt0) cc_final: 0.8101 (mt0) REVERT: H 78 MET cc_start: 0.9375 (tpp) cc_final: 0.9143 (tpp) REVERT: H 243 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7618 (mm-40) REVERT: H 292 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7941 (tm130) REVERT: H 441 GLN cc_start: 0.8471 (mt0) cc_final: 0.8111 (mt0) outliers start: 30 outliers final: 10 residues processed: 505 average time/residue: 2.5682 time to fit residues: 1494.1897 Evaluate side-chains 470 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 458 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 277 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 265 optimal weight: 0.7980 chunk 295 optimal weight: 0.0570 chunk 101 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 454 GLN B 441 GLN B 454 GLN C 21 GLN C 454 GLN D 21 GLN D 454 GLN E 21 GLN E 441 GLN E 454 GLN F 21 GLN F 454 GLN G 21 GLN G 454 GLN H 21 GLN H 454 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25960 Z= 0.271 Angle : 0.552 4.236 35128 Z= 0.293 Chirality : 0.043 0.152 4064 Planarity : 0.004 0.049 4424 Dihedral : 9.312 106.583 4071 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.28 % Allowed : 16.09 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3248 helix: 1.01 (0.15), residues: 1320 sheet: 0.23 (0.29), residues: 288 loop : -0.65 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 466 PHE 0.011 0.002 PHE C 357 TYR 0.011 0.001 TYR B 348 ARG 0.004 0.001 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 474 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.7879 (mmtp) cc_final: 0.7593 (mmtm) REVERT: A 243 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7650 (mm-40) REVERT: A 292 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7933 (tm130) REVERT: A 441 GLN cc_start: 0.8502 (mt0) cc_final: 0.8132 (mt0) REVERT: B 109 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7614 (mmtm) REVERT: B 243 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7673 (mm-40) REVERT: B 292 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7916 (tm130) REVERT: C 109 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7563 (mmtm) REVERT: C 243 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7678 (mm-40) REVERT: C 292 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7920 (tm130) REVERT: C 441 GLN cc_start: 0.8473 (mt0) cc_final: 0.8168 (mt0) REVERT: C 512 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7397 (mt) REVERT: D 109 LYS cc_start: 0.7827 (mmtp) cc_final: 0.7555 (mmtm) REVERT: D 111 GLU cc_start: 0.7128 (tp30) cc_final: 0.6904 (tp30) REVERT: D 224 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7609 (ptp-170) REVERT: D 243 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7683 (mm-40) REVERT: D 292 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7922 (tm130) REVERT: D 441 GLN cc_start: 0.8412 (mt0) cc_final: 0.7988 (mt0) REVERT: D 495 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6728 (tpt) REVERT: E 109 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7636 (mmtm) REVERT: E 243 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7639 (mm-40) REVERT: E 292 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7903 (tm130) REVERT: F 109 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7571 (mmtm) REVERT: F 243 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7711 (mm-40) REVERT: F 292 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7931 (tm130) REVERT: F 441 GLN cc_start: 0.8476 (mt0) cc_final: 0.8187 (mt0) REVERT: G 109 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7601 (mmtm) REVERT: G 243 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7647 (mm-40) REVERT: G 292 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7925 (tm130) REVERT: G 441 GLN cc_start: 0.8431 (mt0) cc_final: 0.7991 (mt0) REVERT: H 243 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7656 (mm-40) REVERT: H 292 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7933 (tm130) REVERT: H 441 GLN cc_start: 0.8465 (mt0) cc_final: 0.8152 (mt0) outliers start: 34 outliers final: 12 residues processed: 501 average time/residue: 2.4606 time to fit residues: 1426.9583 Evaluate side-chains 476 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 461 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 227 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 283 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 454 GLN B 454 GLN C 21 GLN C 454 GLN C 498 GLN D 21 GLN D 454 GLN D 498 GLN E 21 GLN E 454 GLN F 454 GLN F 498 GLN G 21 GLN G 454 GLN G 498 GLN H 21 GLN H 198 ASN H 454 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 25960 Z= 0.243 Angle : 0.531 4.539 35128 Z= 0.280 Chirality : 0.042 0.149 4064 Planarity : 0.004 0.048 4424 Dihedral : 8.745 96.018 4055 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.40 % Allowed : 15.18 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3248 helix: 1.29 (0.15), residues: 1320 sheet: 0.32 (0.30), residues: 288 loop : -0.50 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 466 PHE 0.010 0.001 PHE C 357 TYR 0.011 0.001 TYR C 348 ARG 0.003 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 471 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: A 109 LYS cc_start: 0.7802 (mmtp) cc_final: 0.7505 (mmtm) REVERT: A 243 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7637 (mm-40) REVERT: A 277 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: A 292 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7903 (tm130) REVERT: A 441 GLN cc_start: 0.8508 (mt0) cc_final: 0.8153 (mt0) REVERT: B 109 LYS cc_start: 0.7805 (mmtp) cc_final: 0.7527 (mmtm) REVERT: B 111 GLU cc_start: 0.7143 (tp30) cc_final: 0.6920 (tp30) REVERT: B 243 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7658 (mm-40) REVERT: B 277 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: B 292 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7913 (tm130) REVERT: C 109 LYS cc_start: 0.7803 (mmtp) cc_final: 0.7502 (mmtm) REVERT: C 243 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7646 (mm-40) REVERT: C 277 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: C 292 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7884 (tm130) REVERT: C 441 GLN cc_start: 0.8467 (mt0) cc_final: 0.8176 (mt0) REVERT: D 109 LYS cc_start: 0.7784 (mmtp) cc_final: 0.7500 (mmtm) REVERT: D 111 GLU cc_start: 0.7105 (tp30) cc_final: 0.6881 (tp30) REVERT: D 224 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7675 (ptp-170) REVERT: D 243 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7661 (mm-40) REVERT: D 277 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: D 292 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7888 (tm130) REVERT: D 441 GLN cc_start: 0.8397 (mt0) cc_final: 0.7985 (mt0) REVERT: D 495 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6720 (tpt) REVERT: E 109 LYS cc_start: 0.7827 (mmtp) cc_final: 0.7526 (mmtm) REVERT: E 243 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7637 (mm-40) REVERT: E 277 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: E 292 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7908 (tm130) REVERT: F 109 LYS cc_start: 0.7806 (mmtp) cc_final: 0.7530 (mmtm) REVERT: F 243 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7697 (mm-40) REVERT: F 277 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: F 292 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7918 (tm130) REVERT: F 441 GLN cc_start: 0.8446 (mt0) cc_final: 0.8153 (mt0) REVERT: G 109 LYS cc_start: 0.7814 (mmtp) cc_final: 0.7516 (mmtm) REVERT: G 111 GLU cc_start: 0.7134 (tp30) cc_final: 0.6919 (tp30) REVERT: G 243 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7651 (mm-40) REVERT: G 277 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: G 292 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7888 (tm130) REVERT: G 441 GLN cc_start: 0.8414 (mt0) cc_final: 0.7961 (mt0) REVERT: H 109 LYS cc_start: 0.7784 (mmtp) cc_final: 0.7470 (mmtm) REVERT: H 243 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7638 (mm-40) REVERT: H 277 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: H 292 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7921 (tm130) REVERT: H 441 GLN cc_start: 0.8490 (mt0) cc_final: 0.8157 (mt0) outliers start: 37 outliers final: 18 residues processed: 496 average time/residue: 2.4543 time to fit residues: 1412.5768 Evaluate side-chains 495 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 466 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 236 optimal weight: 0.0050 chunk 130 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 161 optimal weight: 0.0170 chunk 284 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN A 498 GLN B 441 GLN B 454 GLN C 454 GLN D 21 GLN D 454 GLN E 441 GLN E 454 GLN F 454 GLN G 21 GLN G 454 GLN H 21 GLN H 454 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 25960 Z= 0.157 Angle : 0.488 5.234 35128 Z= 0.254 Chirality : 0.041 0.140 4064 Planarity : 0.004 0.045 4424 Dihedral : 8.152 83.921 4055 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.32 % Allowed : 14.84 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3248 helix: 1.64 (0.15), residues: 1320 sheet: 0.21 (0.30), residues: 288 loop : -0.37 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 92 PHE 0.009 0.001 PHE H 401 TYR 0.008 0.001 TYR C 353 ARG 0.002 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 480 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7573 (mm-40) REVERT: A 277 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.6847 (tm-30) REVERT: A 292 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7869 (tm130) REVERT: A 441 GLN cc_start: 0.8477 (mt0) cc_final: 0.8127 (mt0) REVERT: B 111 GLU cc_start: 0.7093 (tp30) cc_final: 0.6889 (tp30) REVERT: B 243 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7618 (mm-40) REVERT: B 277 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: B 292 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7837 (tm130) REVERT: B 512 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7543 (mt) REVERT: C 243 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7590 (mm-40) REVERT: C 277 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: C 292 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7835 (tm130) REVERT: C 441 GLN cc_start: 0.8440 (mt0) cc_final: 0.8177 (mt0) REVERT: C 512 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7450 (mt) REVERT: D 111 GLU cc_start: 0.7080 (tp30) cc_final: 0.6853 (tp30) REVERT: D 224 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7733 (ptp-170) REVERT: D 243 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7620 (mm-40) REVERT: D 277 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: D 292 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7834 (tm130) REVERT: D 441 GLN cc_start: 0.8431 (mt0) cc_final: 0.8051 (mt0) REVERT: D 443 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8327 (t) REVERT: D 495 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6697 (tpt) REVERT: E 243 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7595 (mm-40) REVERT: E 277 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: E 292 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7831 (tm130) REVERT: E 495 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6651 (tpt) REVERT: F 243 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7621 (mm-40) REVERT: F 277 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: F 292 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7866 (tm130) REVERT: F 441 GLN cc_start: 0.8448 (mt0) cc_final: 0.8165 (mt0) REVERT: F 512 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7536 (mt) REVERT: G 111 GLU cc_start: 0.7100 (tp30) cc_final: 0.6881 (tp30) REVERT: G 243 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7593 (mm-40) REVERT: G 277 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: G 292 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7854 (tm130) REVERT: G 441 GLN cc_start: 0.8447 (mt0) cc_final: 0.8064 (mt0) REVERT: G 443 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8359 (t) REVERT: G 512 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7547 (mt) REVERT: H 243 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7613 (mm-40) REVERT: H 277 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: H 292 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7845 (tm130) REVERT: H 441 GLN cc_start: 0.8473 (mt0) cc_final: 0.8166 (mt0) REVERT: H 512 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7585 (mt) outliers start: 35 outliers final: 10 residues processed: 502 average time/residue: 2.4374 time to fit residues: 1432.3981 Evaluate side-chains 482 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 454 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 512 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 512 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 454 GLN B 21 GLN B 454 GLN B 498 GLN C 454 GLN D 454 GLN E 454 GLN E 498 GLN F 21 GLN F 230 ASN F 454 GLN G 454 GLN H 454 GLN H 498 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 25960 Z= 0.332 Angle : 0.575 5.966 35128 Z= 0.304 Chirality : 0.044 0.157 4064 Planarity : 0.005 0.052 4424 Dihedral : 8.843 87.389 4055 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.25 % Allowed : 15.26 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3248 helix: 1.34 (0.15), residues: 1320 sheet: 0.29 (0.31), residues: 288 loop : -0.41 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 466 PHE 0.015 0.002 PHE C 401 TYR 0.010 0.002 TYR C 353 ARG 0.004 0.000 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 465 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.7929 (mmtp) cc_final: 0.7640 (mmtm) REVERT: A 243 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7637 (mm-40) REVERT: A 277 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: A 292 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7943 (tm130) REVERT: A 441 GLN cc_start: 0.8496 (mt0) cc_final: 0.8123 (mt0) REVERT: B 109 LYS cc_start: 0.7922 (mmtp) cc_final: 0.7651 (mmtm) REVERT: B 111 GLU cc_start: 0.7186 (tp30) cc_final: 0.6959 (tp30) REVERT: B 243 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7722 (mm-40) REVERT: B 277 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: B 292 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7929 (tm130) REVERT: C 109 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7618 (mmtm) REVERT: C 243 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7714 (mm-40) REVERT: C 277 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: C 292 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7913 (tm130) REVERT: C 441 GLN cc_start: 0.8453 (mt0) cc_final: 0.8139 (mt0) REVERT: D 109 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7599 (mmtm) REVERT: D 111 GLU cc_start: 0.7161 (tp30) cc_final: 0.6943 (tp30) REVERT: D 224 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7741 (ptp-170) REVERT: D 243 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7704 (mm-40) REVERT: D 277 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: D 292 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7919 (tm130) REVERT: D 441 GLN cc_start: 0.8424 (mt0) cc_final: 0.8007 (mt0) REVERT: D 495 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6755 (tpt) REVERT: E 15 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: E 109 LYS cc_start: 0.7936 (mmtp) cc_final: 0.7645 (mmtm) REVERT: E 243 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7667 (mm-40) REVERT: E 277 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: E 292 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7926 (tm130) REVERT: E 495 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6707 (tpt) REVERT: F 109 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7622 (mmtm) REVERT: F 243 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7735 (mm-40) REVERT: F 277 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: F 292 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7941 (tm130) REVERT: F 441 GLN cc_start: 0.8479 (mt0) cc_final: 0.8181 (mt0) REVERT: G 109 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7644 (mmtm) REVERT: G 111 GLU cc_start: 0.7188 (tp30) cc_final: 0.6956 (tp30) REVERT: G 243 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7704 (mm-40) REVERT: G 277 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: G 292 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7909 (tm130) REVERT: G 441 GLN cc_start: 0.8453 (mt0) cc_final: 0.7988 (mt0) REVERT: H 109 LYS cc_start: 0.7879 (mmtp) cc_final: 0.7635 (mmtm) REVERT: H 243 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7678 (mm-40) REVERT: H 277 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: H 292 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7898 (tm130) REVERT: H 441 GLN cc_start: 0.8516 (mt0) cc_final: 0.8174 (mt0) outliers start: 33 outliers final: 16 residues processed: 482 average time/residue: 2.4576 time to fit residues: 1371.5110 Evaluate side-chains 490 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 462 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 267 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 454 GLN B 21 GLN B 441 GLN B 454 GLN C 21 GLN C 454 GLN D 21 GLN D 454 GLN E 21 GLN E 454 GLN F 21 GLN F 454 GLN G 454 GLN H 21 GLN H 454 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25960 Z= 0.230 Angle : 0.531 6.493 35128 Z= 0.277 Chirality : 0.042 0.148 4064 Planarity : 0.004 0.051 4424 Dihedral : 8.514 81.346 4055 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.13 % Allowed : 15.94 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3248 helix: 1.51 (0.15), residues: 1320 sheet: 0.40 (0.32), residues: 272 loop : -0.41 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 466 PHE 0.009 0.001 PHE A 401 TYR 0.010 0.001 TYR C 348 ARG 0.002 0.000 ARG E 412 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 459 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7599 (mm-40) REVERT: A 277 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: A 292 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7911 (tm130) REVERT: A 441 GLN cc_start: 0.8484 (mt0) cc_final: 0.8119 (mt0) REVERT: B 15 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: B 109 LYS cc_start: 0.7774 (mmtp) cc_final: 0.7494 (mmtm) REVERT: B 111 GLU cc_start: 0.7124 (tp30) cc_final: 0.6908 (tp30) REVERT: B 243 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7673 (mm-40) REVERT: B 277 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: B 292 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7880 (tm130) REVERT: B 512 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7524 (mt) REVERT: C 243 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7640 (mm-40) REVERT: C 277 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.6938 (tm-30) REVERT: C 292 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7874 (tm130) REVERT: C 441 GLN cc_start: 0.8450 (mt0) cc_final: 0.8169 (mt0) REVERT: D 109 LYS cc_start: 0.7748 (mmtp) cc_final: 0.7474 (mmtm) REVERT: D 111 GLU cc_start: 0.7117 (tp30) cc_final: 0.6907 (tp30) REVERT: D 224 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7751 (ptp-170) REVERT: D 243 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7677 (mm-40) REVERT: D 277 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: D 292 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7887 (tm130) REVERT: D 441 GLN cc_start: 0.8396 (mt0) cc_final: 0.7970 (mt0) REVERT: D 495 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6741 (tpt) REVERT: E 243 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7633 (mm-40) REVERT: E 277 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: E 292 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7893 (tm130) REVERT: E 495 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6656 (tpt) REVERT: F 243 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7672 (mm-40) REVERT: F 277 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: F 292 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7908 (tm130) REVERT: F 441 GLN cc_start: 0.8459 (mt0) cc_final: 0.8169 (mt0) REVERT: G 109 LYS cc_start: 0.7802 (mmtp) cc_final: 0.7509 (mmtm) REVERT: G 111 GLU cc_start: 0.7150 (tp30) cc_final: 0.6921 (tp30) REVERT: G 243 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7664 (mm-40) REVERT: G 277 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: G 292 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7876 (tm130) REVERT: G 441 GLN cc_start: 0.8430 (mt0) cc_final: 0.7969 (mt0) REVERT: G 512 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7546 (mt) REVERT: H 243 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7624 (mm-40) REVERT: H 277 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: H 292 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7934 (tm130) REVERT: H 441 GLN cc_start: 0.8489 (mt0) cc_final: 0.8147 (mt0) outliers start: 30 outliers final: 11 residues processed: 474 average time/residue: 2.4695 time to fit residues: 1357.9296 Evaluate side-chains 479 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 454 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 441 GLN B 454 GLN C 21 GLN C 454 GLN D 21 GLN D 454 GLN E 441 GLN E 454 GLN F 454 GLN G 21 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25960 Z= 0.200 Angle : 0.516 6.744 35128 Z= 0.269 Chirality : 0.041 0.146 4064 Planarity : 0.004 0.049 4424 Dihedral : 8.261 77.533 4052 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.10 % Allowed : 16.09 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3248 helix: 1.58 (0.15), residues: 1320 sheet: 0.32 (0.32), residues: 272 loop : -0.37 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 466 PHE 0.010 0.001 PHE C 401 TYR 0.009 0.001 TYR C 348 ARG 0.002 0.000 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 457 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7594 (mm-40) REVERT: A 277 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: A 292 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7907 (tm130) REVERT: A 441 GLN cc_start: 0.8471 (mt0) cc_final: 0.8108 (mt0) REVERT: B 111 GLU cc_start: 0.7137 (tp30) cc_final: 0.6913 (tp30) REVERT: B 243 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7637 (mm-40) REVERT: B 277 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: B 292 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7875 (tm130) REVERT: B 330 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8948 (pp) REVERT: B 512 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7535 (mt) REVERT: C 243 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7626 (mm-40) REVERT: C 277 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: C 292 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7855 (tm130) REVERT: C 441 GLN cc_start: 0.8445 (mt0) cc_final: 0.8179 (mt0) REVERT: D 111 GLU cc_start: 0.7099 (tp30) cc_final: 0.6885 (tp30) REVERT: D 224 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7763 (ptp-170) REVERT: D 243 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7648 (mm-40) REVERT: D 277 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: D 292 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7845 (tm130) REVERT: D 441 GLN cc_start: 0.8409 (mt0) cc_final: 0.7990 (mt0) REVERT: D 495 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6742 (tpt) REVERT: E 243 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7624 (mm-40) REVERT: E 277 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: E 292 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7856 (tm130) REVERT: E 495 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6647 (tpt) REVERT: F 243 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7658 (mm-40) REVERT: F 277 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: F 292 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7904 (tm130) REVERT: F 441 GLN cc_start: 0.8461 (mt0) cc_final: 0.8168 (mt0) REVERT: G 78 MET cc_start: 0.9379 (tpp) cc_final: 0.9115 (tpp) REVERT: G 111 GLU cc_start: 0.7131 (tp30) cc_final: 0.6898 (tp30) REVERT: G 243 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7626 (mm-40) REVERT: G 277 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: G 292 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7880 (tm130) REVERT: G 441 GLN cc_start: 0.8425 (mt0) cc_final: 0.7967 (mt0) REVERT: G 512 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7543 (mt) REVERT: H 243 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7593 (mm-40) REVERT: H 277 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: H 292 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7878 (tm130) REVERT: H 441 GLN cc_start: 0.8495 (mt0) cc_final: 0.8181 (mt0) outliers start: 29 outliers final: 13 residues processed: 471 average time/residue: 2.4365 time to fit residues: 1331.6763 Evaluate side-chains 479 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 452 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 177 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 278 optimal weight: 0.6980 chunk 293 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 454 GLN B 21 GLN B 441 GLN B 454 GLN C 454 GLN D 454 GLN E 21 GLN E 441 GLN E 454 GLN F 454 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 25960 Z= 0.188 Angle : 0.512 6.977 35128 Z= 0.266 Chirality : 0.041 0.145 4064 Planarity : 0.004 0.049 4424 Dihedral : 8.102 77.146 4052 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.02 % Allowed : 16.20 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3248 helix: 1.66 (0.15), residues: 1320 sheet: 0.27 (0.32), residues: 272 loop : -0.37 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 466 PHE 0.010 0.001 PHE B 401 TYR 0.009 0.001 TYR C 348 ARG 0.002 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 459 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7612 (mm-40) REVERT: A 277 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: A 292 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7898 (tm130) REVERT: A 441 GLN cc_start: 0.8465 (mt0) cc_final: 0.8105 (mt0) REVERT: B 111 GLU cc_start: 0.7138 (tp30) cc_final: 0.6916 (tp30) REVERT: B 243 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7630 (mm-40) REVERT: B 277 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: B 292 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7869 (tm130) REVERT: B 512 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7546 (mt) REVERT: C 243 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7623 (mm-40) REVERT: C 277 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: C 292 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7847 (tm130) REVERT: C 441 GLN cc_start: 0.8438 (mt0) cc_final: 0.8176 (mt0) REVERT: D 78 MET cc_start: 0.9379 (tpp) cc_final: 0.9118 (tpp) REVERT: D 224 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (ptp-170) REVERT: D 243 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7637 (mm-40) REVERT: D 277 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: D 292 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7843 (tm130) REVERT: D 441 GLN cc_start: 0.8410 (mt0) cc_final: 0.7991 (mt0) REVERT: D 443 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8349 (t) REVERT: E 243 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7589 (mm-40) REVERT: E 277 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: E 292 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7855 (tm130) REVERT: E 495 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6649 (tpt) REVERT: F 243 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7657 (mm-40) REVERT: F 277 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: F 292 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7881 (tm130) REVERT: F 441 GLN cc_start: 0.8452 (mt0) cc_final: 0.8155 (mt0) REVERT: G 78 MET cc_start: 0.9380 (tpp) cc_final: 0.9118 (tpp) REVERT: G 111 GLU cc_start: 0.7116 (tp30) cc_final: 0.6906 (tp30) REVERT: G 243 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7616 (mm-40) REVERT: G 277 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: G 292 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7846 (tm130) REVERT: G 441 GLN cc_start: 0.8420 (mt0) cc_final: 0.7956 (mt0) REVERT: G 443 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8330 (t) REVERT: H 243 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7640 (mm-40) REVERT: H 277 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: H 292 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7853 (tm130) REVERT: H 441 GLN cc_start: 0.8480 (mt0) cc_final: 0.8160 (mt0) outliers start: 27 outliers final: 10 residues processed: 473 average time/residue: 2.4730 time to fit residues: 1356.8317 Evaluate side-chains 475 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 452 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 326 optimal weight: 0.9980 chunk 300 optimal weight: 0.5980 chunk 260 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 454 GLN C 21 GLN C 454 GLN D 21 GLN D 454 GLN E 441 GLN E 454 GLN F 454 GLN G 21 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25960 Z= 0.209 Angle : 0.523 6.952 35128 Z= 0.272 Chirality : 0.042 0.147 4064 Planarity : 0.004 0.049 4424 Dihedral : 8.168 78.260 4052 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.87 % Allowed : 16.43 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3248 helix: 1.64 (0.15), residues: 1320 sheet: 0.27 (0.31), residues: 272 loop : -0.36 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 466 PHE 0.010 0.001 PHE C 401 TYR 0.009 0.001 TYR B 348 ARG 0.002 0.000 ARG E 412 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 455 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7620 (mm-40) REVERT: A 277 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: A 292 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7912 (tm130) REVERT: A 441 GLN cc_start: 0.8477 (mt0) cc_final: 0.8122 (mt0) REVERT: B 109 LYS cc_start: 0.7796 (mmtp) cc_final: 0.7511 (mmtm) REVERT: B 111 GLU cc_start: 0.7154 (tp30) cc_final: 0.6933 (tp30) REVERT: B 243 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7656 (mm-40) REVERT: B 277 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: B 292 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7873 (tm130) REVERT: C 243 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7624 (mm-40) REVERT: C 277 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: C 292 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7855 (tm130) REVERT: C 441 GLN cc_start: 0.8448 (mt0) cc_final: 0.8180 (mt0) REVERT: D 78 MET cc_start: 0.9386 (tpp) cc_final: 0.9120 (tpp) REVERT: D 109 LYS cc_start: 0.7800 (mmtp) cc_final: 0.7524 (mmtm) REVERT: D 243 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7673 (mm-40) REVERT: D 277 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: D 292 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7845 (tm130) REVERT: D 441 GLN cc_start: 0.8406 (mt0) cc_final: 0.7969 (mt0) REVERT: D 443 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8379 (t) REVERT: E 243 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7625 (mm-40) REVERT: E 277 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: E 292 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7884 (tm130) REVERT: E 495 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6674 (tpt) REVERT: F 243 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7656 (mm-40) REVERT: F 277 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: F 292 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7894 (tm130) REVERT: F 441 GLN cc_start: 0.8477 (mt0) cc_final: 0.8174 (mt0) REVERT: G 78 MET cc_start: 0.9387 (tpp) cc_final: 0.9116 (tpp) REVERT: G 109 LYS cc_start: 0.7814 (mmtp) cc_final: 0.7519 (mmtm) REVERT: G 111 GLU cc_start: 0.7134 (tp30) cc_final: 0.6927 (tp30) REVERT: G 243 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7646 (mm-40) REVERT: G 277 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: G 292 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7881 (tm130) REVERT: G 441 GLN cc_start: 0.8439 (mt0) cc_final: 0.7980 (mt0) REVERT: G 443 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8371 (t) REVERT: H 243 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7652 (mm-40) REVERT: H 277 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: H 292 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7885 (tm130) REVERT: H 441 GLN cc_start: 0.8483 (mt0) cc_final: 0.8163 (mt0) outliers start: 23 outliers final: 10 residues processed: 467 average time/residue: 2.5007 time to fit residues: 1355.3682 Evaluate side-chains 476 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 455 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 0.2980 chunk 277 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 260 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 454 GLN B 21 GLN B 441 GLN B 454 GLN C 454 GLN D 454 GLN E 441 GLN E 454 GLN F 454 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.086693 restraints weight = 78969.267| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.72 r_work: 0.2776 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 25960 Z= 0.158 Angle : 0.496 6.812 35128 Z= 0.256 Chirality : 0.041 0.143 4064 Planarity : 0.004 0.047 4424 Dihedral : 7.738 74.695 4048 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.79 % Allowed : 16.47 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3248 helix: 1.83 (0.15), residues: 1320 sheet: -0.21 (0.39), residues: 192 loop : -0.27 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 92 PHE 0.015 0.001 PHE E 401 TYR 0.008 0.001 TYR B 348 ARG 0.002 0.000 ARG G 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18982.43 seconds wall clock time: 324 minutes 8.08 seconds (19448.08 seconds total)