Starting phenix.real_space_refine on Wed May 28 02:30:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8o_42026/05_2025/8u8o_42026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8o_42026/05_2025/8u8o_42026.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/8u8o_42026/05_2025/8u8o_42026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8o_42026/05_2025/8u8o_42026.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8o_42026/05_2025/8u8o_42026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8o_42026/05_2025/8u8o_42026.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= 0.008 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 192 5.16 5 C 18760 2.51 5 N 5136 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "B" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "C" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "D" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "E" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "F" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "G" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "H" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3631 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 2 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 15.87, per 1000 atoms: 0.53 Number of scatterers: 30080 At special positions: 0 Unit cell: (159.327, 159.327, 134.037, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 192 16.00 P 72 15.00 O 5920 8.00 N 5136 7.00 C 18760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.00 Conformation dependent library (CDL) restraints added in 3.4 seconds 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 48 sheets defined 41.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... 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 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.630A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.601A 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 removed outlier: 3.736A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 417 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 486 Processing helix chain 'A' and resid 494 through 501 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 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.638A pdb=" N LYS B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.602A 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 removed outlier: 3.737A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 486 Processing helix chain 'B' and resid 494 through 501 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 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.633A pdb=" N LYS C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.612A 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 removed outlier: 3.738A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 417 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 486 Processing helix chain 'C' and resid 494 through 501 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 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.629A pdb=" N LYS D 229 " --> pdb=" O THR D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.589A 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 removed outlier: 3.737A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 417 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 486 Processing helix chain 'D' and resid 494 through 501 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 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 229 removed outlier: 3.638A pdb=" N LYS E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.602A 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 removed outlier: 3.736A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 417 through 421 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 486 Processing helix chain 'E' and resid 494 through 501 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 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.636A pdb=" N LYS F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.612A 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 removed outlier: 3.737A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 417 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 486 Processing helix chain 'F' and resid 494 through 501 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 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 164 Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 229 removed outlier: 3.634A pdb=" N LYS G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.594A 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 removed outlier: 3.736A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 417 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 486 Processing helix chain 'G' and resid 494 through 501 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 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 229 removed outlier: 3.634A pdb=" N LYS H 229 " --> pdb=" O THR H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.595A 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 removed outlier: 3.736A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 417 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 486 Processing helix chain 'H' and resid 494 through 501 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: 3.630A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.357A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 4.116A pdb=" N SER A 444 " --> pdb=" O THR D 510 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER D 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.940A pdb=" N SER A 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 444 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.621A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.361A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.967A 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=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.617A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.375A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.966A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER D 444 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.631A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.652A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.375A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.619A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.651A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.359A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 402 removed outlier: 4.112A pdb=" N SER E 444 " --> pdb=" O THR H 510 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.917A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER F 444 " --> pdb=" O THR E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.620A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.370A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.902A pdb=" N SER F 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER G 444 " --> pdb=" O THR F 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.622A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.653A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.369A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.974A pdb=" N SER G 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER H 444 " --> pdb=" O THR G 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.631A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.651A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.374A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) 1169 hydrogen bonds defined for protein. 3267 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: 12.87 Time building geometry restraints manager: 8.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4969 1.30 - 1.43: 7402 1.43 - 1.56: 17765 1.56 - 1.69: 128 1.69 - 1.82: 328 Bond restraints: 30592 Sorted by residual: bond pdb=" C5 IMP A 603 " pdb=" C6 IMP A 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 IMP H 603 " pdb=" C6 IMP H 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 IMP D 603 " pdb=" C6 IMP D 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C5 IMP E 603 " pdb=" C6 IMP E 603 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C5 IMP G 603 " pdb=" C6 IMP G 603 " ideal model delta sigma weight residual 1.390 1.533 -0.143 2.00e-02 2.50e+03 5.15e+01 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 40050 1.79 - 3.58: 1246 3.58 - 5.36: 165 5.36 - 7.15: 51 7.15 - 8.94: 24 Bond angle restraints: 41536 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 130.93 8.94 1.00e+00 1.00e+00 7.99e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 131.00 8.87 1.00e+00 1.00e+00 7.86e+01 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 131.03 8.84 1.00e+00 1.00e+00 7.81e+01 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 131.06 8.81 1.00e+00 1.00e+00 7.77e+01 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 131.87 8.00 1.00e+00 1.00e+00 6.40e+01 ... (remaining 41531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.18: 17766 31.18 - 62.37: 1042 62.37 - 93.55: 92 93.55 - 124.73: 0 124.73 - 155.92: 4 Dihedral angle restraints: 18904 sinusoidal: 8016 harmonic: 10888 Sorted by residual: dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.15 -155.92 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.17 -155.90 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' IMP E 603 " pdb=" O5' IMP E 603 " pdb=" P IMP E 603 " pdb=" O2P IMP E 603 " ideal model delta sinusoidal sigma weight residual -168.07 -12.27 -155.80 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 18901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2650 0.030 - 0.060: 1280 0.060 - 0.090: 539 0.090 - 0.119: 291 0.119 - 0.149: 80 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ILE C 439 " pdb=" N ILE C 439 " pdb=" C ILE C 439 " pdb=" CB ILE C 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE D 439 " pdb=" N ILE D 439 " pdb=" C ILE D 439 " pdb=" CB ILE D 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE F 439 " pdb=" N ILE F 439 " pdb=" C ILE F 439 " pdb=" CB ILE F 439 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 4837 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 63 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO G 64 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 64 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 63 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO D 64 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.027 5.00e-02 4.00e+02 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6185 2.79 - 3.31: 28229 3.31 - 3.84: 51888 3.84 - 4.37: 63870 4.37 - 4.90: 102765 Nonbonded interactions: 252937 Sorted by model distance: nonbonded pdb=" O ALA G 396 " pdb=" NZ LYS G 409 " model vdw 2.256 3.120 nonbonded pdb=" O ALA F 396 " pdb=" NZ LYS F 409 " model vdw 2.261 3.120 nonbonded pdb=" O ALA E 396 " pdb=" NZ LYS E 409 " model vdw 2.264 3.120 nonbonded pdb=" O ALA B 396 " pdb=" NZ LYS B 409 " model vdw 2.264 3.120 nonbonded pdb=" O ALA C 396 " pdb=" NZ LYS C 409 " model vdw 2.265 3.120 ... (remaining 252932 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: 0.25 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 4.670 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: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 66.050 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.006 0.144 30592 Z= 0.313 Angle : 0.783 8.941 41536 Z= 0.442 Chirality : 0.046 0.149 4840 Planarity : 0.005 0.049 5160 Dihedral : 18.028 155.916 11960 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.24 % Allowed : 12.15 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 3808 helix: 0.80 (0.13), residues: 1464 sheet: 0.15 (0.25), residues: 448 loop : -0.44 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 92 PHE 0.014 0.002 PHE C 357 TYR 0.012 0.002 TYR H 353 ARG 0.004 0.001 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.15353 ( 1169) hydrogen bonds : angle 6.30070 ( 3267) covalent geometry : bond 0.00642 (30592) covalent geometry : angle 0.78311 (41536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 855 time to evaluate : 3.480 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 outliers start: 39 outliers final: 11 residues processed: 875 average time/residue: 1.5391 time to fit residues: 1558.3639 Evaluate side-chains 664 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 653 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 300 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 348 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN A 368 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 441 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 368 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 368 GLN ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.093060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081800 restraints weight = 54426.810| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.94 r_work: 0.3138 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30592 Z= 0.140 Angle : 0.574 6.376 41536 Z= 0.304 Chirality : 0.043 0.151 4840 Planarity : 0.004 0.047 5160 Dihedral : 12.808 179.384 5178 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.20 % Allowed : 17.12 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.14), residues: 3808 helix: 1.57 (0.14), residues: 1464 sheet: 0.30 (0.24), residues: 448 loop : -0.26 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 92 PHE 0.010 0.001 PHE D 165 TYR 0.012 0.001 TYR G 400 ARG 0.009 0.001 ARG G 136 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 1169) hydrogen bonds : angle 5.49357 ( 3267) covalent geometry : bond 0.00332 (30592) covalent geometry : angle 0.57371 (41536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 689 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8097 (tmm-80) REVERT: A 352 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8692 (tp30) REVERT: A 447 ILE cc_start: 0.8962 (mm) cc_final: 0.8756 (mt) REVERT: B 438 LYS cc_start: 0.8757 (ptmt) cc_final: 0.8523 (mtmm) REVERT: B 447 ILE cc_start: 0.8899 (mm) cc_final: 0.8654 (mt) REVERT: C 136 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8055 (ttp80) REVERT: C 491 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8529 (tp30) REVERT: D 136 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8055 (ttp80) REVERT: D 410 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8218 (ttpp) REVERT: E 410 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8265 (ttpp) REVERT: F 136 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7653 (tmm-80) REVERT: F 410 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8303 (ttpp) REVERT: G 136 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7768 (tmm-80) REVERT: H 352 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8499 (tp30) outliers start: 69 outliers final: 19 residues processed: 726 average time/residue: 1.5995 time to fit residues: 1336.9528 Evaluate side-chains 648 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 628 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 418 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 290 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 170 optimal weight: 7.9990 chunk 322 optimal weight: 4.9990 chunk 339 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 368 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 441 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN H 303 ASN H 441 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080729 restraints weight = 54983.930| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.93 r_work: 0.3122 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30592 Z= 0.125 Angle : 0.522 6.551 41536 Z= 0.280 Chirality : 0.042 0.155 4840 Planarity : 0.004 0.037 5160 Dihedral : 11.861 149.512 5160 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.81 % Allowed : 17.09 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3808 helix: 1.60 (0.14), residues: 1520 sheet: 0.71 (0.26), residues: 352 loop : -0.14 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 92 PHE 0.007 0.001 PHE D 114 TYR 0.011 0.001 TYR F 353 ARG 0.009 0.001 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 1169) hydrogen bonds : angle 5.31857 ( 3267) covalent geometry : bond 0.00295 (30592) covalent geometry : angle 0.52229 (41536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 646 time to evaluate : 3.172 Fit side-chains REVERT: A 132 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 136 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8070 (ttp80) REVERT: A 153 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8252 (mmmm) REVERT: A 447 ILE cc_start: 0.9054 (mm) cc_final: 0.8839 (mt) REVERT: B 132 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7758 (tp30) REVERT: B 136 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7865 (mtm110) REVERT: B 438 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8457 (mtmm) REVERT: B 447 ILE cc_start: 0.8958 (mm) cc_final: 0.8729 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 136 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8070 (ttp80) REVERT: C 153 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8411 (tppp) REVERT: C 491 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8511 (tp30) REVERT: D 132 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7668 (tm-30) REVERT: D 410 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8365 (ttpp) REVERT: E 132 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7660 (tm-30) REVERT: E 136 ARG cc_start: 0.7946 (tmm-80) cc_final: 0.7527 (ttp80) REVERT: E 137 HIS cc_start: 0.8711 (OUTLIER) cc_final: 0.8345 (m-70) REVERT: E 410 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8410 (ttpp) REVERT: E 487 GLU cc_start: 0.5368 (mm-30) cc_final: 0.3535 (mm-30) REVERT: F 132 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7435 (tm-30) REVERT: F 136 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7516 (ttp80) REVERT: F 410 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8412 (ttpp) REVERT: F 487 GLU cc_start: 0.5652 (mm-30) cc_final: 0.3579 (mm-30) REVERT: G 487 GLU cc_start: 0.5758 (mm-30) cc_final: 0.3933 (mm-30) REVERT: G 495 MET cc_start: 0.8629 (tpp) cc_final: 0.8412 (tpp) REVERT: H 132 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7508 (tm-30) REVERT: H 352 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8496 (tp30) REVERT: H 410 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8412 (ttpp) REVERT: H 487 GLU cc_start: 0.5468 (mm-30) cc_final: 0.4788 (mm-30) outliers start: 88 outliers final: 31 residues processed: 696 average time/residue: 1.5219 time to fit residues: 1222.6720 Evaluate side-chains 670 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 636 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 91 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 260 optimal weight: 0.0370 chunk 35 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078370 restraints weight = 55568.440| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.93 r_work: 0.3089 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30592 Z= 0.168 Angle : 0.559 7.322 41536 Z= 0.297 Chirality : 0.043 0.161 4840 Planarity : 0.004 0.038 5160 Dihedral : 11.364 104.524 5160 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 17.86 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3808 helix: 1.79 (0.14), residues: 1472 sheet: 0.38 (0.24), residues: 432 loop : -0.15 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 92 PHE 0.011 0.002 PHE D 114 TYR 0.011 0.001 TYR A 353 ARG 0.009 0.001 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 1169) hydrogen bonds : angle 5.25529 ( 3267) covalent geometry : bond 0.00411 (30592) covalent geometry : angle 0.55866 (41536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 659 time to evaluate : 3.282 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 136 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8087 (ttp80) REVERT: A 447 ILE cc_start: 0.9109 (mm) cc_final: 0.8903 (mt) REVERT: B 132 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7870 (tp30) REVERT: B 136 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8011 (mtm110) REVERT: B 149 THR cc_start: 0.8668 (t) cc_final: 0.8402 (p) REVERT: B 447 ILE cc_start: 0.9044 (mm) cc_final: 0.8817 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7431 (tm-30) REVERT: C 136 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8113 (ttp80) REVERT: C 303 ASN cc_start: 0.8413 (m-40) cc_final: 0.8204 (m-40) REVERT: C 491 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8526 (tp30) REVERT: D 132 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7573 (tm-30) REVERT: D 153 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8443 (tppt) REVERT: D 196 GLU cc_start: 0.8334 (mp0) cc_final: 0.8055 (mp0) REVERT: D 410 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8516 (ttpp) REVERT: E 132 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7248 (tm-30) REVERT: E 199 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8242 (tm-30) REVERT: E 410 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8515 (ttpp) REVERT: E 487 GLU cc_start: 0.5640 (mm-30) cc_final: 0.3568 (mm-30) REVERT: F 132 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7315 (tm-30) REVERT: F 136 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7671 (ttp80) REVERT: F 487 GLU cc_start: 0.5969 (mm-30) cc_final: 0.3737 (mm-30) REVERT: G 153 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8334 (tppt) REVERT: G 487 GLU cc_start: 0.6176 (mm-30) cc_final: 0.4394 (mm-30) REVERT: G 495 MET cc_start: 0.8640 (tpp) cc_final: 0.8391 (tpp) REVERT: H 132 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7585 (tm-30) REVERT: H 410 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8521 (ttpp) REVERT: H 487 GLU cc_start: 0.5891 (mm-30) cc_final: 0.5115 (mm-30) outliers start: 94 outliers final: 45 residues processed: 708 average time/residue: 1.5462 time to fit residues: 1267.6105 Evaluate side-chains 676 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 630 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 333 optimal weight: 0.8980 chunk 338 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 325 optimal weight: 7.9990 chunk 377 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 237 optimal weight: 0.9980 chunk 378 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN H 303 ASN H 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.079414 restraints weight = 55224.509| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.92 r_work: 0.3113 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30592 Z= 0.121 Angle : 0.537 7.073 41536 Z= 0.285 Chirality : 0.042 0.153 4840 Planarity : 0.004 0.039 5160 Dihedral : 10.993 88.759 5160 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.58 % Allowed : 19.67 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3808 helix: 1.78 (0.14), residues: 1520 sheet: 1.00 (0.30), residues: 272 loop : -0.07 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 92 PHE 0.007 0.001 PHE E 99 TYR 0.010 0.001 TYR E 353 ARG 0.010 0.001 ARG F 203 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1169) hydrogen bonds : angle 5.16990 ( 3267) covalent geometry : bond 0.00285 (30592) covalent geometry : angle 0.53733 (41536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 651 time to evaluate : 3.529 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7899 (tm-30) cc_final: 0.6731 (tm-30) REVERT: A 136 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8126 (ttm-80) REVERT: A 447 ILE cc_start: 0.9090 (mm) cc_final: 0.8886 (mt) REVERT: B 132 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7880 (tp30) REVERT: B 136 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8099 (mtm110) REVERT: B 149 THR cc_start: 0.8669 (t) cc_final: 0.8459 (p) REVERT: B 153 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8209 (tppt) REVERT: B 447 ILE cc_start: 0.9046 (mm) cc_final: 0.8816 (OUTLIER) REVERT: C 132 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 136 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8111 (ttp80) REVERT: C 149 THR cc_start: 0.8651 (t) cc_final: 0.8372 (p) REVERT: D 132 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7483 (tm-30) REVERT: D 199 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7478 (tm-30) REVERT: E 132 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7492 (tm-30) REVERT: E 196 GLU cc_start: 0.8283 (mp0) cc_final: 0.8068 (mp0) REVERT: E 487 GLU cc_start: 0.5662 (mm-30) cc_final: 0.3512 (mm-30) REVERT: F 132 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7074 (tm-30) REVERT: F 136 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7606 (ttp80) REVERT: F 149 THR cc_start: 0.8607 (t) cc_final: 0.8342 (p) REVERT: F 153 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8510 (tppt) REVERT: F 487 GLU cc_start: 0.5880 (mm-30) cc_final: 0.3613 (mm-30) REVERT: G 136 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7623 (tmm-80) REVERT: G 410 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8529 (ttpp) REVERT: G 487 GLU cc_start: 0.6109 (mm-30) cc_final: 0.4063 (mm-30) REVERT: G 495 MET cc_start: 0.8616 (tpp) cc_final: 0.8353 (tpp) REVERT: H 132 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7417 (tm-30) REVERT: H 196 GLU cc_start: 0.8247 (mp0) cc_final: 0.7968 (mp0) REVERT: H 410 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8491 (ttpp) REVERT: H 487 GLU cc_start: 0.5783 (mm-30) cc_final: 0.3838 (mm-30) outliers start: 81 outliers final: 39 residues processed: 700 average time/residue: 1.4840 time to fit residues: 1204.3690 Evaluate side-chains 686 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 646 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 410 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 290 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 286 optimal weight: 0.7980 chunk 346 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 223 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078631 restraints weight = 55486.857| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.92 r_work: 0.3096 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30592 Z= 0.140 Angle : 0.559 7.984 41536 Z= 0.295 Chirality : 0.042 0.148 4840 Planarity : 0.004 0.044 5160 Dihedral : 10.875 87.947 5160 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.12 % Allowed : 19.83 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.14), residues: 3808 helix: 2.02 (0.14), residues: 1464 sheet: 0.68 (0.27), residues: 352 loop : -0.12 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 137 PHE 0.009 0.001 PHE D 114 TYR 0.011 0.001 TYR B 353 ARG 0.011 0.001 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 1169) hydrogen bonds : angle 5.13533 ( 3267) covalent geometry : bond 0.00339 (30592) covalent geometry : angle 0.55937 (41536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 656 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8005 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 136 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8138 (ttm-80) REVERT: B 132 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7913 (tp30) REVERT: B 136 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8214 (mtm110) REVERT: B 196 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: C 132 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7423 (tm-30) REVERT: C 136 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8177 (ttp80) REVERT: C 149 THR cc_start: 0.8694 (t) cc_final: 0.8435 (p) REVERT: D 132 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7635 (tm-30) REVERT: D 199 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7450 (tm-30) REVERT: D 203 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7840 (mtm110) REVERT: E 132 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7579 (tm-30) REVERT: E 196 GLU cc_start: 0.8364 (mp0) cc_final: 0.8095 (mp0) REVERT: E 487 GLU cc_start: 0.5689 (mm-30) cc_final: 0.3432 (mm-30) REVERT: F 132 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7182 (tm-30) REVERT: F 136 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7805 (ttp80) REVERT: F 149 THR cc_start: 0.8607 (t) cc_final: 0.8380 (p) REVERT: F 153 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8550 (tppt) REVERT: F 196 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: F 487 GLU cc_start: 0.5991 (mm-30) cc_final: 0.3764 (mm-30) REVERT: G 109 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8348 (mptm) REVERT: G 132 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7417 (tm-30) REVERT: G 410 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8533 (ttpp) REVERT: G 487 GLU cc_start: 0.6138 (mm-30) cc_final: 0.4175 (mm-30) REVERT: G 495 MET cc_start: 0.8692 (tpp) cc_final: 0.8402 (tpp) REVERT: H 132 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7375 (tm-30) REVERT: H 136 ARG cc_start: 0.8376 (mtm110) cc_final: 0.7990 (mtm110) REVERT: H 196 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: H 410 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8518 (ttpp) REVERT: H 487 GLU cc_start: 0.5760 (mm-30) cc_final: 0.3739 (mm-30) outliers start: 98 outliers final: 49 residues processed: 711 average time/residue: 1.4836 time to fit residues: 1221.4666 Evaluate side-chains 702 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 647 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 111 optimal weight: 0.0040 chunk 216 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 297 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 367 optimal weight: 0.0020 chunk 321 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080901 restraints weight = 55622.576| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.91 r_work: 0.3135 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30592 Z= 0.108 Angle : 0.549 8.267 41536 Z= 0.288 Chirality : 0.041 0.150 4840 Planarity : 0.004 0.050 5160 Dihedral : 10.451 88.798 5160 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.42 % Allowed : 20.66 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3808 helix: 1.98 (0.14), residues: 1512 sheet: 1.01 (0.29), residues: 272 loop : -0.04 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 92 PHE 0.006 0.001 PHE E 401 TYR 0.009 0.001 TYR C 353 ARG 0.013 0.001 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 1169) hydrogen bonds : angle 5.04638 ( 3267) covalent geometry : bond 0.00252 (30592) covalent geometry : angle 0.54914 (41536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 662 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7995 (tm-30) cc_final: 0.6821 (tm-30) REVERT: A 136 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8120 (ttm-80) REVERT: B 132 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7854 (OUTLIER) REVERT: B 136 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8200 (mtm110) REVERT: B 196 GLU cc_start: 0.8196 (mp0) cc_final: 0.7906 (mp0) REVERT: C 132 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7683 (tm-30) REVERT: C 149 THR cc_start: 0.8651 (t) cc_final: 0.8422 (p) REVERT: C 216 ASP cc_start: 0.7858 (m-30) cc_final: 0.7649 (t0) REVERT: D 132 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7571 (tm-30) REVERT: D 199 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7552 (tm-30) REVERT: E 132 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7502 (tm-30) REVERT: E 487 GLU cc_start: 0.5670 (mm-30) cc_final: 0.3536 (mm-30) REVERT: F 132 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7594 (tm-30) REVERT: F 196 GLU cc_start: 0.8256 (mp0) cc_final: 0.8005 (mp0) REVERT: F 487 GLU cc_start: 0.5846 (mm-30) cc_final: 0.3703 (mm-30) REVERT: G 410 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8514 (ttpp) REVERT: G 487 GLU cc_start: 0.5947 (mm-30) cc_final: 0.3884 (mm-30) REVERT: G 495 MET cc_start: 0.8665 (tpp) cc_final: 0.8365 (tpp) REVERT: H 132 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7322 (tm-30) REVERT: H 136 ARG cc_start: 0.8356 (mtm110) cc_final: 0.7957 (mtm110) REVERT: H 196 GLU cc_start: 0.8336 (mp0) cc_final: 0.8065 (mp0) REVERT: H 241 GLN cc_start: 0.8841 (mm110) cc_final: 0.8562 (mm110) REVERT: H 410 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8501 (ttpp) REVERT: H 487 GLU cc_start: 0.5693 (mm-30) cc_final: 0.4179 (mm-30) outliers start: 76 outliers final: 36 residues processed: 711 average time/residue: 1.4808 time to fit residues: 1222.7828 Evaluate side-chains 686 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 649 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 354 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 357 optimal weight: 0.0040 chunk 281 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN E 441 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.080738 restraints weight = 55451.010| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.91 r_work: 0.3133 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30592 Z= 0.113 Angle : 0.566 11.048 41536 Z= 0.295 Chirality : 0.041 0.178 4840 Planarity : 0.004 0.057 5160 Dihedral : 10.235 89.647 5160 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.88 % Allowed : 21.97 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 3808 helix: 2.00 (0.14), residues: 1512 sheet: 1.00 (0.28), residues: 272 loop : -0.03 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 92 PHE 0.024 0.001 PHE G 401 TYR 0.009 0.001 TYR B 353 ARG 0.014 0.001 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 1169) hydrogen bonds : angle 5.00756 ( 3267) covalent geometry : bond 0.00266 (30592) covalent geometry : angle 0.56649 (41536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 657 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8006 (tm-30) cc_final: 0.6892 (tm-30) REVERT: A 136 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8202 (ttm-80) REVERT: B 132 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7828 (OUTLIER) REVERT: B 136 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8188 (mtm110) REVERT: B 196 GLU cc_start: 0.8249 (mp0) cc_final: 0.8001 (mp0) REVERT: C 132 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 149 THR cc_start: 0.8609 (t) cc_final: 0.8400 (p) REVERT: D 132 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7541 (tm-30) REVERT: D 199 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7433 (tm-30) REVERT: D 203 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7726 (mtm110) REVERT: E 132 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7501 (tm-30) REVERT: E 487 GLU cc_start: 0.5753 (mm-30) cc_final: 0.3710 (mm-30) REVERT: F 132 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7291 (tm-30) REVERT: F 196 GLU cc_start: 0.8280 (mp0) cc_final: 0.8072 (mp0) REVERT: F 487 GLU cc_start: 0.5847 (mm-30) cc_final: 0.3750 (mm-30) REVERT: G 410 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8534 (ttpp) REVERT: G 487 GLU cc_start: 0.5980 (mm-30) cc_final: 0.4133 (mm-30) REVERT: G 495 MET cc_start: 0.8681 (tpp) cc_final: 0.8384 (tpp) REVERT: H 132 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7300 (tm-30) REVERT: H 136 ARG cc_start: 0.8381 (mtm110) cc_final: 0.8026 (mtm110) REVERT: H 410 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8541 (ttpp) REVERT: H 487 GLU cc_start: 0.5721 (mm-30) cc_final: 0.3943 (mm-30) outliers start: 59 outliers final: 38 residues processed: 689 average time/residue: 1.5101 time to fit residues: 1206.3757 Evaluate side-chains 673 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 634 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 406 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 410 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 201 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 359 optimal weight: 0.0470 chunk 343 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080560 restraints weight = 55192.219| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.90 r_work: 0.3131 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30592 Z= 0.121 Angle : 0.594 12.680 41536 Z= 0.308 Chirality : 0.041 0.164 4840 Planarity : 0.004 0.064 5160 Dihedral : 10.060 89.854 5160 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.43 % Allowed : 22.61 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3808 helix: 2.11 (0.14), residues: 1472 sheet: 1.02 (0.28), residues: 272 loop : -0.03 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 92 PHE 0.024 0.001 PHE F 401 TYR 0.009 0.001 TYR A 353 ARG 0.014 0.001 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 1169) hydrogen bonds : angle 4.97593 ( 3267) covalent geometry : bond 0.00288 (30592) covalent geometry : angle 0.59358 (41536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 648 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8000 (tm-30) cc_final: 0.6853 (tm-30) REVERT: A 136 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8163 (ttm-80) REVERT: A 303 ASN cc_start: 0.8144 (m-40) cc_final: 0.7918 (m-40) REVERT: B 132 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7813 (OUTLIER) REVERT: B 136 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8180 (mtm110) REVERT: B 196 GLU cc_start: 0.8261 (mp0) cc_final: 0.8037 (mp0) REVERT: B 438 LYS cc_start: 0.8738 (ptmt) cc_final: 0.8496 (ptmt) REVERT: C 132 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7698 (tm-30) REVERT: D 132 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7585 (tm-30) REVERT: D 199 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7490 (tm-30) REVERT: D 203 ARG cc_start: 0.8110 (mtm110) cc_final: 0.7792 (mtm110) REVERT: E 132 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7531 (tm-30) REVERT: E 487 GLU cc_start: 0.5732 (mm-30) cc_final: 0.3768 (mm-30) REVERT: F 132 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7408 (tm-30) REVERT: F 136 ARG cc_start: 0.8293 (mtm110) cc_final: 0.7920 (mtm110) REVERT: F 216 ASP cc_start: 0.7933 (m-30) cc_final: 0.7686 (t0) REVERT: F 487 GLU cc_start: 0.5829 (mm-30) cc_final: 0.3742 (mm-30) REVERT: G 132 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7027 (tm-30) REVERT: G 410 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8548 (ttpp) REVERT: G 487 GLU cc_start: 0.6034 (mm-30) cc_final: 0.4267 (mm-30) REVERT: G 495 MET cc_start: 0.8654 (tpp) cc_final: 0.8358 (tpp) REVERT: H 132 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7462 (tp30) REVERT: H 136 ARG cc_start: 0.8452 (mtm110) cc_final: 0.7938 (mtm110) REVERT: H 216 ASP cc_start: 0.6832 (t0) cc_final: 0.6627 (t0) REVERT: H 410 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8569 (ttpp) REVERT: H 487 GLU cc_start: 0.5661 (mm-30) cc_final: 0.3923 (mm-30) outliers start: 45 outliers final: 34 residues processed: 678 average time/residue: 1.5081 time to fit residues: 1191.6326 Evaluate side-chains 665 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 630 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 76 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 339 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 280 optimal weight: 6.9990 chunk 286 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 441 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.079703 restraints weight = 55254.687| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.90 r_work: 0.3116 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30592 Z= 0.134 Angle : 0.619 13.055 41536 Z= 0.321 Chirality : 0.042 0.160 4840 Planarity : 0.005 0.062 5160 Dihedral : 10.004 89.637 5160 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.53 % Allowed : 22.58 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3808 helix: 2.23 (0.14), residues: 1424 sheet: 0.71 (0.25), residues: 352 loop : -0.14 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 137 PHE 0.008 0.001 PHE F 401 TYR 0.010 0.001 TYR C 353 ARG 0.015 0.001 ARG E 203 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 1169) hydrogen bonds : angle 5.01877 ( 3267) covalent geometry : bond 0.00321 (30592) covalent geometry : angle 0.61936 (41536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 641 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7987 (tm-30) cc_final: 0.6904 (tp30) REVERT: A 136 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8150 (ttm-80) REVERT: A 303 ASN cc_start: 0.8199 (m-40) cc_final: 0.7983 (m-40) REVERT: B 132 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7811 (tp30) REVERT: B 136 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8201 (mtm110) REVERT: B 438 LYS cc_start: 0.8724 (ptmt) cc_final: 0.8477 (ptmt) REVERT: C 132 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 216 ASP cc_start: 0.7076 (t0) cc_final: 0.6873 (t0) REVERT: D 132 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7532 (tm-30) REVERT: D 199 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7534 (tm-30) REVERT: D 203 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7847 (mtm110) REVERT: E 132 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7524 (tm-30) REVERT: E 487 GLU cc_start: 0.5868 (mm-30) cc_final: 0.3758 (mm-30) REVERT: F 132 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7350 (tm-30) REVERT: F 136 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7986 (mtm110) REVERT: F 487 GLU cc_start: 0.5907 (mm-30) cc_final: 0.3799 (mm-30) REVERT: G 132 GLU cc_start: 0.8022 (tm-30) cc_final: 0.6759 (tm-30) REVERT: G 410 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8553 (ttpp) REVERT: G 487 GLU cc_start: 0.6129 (mm-30) cc_final: 0.4363 (mm-30) REVERT: G 495 MET cc_start: 0.8679 (tpp) cc_final: 0.8390 (tpp) REVERT: H 132 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7455 (tp30) REVERT: H 136 ARG cc_start: 0.8383 (mtm110) cc_final: 0.7907 (mtm110) REVERT: H 410 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8592 (ttpp) REVERT: H 487 GLU cc_start: 0.5798 (mm-30) cc_final: 0.3770 (mm-30) outliers start: 48 outliers final: 35 residues processed: 673 average time/residue: 1.4790 time to fit residues: 1155.5345 Evaluate side-chains 670 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 633 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 219 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 356 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078702 restraints weight = 54749.734| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.95 r_work: 0.3096 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30592 Z= 0.147 Angle : 0.638 13.170 41536 Z= 0.330 Chirality : 0.042 0.161 4840 Planarity : 0.005 0.069 5160 Dihedral : 10.033 89.927 5160 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.66 % Allowed : 22.86 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3808 helix: 2.14 (0.14), residues: 1424 sheet: 0.39 (0.23), residues: 448 loop : -0.16 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 92 PHE 0.008 0.001 PHE C 114 TYR 0.011 0.001 TYR F 353 ARG 0.015 0.001 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 1169) hydrogen bonds : angle 5.05113 ( 3267) covalent geometry : bond 0.00356 (30592) covalent geometry : angle 0.63833 (41536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28024.91 seconds wall clock time: 482 minutes 54.45 seconds (28974.45 seconds total)