Starting phenix.real_space_refine on Sat Aug 8 02:46:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdo_64990/08_2026/9vdo_64990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdo_64990/08_2026/9vdo_64990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vdo_64990/08_2026/9vdo_64990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdo_64990/08_2026/9vdo_64990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vdo_64990/08_2026/9vdo_64990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdo_64990/08_2026/9vdo_64990.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 12 7.51 5 P 48 5.49 5 S 132 5.16 5 C 15834 2.51 5 N 4152 2.21 5 O 4848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25026 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "B" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "F" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "H" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "K" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MN': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MN': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MN': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MN': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MN': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MN': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.56, per 1000 atoms: 0.18 Number of scatterers: 25026 At special positions: 0 Unit cell: (135.85, 132.05, 105.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 12 24.99 S 132 16.00 P 48 15.00 O 4848 8.00 N 4152 7.00 C 15834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 993.1 milliseconds 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 12 sheets defined 60.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.586A pdb=" N ALA A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.666A pdb=" N ASN A 95 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 160 through 168 removed outlier: 4.227A pdb=" N TRP A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.824A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.663A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.690A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.563A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 Processing helix chain 'A' and resid 366 through 375 Proline residue: A 370 - end of helix removed outlier: 3.722A pdb=" N GLY A 373 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 402 removed outlier: 3.587A pdb=" N ASN A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 422 through 433 Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.820A pdb=" N ASP A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.559A pdb=" N ALA B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.686A pdb=" N ASN B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.524A pdb=" N PHE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 4.247A pdb=" N TRP B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.787A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.667A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.685A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.535A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 Processing helix chain 'B' and resid 366 through 370 Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.895A pdb=" N LEU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 401 removed outlier: 3.569A pdb=" N ASN B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.778A pdb=" N ASP B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 81 through 95 removed outlier: 3.684A pdb=" N ASN D 95 " --> pdb=" O HIS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 127 through 140 Processing helix chain 'D' and resid 160 through 168 removed outlier: 4.248A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.786A pdb=" N LYS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.662A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.705A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.535A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 365 Processing helix chain 'D' and resid 366 through 370 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.893A pdb=" N LEU D 375 " --> pdb=" O TYR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 402 removed outlier: 3.513A pdb=" N ASN D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.802A pdb=" N ASP D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 40 through 50 removed outlier: 3.597A pdb=" N ALA F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.615A pdb=" N ASN F 95 " --> pdb=" O HIS F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 127 through 140 removed outlier: 3.550A pdb=" N PHE F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 removed outlier: 4.191A pdb=" N TRP F 164 " --> pdb=" O HIS F 160 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.818A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 230 removed outlier: 3.670A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 266 removed outlier: 4.016A pdb=" N TYR F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 3.701A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 329 removed outlier: 3.514A pdb=" N VAL F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 343 removed outlier: 3.585A pdb=" N VAL F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 365 Processing helix chain 'F' and resid 366 through 370 Proline residue: F 370 - end of helix Processing helix chain 'F' and resid 371 through 376 removed outlier: 3.899A pdb=" N LEU F 375 " --> pdb=" O TYR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 402 removed outlier: 3.597A pdb=" N ASN F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 417 Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 447 through 462 removed outlier: 3.803A pdb=" N ASP F 462 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 469 Processing helix chain 'F' and resid 470 through 480 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 81 through 95 removed outlier: 3.678A pdb=" N ASN H 95 " --> pdb=" O HIS H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 100 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 126 through 140 removed outlier: 4.264A pdb=" N THR H 130 " --> pdb=" O GLU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 removed outlier: 4.278A pdb=" N TRP H 164 " --> pdb=" O HIS H 160 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL H 166 " --> pdb=" O ILE H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 176 Processing helix chain 'H' and resid 186 through 199 removed outlier: 3.798A pdb=" N LYS H 199 " --> pdb=" O GLN H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 230 removed outlier: 3.713A pdb=" N SER H 214 " --> pdb=" O PRO H 210 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA H 223 " --> pdb=" O ILE H 219 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL H 224 " --> pdb=" O ILE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 265 Processing helix chain 'H' and resid 286 through 295 removed outlier: 3.724A pdb=" N SER H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 329 Processing helix chain 'H' and resid 333 through 343 removed outlier: 3.546A pdb=" N VAL H 342 " --> pdb=" O ALA H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 365 Processing helix chain 'H' and resid 366 through 370 Proline residue: H 370 - end of helix Processing helix chain 'H' and resid 371 through 376 removed outlier: 3.927A pdb=" N LEU H 375 " --> pdb=" O TYR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 402 removed outlier: 3.537A pdb=" N ASN H 389 " --> pdb=" O ASP H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 417 Processing helix chain 'H' and resid 422 through 433 Processing helix chain 'H' and resid 434 through 445 Processing helix chain 'H' and resid 447 through 462 removed outlier: 3.803A pdb=" N ASP H 462 " --> pdb=" O ILE H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 469 Processing helix chain 'H' and resid 470 through 480 Processing helix chain 'H' and resid 490 through 498 Processing helix chain 'K' and resid 6 through 17 Processing helix chain 'K' and resid 40 through 50 Processing helix chain 'K' and resid 81 through 95 removed outlier: 3.686A pdb=" N ASN K 95 " --> pdb=" O HIS K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 100 Processing helix chain 'K' and resid 101 through 103 No H-bonds generated for 'chain 'K' and resid 101 through 103' Processing helix chain 'K' and resid 127 through 140 removed outlier: 3.504A pdb=" N PHE K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 168 removed outlier: 4.215A pdb=" N TRP K 164 " --> pdb=" O HIS K 160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL K 166 " --> pdb=" O ILE K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 176 Processing helix chain 'K' and resid 186 through 199 removed outlier: 3.782A pdb=" N LYS K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 230 removed outlier: 3.710A pdb=" N SER K 214 " --> pdb=" O PRO K 210 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA K 223 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL K 224 " --> pdb=" O ILE K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 265 Processing helix chain 'K' and resid 286 through 295 removed outlier: 3.719A pdb=" N SER K 290 " --> pdb=" O ASP K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 329 Processing helix chain 'K' and resid 333 through 343 removed outlier: 3.544A pdb=" N VAL K 342 " --> pdb=" O ALA K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 365 Processing helix chain 'K' and resid 366 through 370 Proline residue: K 370 - end of helix Processing helix chain 'K' and resid 371 through 376 removed outlier: 3.929A pdb=" N LEU K 375 " --> pdb=" O TYR K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 401 removed outlier: 3.560A pdb=" N ASN K 389 " --> pdb=" O ASP K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 417 Processing helix chain 'K' and resid 422 through 433 Processing helix chain 'K' and resid 434 through 445 Processing helix chain 'K' and resid 447 through 462 removed outlier: 3.791A pdb=" N ASP K 462 " --> pdb=" O ILE K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 469 Processing helix chain 'K' and resid 470 through 480 Processing helix chain 'K' and resid 490 through 498 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 238 removed outlier: 11.188A pdb=" N LYS A 145 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N THR A 275 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ASN A 147 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS A 273 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 149 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 238 removed outlier: 11.178A pdb=" N LYS B 145 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N THR B 275 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N ASN B 147 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS B 273 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP B 149 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 63 through 68 Processing sheet with id=AA6, first strand: chain 'D' and resid 235 through 238 removed outlier: 11.248A pdb=" N LYS D 145 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N THR D 275 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ASN D 147 " --> pdb=" O HIS D 273 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N HIS D 273 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP D 149 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 63 through 68 Processing sheet with id=AA8, first strand: chain 'F' and resid 235 through 238 removed outlier: 11.185A pdb=" N LYS F 145 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N THR F 275 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASN F 147 " --> pdb=" O HIS F 273 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N HIS F 273 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP F 149 " --> pdb=" O ASN F 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 63 through 68 Processing sheet with id=AB1, first strand: chain 'H' and resid 235 through 238 removed outlier: 11.163A pdb=" N LYS H 145 " --> pdb=" O THR H 275 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N THR H 275 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ASN H 147 " --> pdb=" O HIS H 273 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS H 273 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP H 149 " --> pdb=" O ASN H 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 63 through 68 Processing sheet with id=AB3, first strand: chain 'K' and resid 235 through 238 removed outlier: 11.166A pdb=" N LYS K 145 " --> pdb=" O THR K 275 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N THR K 275 " --> pdb=" O LYS K 145 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASN K 147 " --> pdb=" O HIS K 273 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N HIS K 273 " --> pdb=" O ASN K 147 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP K 149 " --> pdb=" O ASN K 271 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7980 1.34 - 1.46: 6044 1.46 - 1.58: 11377 1.58 - 1.70: 75 1.70 - 1.82: 186 Bond restraints: 25662 Sorted by residual: bond pdb=" O3B DCP F 601 " pdb=" PG DCP F 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" O3B DCP K 601 " pdb=" PG DCP K 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3B DCP H 601 " pdb=" PG DCP H 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" O3B DCP D 601 " pdb=" PG DCP D 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" O3B DCP B 601 " pdb=" PG DCP B 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.38e+01 ... (remaining 25657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 34238 2.80 - 5.60: 544 5.60 - 8.39: 75 8.39 - 11.19: 8 11.19 - 13.99: 7 Bond angle restraints: 34872 Sorted by residual: angle pdb=" CA PRO D 41 " pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 112.00 99.87 12.13 1.40e+00 5.10e-01 7.51e+01 angle pdb=" C GLU K 126 " pdb=" N ASP K 127 " pdb=" CA ASP K 127 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" CA LYS K 460 " pdb=" CB LYS K 460 " pdb=" CG LYS K 460 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" CA LYS B 460 " pdb=" CB LYS B 460 " pdb=" CG LYS B 460 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 angle pdb=" C3' DC I 5 " pdb=" O3' DC I 5 " pdb=" P DC I 6 " ideal model delta sigma weight residual 119.70 125.37 -5.67 1.20e+00 6.94e-01 2.23e+01 ... (remaining 34867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 14839 35.96 - 71.92: 522 71.92 - 107.88: 17 107.88 - 143.84: 0 143.84 - 179.80: 12 Dihedral angle restraints: 15390 sinusoidal: 6594 harmonic: 8796 Sorted by residual: dihedral pdb=" CA GLY D 152 " pdb=" C GLY D 152 " pdb=" N CYS D 153 " pdb=" CA CYS D 153 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLY H 152 " pdb=" C GLY H 152 " pdb=" N CYS H 153 " pdb=" CA CYS H 153 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLY F 152 " pdb=" C GLY F 152 " pdb=" N CYS F 153 " pdb=" CA CYS F 153 " ideal model delta harmonic sigma weight residual -180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 15387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2747 0.053 - 0.105: 790 0.105 - 0.158: 191 0.158 - 0.210: 27 0.210 - 0.263: 7 Chirality restraints: 3762 Sorted by residual: chirality pdb=" CG LEU A 10 " pdb=" CB LEU A 10 " pdb=" CD1 LEU A 10 " pdb=" CD2 LEU A 10 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU F 10 " pdb=" CB LEU F 10 " pdb=" CD1 LEU F 10 " pdb=" CD2 LEU F 10 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 3759 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 40 " 0.110 5.00e-02 4.00e+02 1.57e-01 3.94e+01 pdb=" N PRO D 41 " -0.271 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 96 " -0.015 2.00e-02 2.50e+03 1.58e-02 6.22e+00 pdb=" CG TRP A 96 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 96 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 96 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 96 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 96 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 96 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 126 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLU H 126 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU H 126 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP H 127 " -0.015 2.00e-02 2.50e+03 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 716 2.69 - 3.24: 24679 3.24 - 3.80: 41818 3.80 - 4.35: 57952 4.35 - 4.90: 93987 Nonbonded interactions: 219152 Sorted by model distance: nonbonded pdb=" O ILE A 150 " pdb="MN MN A 603 " model vdw 2.141 2.320 nonbonded pdb=" O ILE B 150 " pdb="MN MN B 603 " model vdw 2.142 2.320 nonbonded pdb=" O ILE K 150 " pdb="MN MN K 603 " model vdw 2.143 2.320 nonbonded pdb=" O ILE D 150 " pdb="MN MN D 603 " model vdw 2.144 2.320 nonbonded pdb=" O ILE F 150 " pdb="MN MN F 603 " model vdw 2.146 2.320 ... (remaining 219147 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.710 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 0.147 25662 Z= 0.301 Angle : 0.873 13.991 34872 Z= 0.487 Chirality : 0.052 0.263 3762 Planarity : 0.007 0.157 4350 Dihedral : 18.482 179.801 9726 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.11 % Rotamer: Outliers : 0.37 % Allowed : 22.17 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 2940 helix: -0.40 (0.11), residues: 1680 sheet: -0.10 (0.36), residues: 204 loop : -1.20 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 477 TYR 0.030 0.002 TYR B 11 PHE 0.034 0.002 PHE B 140 TRP 0.043 0.003 TRP A 96 HIS 0.008 0.002 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.30 (25662) covalent geometry : angle 0.87349 / 0.49 (34872) hydrogen bonds : bond 0.16151 / 10.63 ( 1217) hydrogen bonds : angle 6.16326 / 4.28 ( 3573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 276 time to evaluate : 0.745 Fit side-chains REVERT: A 313 SER cc_start: 0.8453 (p) cc_final: 0.8223 (p) REVERT: A 397 MET cc_start: 0.4931 (tmm) cc_final: 0.4533 (pp-130) REVERT: B 313 SER cc_start: 0.8685 (t) cc_final: 0.8307 (m) REVERT: F 397 MET cc_start: 0.4796 (tmm) cc_final: 0.4246 (pp-130) REVERT: H 313 SER cc_start: 0.8297 (t) cc_final: 0.7994 (m) REVERT: H 407 MET cc_start: 0.7159 (tpp) cc_final: 0.6606 (tmm) REVERT: K 123 MET cc_start: 0.7157 (mtp) cc_final: 0.6886 (mtm) REVERT: K 407 MET cc_start: 0.7214 (tpp) cc_final: 0.6698 (tmm) outliers start: 10 outliers final: 4 residues processed: 283 average time/residue: 0.4519 time to fit residues: 152.3786 Evaluate side-chains 252 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain H residue 11 TYR Chi-restraints excluded: chain K residue 11 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN F 95 ASN F 295 ASN K 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.193558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.166981 restraints weight = 25985.004| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.57 r_work: 0.3723 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25662 Z= 0.167 Angle : 0.606 6.826 34872 Z= 0.334 Chirality : 0.046 0.309 3762 Planarity : 0.005 0.078 4350 Dihedral : 15.694 176.810 3800 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 2.96 % Allowed : 21.32 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 2940 helix: 0.45 (0.12), residues: 1728 sheet: -0.22 (0.37), residues: 204 loop : -1.19 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 75 TYR 0.015 0.001 TYR A 245 PHE 0.019 0.001 PHE H 140 TRP 0.018 0.002 TRP F 96 HIS 0.005 0.001 HIS F 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (25662) covalent geometry : angle 0.60595 / 0.33 (34872) hydrogen bonds : bond 0.05517 / 3.67 ( 1217) hydrogen bonds : angle 4.81081 / 3.37 ( 3573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 282 time to evaluate : 0.867 Fit side-chains REVERT: A 188 SER cc_start: 0.8373 (t) cc_final: 0.8135 (p) REVERT: A 261 MET cc_start: 0.5916 (mmm) cc_final: 0.5627 (mmm) REVERT: A 313 SER cc_start: 0.7487 (p) cc_final: 0.7187 (p) REVERT: A 397 MET cc_start: 0.4185 (tmm) cc_final: 0.3677 (pp-130) REVERT: B 113 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: B 313 SER cc_start: 0.7887 (t) cc_final: 0.7354 (m) REVERT: B 374 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7810 (p) REVERT: D 113 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: D 227 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6786 (mpp-170) REVERT: D 349 TYR cc_start: 0.7817 (m-80) cc_final: 0.7600 (m-80) REVERT: D 374 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7785 (p) REVERT: D 498 TYR cc_start: 0.7741 (m-80) cc_final: 0.7507 (m-80) REVERT: F 97 GLU cc_start: 0.7718 (mm-30) cc_final: 0.6760 (pm20) REVERT: F 374 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.7857 (p) REVERT: F 397 MET cc_start: 0.4366 (tmm) cc_final: 0.3505 (pp-130) REVERT: H 97 GLU cc_start: 0.7727 (mm-30) cc_final: 0.6637 (pm20) REVERT: H 313 SER cc_start: 0.7856 (t) cc_final: 0.7392 (m) REVERT: K 261 MET cc_start: 0.5881 (OUTLIER) cc_final: 0.5044 (mmm) outliers start: 80 outliers final: 23 residues processed: 338 average time/residue: 0.4208 time to fit residues: 171.6926 Evaluate side-chains 291 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 374 VAL Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 374 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 99 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 156 optimal weight: 0.0000 chunk 269 optimal weight: 0.7980 chunk 264 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 212 optimal weight: 0.1980 chunk 261 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN A 201 ASN B 201 ASN D 58 GLN F 257 HIS H 124 ASN H 201 ASN K 257 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.196171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.170129 restraints weight = 25933.431| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.57 r_work: 0.3766 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25662 Z= 0.119 Angle : 0.537 9.428 34872 Z= 0.293 Chirality : 0.044 0.327 3762 Planarity : 0.005 0.076 4350 Dihedral : 15.436 176.131 3792 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.80 % Rotamer: Outliers : 2.51 % Allowed : 21.84 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 2940 helix: 0.86 (0.12), residues: 1728 sheet: -0.32 (0.37), residues: 204 loop : -1.06 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 134 TYR 0.014 0.001 TYR F 355 PHE 0.018 0.001 PHE F 39 TRP 0.011 0.001 TRP A 96 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (25662) covalent geometry : angle 0.53699 / 0.29 (34872) hydrogen bonds : bond 0.04519 / 3.02 ( 1217) hydrogen bonds : angle 4.58090 / 3.21 ( 3573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 305 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 188 SER cc_start: 0.8338 (t) cc_final: 0.8080 (p) REVERT: A 227 ARG cc_start: 0.6862 (mpp-170) cc_final: 0.6550 (tpp80) REVERT: A 261 MET cc_start: 0.5622 (mmm) cc_final: 0.5282 (mmm) REVERT: A 300 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7653 (tttp) REVERT: A 313 SER cc_start: 0.7390 (p) cc_final: 0.7066 (p) REVERT: A 374 VAL cc_start: 0.7790 (m) cc_final: 0.7550 (p) REVERT: A 397 MET cc_start: 0.4254 (tmm) cc_final: 0.3606 (pp-130) REVERT: B 113 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: B 158 TYR cc_start: 0.8140 (t80) cc_final: 0.7738 (t80) REVERT: B 202 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 227 ARG cc_start: 0.6550 (mmp-170) cc_final: 0.6062 (mpp-170) REVERT: B 374 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7641 (p) REVERT: B 442 ASP cc_start: 0.6005 (t0) cc_final: 0.5756 (t0) REVERT: D 97 GLU cc_start: 0.7767 (mm-30) cc_final: 0.6918 (mp0) REVERT: D 113 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: D 158 TYR cc_start: 0.8189 (t80) cc_final: 0.7800 (t80) REVERT: D 188 SER cc_start: 0.8383 (t) cc_final: 0.8045 (p) REVERT: D 202 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 374 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7689 (p) REVERT: D 442 ASP cc_start: 0.5987 (t0) cc_final: 0.5786 (t0) REVERT: D 498 TYR cc_start: 0.7771 (m-80) cc_final: 0.7496 (m-80) REVERT: F 97 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6769 (pm20) REVERT: F 374 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7788 (p) REVERT: F 397 MET cc_start: 0.4222 (tmm) cc_final: 0.3299 (pp-130) REVERT: H 54 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7658 (ttp80) REVERT: H 97 GLU cc_start: 0.7676 (mm-30) cc_final: 0.6700 (pm20) REVERT: H 202 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8020 (mt-10) REVERT: H 397 MET cc_start: 0.4952 (tmt) cc_final: 0.4071 (pp-130) REVERT: K 261 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.4898 (mmm) REVERT: K 397 MET cc_start: 0.5137 (tmt) cc_final: 0.4149 (ppp) REVERT: K 407 MET cc_start: 0.7407 (tpp) cc_final: 0.7070 (tpp) outliers start: 68 outliers final: 22 residues processed: 360 average time/residue: 0.4170 time to fit residues: 181.9297 Evaluate side-chains 299 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 421 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 43 optimal weight: 1.9990 chunk 180 optimal weight: 0.0980 chunk 283 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 ASN D 58 GLN D 201 ASN D 392 ASN H 58 GLN H 124 ASN K 201 ASN K 257 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.193840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.167276 restraints weight = 25919.204| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.58 r_work: 0.3728 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25662 Z= 0.139 Angle : 0.551 9.980 34872 Z= 0.299 Chirality : 0.045 0.328 3762 Planarity : 0.005 0.063 4350 Dihedral : 15.357 175.879 3792 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.93 % Favored : 96.84 % Rotamer: Outliers : 2.18 % Allowed : 22.88 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 2940 helix: 0.99 (0.12), residues: 1728 sheet: -0.38 (0.37), residues: 204 loop : -1.06 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 75 TYR 0.016 0.001 TYR F 447 PHE 0.016 0.001 PHE A 39 TRP 0.010 0.001 TRP K 96 HIS 0.004 0.001 HIS K 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (25662) covalent geometry : angle 0.55129 / 0.30 (34872) hydrogen bonds : bond 0.04509 / 3.00 ( 1217) hydrogen bonds : angle 4.53281 / 3.18 ( 3573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 290 time to evaluate : 0.764 Fit side-chains REVERT: A 97 GLU cc_start: 0.7838 (mm-30) cc_final: 0.6890 (pm20) REVERT: A 188 SER cc_start: 0.8367 (t) cc_final: 0.8038 (p) REVERT: A 261 MET cc_start: 0.5585 (mmm) cc_final: 0.5230 (mmm) REVERT: A 300 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7666 (tttp) REVERT: A 313 SER cc_start: 0.7390 (p) cc_final: 0.7066 (p) REVERT: A 374 VAL cc_start: 0.7925 (m) cc_final: 0.7639 (p) REVERT: A 397 MET cc_start: 0.4299 (tmm) cc_final: 0.3374 (pp-130) REVERT: B 97 GLU cc_start: 0.7837 (mm-30) cc_final: 0.6981 (mp0) REVERT: B 113 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: B 158 TYR cc_start: 0.8215 (t80) cc_final: 0.7906 (t80) REVERT: B 227 ARG cc_start: 0.6638 (mmp-170) cc_final: 0.6109 (mpp-170) REVERT: B 265 LYS cc_start: 0.7513 (mttt) cc_final: 0.7128 (mptt) REVERT: D 97 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7072 (mp0) REVERT: D 113 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: D 158 TYR cc_start: 0.8212 (t80) cc_final: 0.7870 (t80) REVERT: D 265 LYS cc_start: 0.7437 (mttt) cc_final: 0.7078 (mptt) REVERT: D 349 TYR cc_start: 0.7811 (m-80) cc_final: 0.7589 (m-80) REVERT: D 498 TYR cc_start: 0.7803 (m-80) cc_final: 0.7510 (m-80) REVERT: F 97 GLU cc_start: 0.7663 (mm-30) cc_final: 0.6822 (pm20) REVERT: F 300 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7470 (tmtm) REVERT: F 397 MET cc_start: 0.4285 (tmm) cc_final: 0.3174 (pp-130) REVERT: F 489 ASP cc_start: 0.7018 (p0) cc_final: 0.6788 (p0) REVERT: H 97 GLU cc_start: 0.7778 (mm-30) cc_final: 0.6845 (pm20) REVERT: H 202 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8096 (mt-10) REVERT: H 261 MET cc_start: 0.5704 (mmm) cc_final: 0.4876 (mmm) REVERT: H 397 MET cc_start: 0.4968 (tmt) cc_final: 0.4173 (ppp) REVERT: K 97 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7092 (pm20) REVERT: K 261 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.4870 (mmm) REVERT: K 397 MET cc_start: 0.5134 (tmt) cc_final: 0.4042 (ppp) outliers start: 59 outliers final: 27 residues processed: 338 average time/residue: 0.4459 time to fit residues: 182.0154 Evaluate side-chains 296 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 149 optimal weight: 0.0170 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN D 58 GLN F 201 ASN H 58 GLN K 257 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.192597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.165777 restraints weight = 25860.285| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.59 r_work: 0.3714 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25662 Z= 0.147 Angle : 0.551 9.957 34872 Z= 0.297 Chirality : 0.045 0.330 3762 Planarity : 0.005 0.059 4350 Dihedral : 15.289 176.126 3792 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.06 % Favored : 96.70 % Rotamer: Outliers : 3.03 % Allowed : 22.65 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 2940 helix: 1.01 (0.12), residues: 1728 sheet: -0.38 (0.37), residues: 204 loop : -0.98 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 54 TYR 0.016 0.001 TYR F 447 PHE 0.016 0.001 PHE F 478 TRP 0.010 0.001 TRP D 96 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (25662) covalent geometry : angle 0.55144 / 0.30 (34872) hydrogen bonds : bond 0.04402 / 2.93 ( 1217) hydrogen bonds : angle 4.50303 / 3.16 ( 3573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 297 time to evaluate : 0.796 Fit side-chains REVERT: A 97 GLU cc_start: 0.7873 (mm-30) cc_final: 0.6967 (pm20) REVERT: A 132 THR cc_start: 0.5008 (OUTLIER) cc_final: 0.4686 (m) REVERT: A 188 SER cc_start: 0.8401 (t) cc_final: 0.8093 (p) REVERT: A 261 MET cc_start: 0.5627 (mmm) cc_final: 0.5324 (mmm) REVERT: A 300 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7707 (tttp) REVERT: A 313 SER cc_start: 0.7527 (p) cc_final: 0.7209 (p) REVERT: A 397 MET cc_start: 0.4400 (tmm) cc_final: 0.3344 (pp-130) REVERT: B 97 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7127 (mp0) REVERT: B 113 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: B 227 ARG cc_start: 0.6704 (mmp-170) cc_final: 0.6121 (mpp-170) REVERT: B 265 LYS cc_start: 0.7263 (mttt) cc_final: 0.6912 (mptt) REVERT: B 374 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7716 (p) REVERT: D 97 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7133 (mp0) REVERT: D 113 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: D 158 TYR cc_start: 0.8274 (t80) cc_final: 0.7957 (t80) REVERT: D 434 ASP cc_start: 0.7835 (m-30) cc_final: 0.7415 (m-30) REVERT: D 498 TYR cc_start: 0.7807 (m-80) cc_final: 0.7533 (m-80) REVERT: F 97 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6885 (pm20) REVERT: F 104 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6718 (pm20) REVERT: F 265 LYS cc_start: 0.7043 (mmtm) cc_final: 0.6813 (mptt) REVERT: F 397 MET cc_start: 0.4333 (tmm) cc_final: 0.3465 (pp-130) REVERT: H 97 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7098 (mp0) REVERT: H 135 GLU cc_start: 0.7010 (tp30) cc_final: 0.6782 (tp30) REVERT: H 202 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8015 (mt-10) REVERT: H 397 MET cc_start: 0.4900 (tmt) cc_final: 0.4087 (ppp) REVERT: K 97 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7100 (pm20) REVERT: K 123 MET cc_start: 0.7708 (mtp) cc_final: 0.7386 (mtm) REVERT: K 132 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.5081 (p) REVERT: K 261 MET cc_start: 0.5718 (OUTLIER) cc_final: 0.4845 (mmm) REVERT: K 397 MET cc_start: 0.5235 (tmt) cc_final: 0.4072 (ppp) REVERT: K 407 MET cc_start: 0.7479 (tpp) cc_final: 0.6992 (tpp) outliers start: 82 outliers final: 38 residues processed: 359 average time/residue: 0.4463 time to fit residues: 192.2195 Evaluate side-chains 318 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 491 CYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 421 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 58 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 207 optimal weight: 0.0070 chunk 129 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 157 optimal weight: 0.0000 chunk 63 optimal weight: 4.9990 overall best weight: 1.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN B 353 GLN D 58 GLN D 124 ASN D 353 GLN F 201 ASN H 58 GLN K 58 GLN K 257 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.191038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164172 restraints weight = 25984.466| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.59 r_work: 0.3695 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25662 Z= 0.165 Angle : 0.572 9.906 34872 Z= 0.308 Chirality : 0.046 0.330 3762 Planarity : 0.005 0.059 4350 Dihedral : 15.293 177.079 3792 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.06 % Favored : 96.67 % Rotamer: Outliers : 3.88 % Allowed : 22.21 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 2940 helix: 1.03 (0.12), residues: 1710 sheet: -0.32 (0.38), residues: 204 loop : -0.98 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 75 TYR 0.020 0.002 TYR A 447 PHE 0.020 0.001 PHE F 478 TRP 0.011 0.001 TRP B 96 HIS 0.005 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (25662) covalent geometry : angle 0.57214 / 0.31 (34872) hydrogen bonds : bond 0.04477 / 2.98 ( 1217) hydrogen bonds : angle 4.54738 / 3.19 ( 3573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 289 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7875 (mm-30) cc_final: 0.6997 (pm20) REVERT: A 132 THR cc_start: 0.5072 (OUTLIER) cc_final: 0.4760 (m) REVERT: A 188 SER cc_start: 0.8473 (t) cc_final: 0.8162 (p) REVERT: A 300 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7786 (tttp) REVERT: A 313 SER cc_start: 0.7574 (p) cc_final: 0.7260 (p) REVERT: A 397 MET cc_start: 0.4277 (tmm) cc_final: 0.3579 (pp-130) REVERT: B 97 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7073 (mp0) REVERT: B 113 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: B 434 ASP cc_start: 0.7887 (m-30) cc_final: 0.7431 (m-30) REVERT: D 75 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.5117 (tpm170) REVERT: D 97 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7160 (mp0) REVERT: D 113 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: D 434 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: D 498 TYR cc_start: 0.7736 (m-80) cc_final: 0.7464 (m-80) REVERT: F 97 GLU cc_start: 0.7678 (mm-30) cc_final: 0.6914 (pm20) REVERT: F 104 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: F 265 LYS cc_start: 0.7085 (mmtm) cc_final: 0.6834 (mptt) REVERT: F 300 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7520 (tmtm) REVERT: F 397 MET cc_start: 0.4420 (tmm) cc_final: 0.3736 (pp-130) REVERT: F 489 ASP cc_start: 0.7005 (p0) cc_final: 0.6723 (p0) REVERT: H 97 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7157 (mp0) REVERT: H 202 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8102 (mt-10) REVERT: H 397 MET cc_start: 0.4903 (OUTLIER) cc_final: 0.4063 (ppp) REVERT: H 434 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: K 75 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.5706 (ttm170) REVERT: K 97 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7178 (pm20) REVERT: K 132 THR cc_start: 0.5429 (OUTLIER) cc_final: 0.5180 (p) REVERT: K 261 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.4964 (mmm) REVERT: K 397 MET cc_start: 0.5339 (tmt) cc_final: 0.4205 (ppp) outliers start: 105 outliers final: 55 residues processed: 370 average time/residue: 0.4285 time to fit residues: 191.6530 Evaluate side-chains 326 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 397 MET Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain H residue 491 CYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 75 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN B 353 GLN F 201 ASN H 58 GLN H 197 GLN H 201 ASN K 58 GLN K 257 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.191294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.164683 restraints weight = 25939.507| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.57 r_work: 0.3703 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25662 Z= 0.153 Angle : 0.571 9.594 34872 Z= 0.305 Chirality : 0.046 0.327 3762 Planarity : 0.005 0.058 4350 Dihedral : 15.256 176.949 3792 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.20 % Favored : 96.53 % Rotamer: Outliers : 3.47 % Allowed : 22.51 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2940 helix: 0.97 (0.12), residues: 1728 sheet: -0.29 (0.38), residues: 204 loop : -0.95 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 75 TYR 0.017 0.002 TYR A 447 PHE 0.020 0.001 PHE F 478 TRP 0.011 0.001 TRP B 96 HIS 0.005 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (25662) covalent geometry : angle 0.57113 / 0.31 (34872) hydrogen bonds : bond 0.04357 / 2.89 ( 1217) hydrogen bonds : angle 4.54246 / 3.19 ( 3573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 284 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7856 (mm-30) cc_final: 0.6972 (pm20) REVERT: A 188 SER cc_start: 0.8466 (t) cc_final: 0.8149 (p) REVERT: A 300 LYS cc_start: 0.8273 (ttmm) cc_final: 0.7751 (tttp) REVERT: A 313 SER cc_start: 0.7552 (p) cc_final: 0.7239 (p) REVERT: A 397 MET cc_start: 0.4227 (tmm) cc_final: 0.3492 (pp-130) REVERT: A 407 MET cc_start: 0.7104 (tpp) cc_final: 0.6904 (tpp) REVERT: A 488 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6760 (p0) REVERT: A 489 ASP cc_start: 0.7059 (p0) cc_final: 0.6846 (p0) REVERT: B 97 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7072 (mp0) REVERT: B 113 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: B 132 THR cc_start: 0.5022 (OUTLIER) cc_final: 0.4799 (p) REVERT: B 434 ASP cc_start: 0.7859 (m-30) cc_final: 0.7460 (m-30) REVERT: D 75 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.5121 (tpm170) REVERT: D 97 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7158 (mp0) REVERT: D 113 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: D 131 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5912 (ttmt) REVERT: D 313 SER cc_start: 0.7750 (OUTLIER) cc_final: 0.7473 (m) REVERT: D 434 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: F 97 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6908 (pm20) REVERT: F 104 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: F 265 LYS cc_start: 0.7113 (mmtm) cc_final: 0.6770 (mptt) REVERT: F 300 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7473 (tmtm) REVERT: F 309 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6281 (mptt) REVERT: F 397 MET cc_start: 0.4367 (tmm) cc_final: 0.3674 (pp-130) REVERT: F 446 ILE cc_start: 0.4999 (mm) cc_final: 0.4474 (mt) REVERT: H 97 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7157 (mp0) REVERT: H 202 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7989 (mt-10) REVERT: H 397 MET cc_start: 0.4931 (tmt) cc_final: 0.4064 (ppp) REVERT: H 434 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6869 (m-30) REVERT: K 75 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7163 (tpp-160) REVERT: K 97 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7161 (pm20) REVERT: K 123 MET cc_start: 0.7766 (mtp) cc_final: 0.7472 (mtm) REVERT: K 132 THR cc_start: 0.5452 (OUTLIER) cc_final: 0.5201 (p) REVERT: K 158 TYR cc_start: 0.7690 (t80) cc_final: 0.7382 (t80) REVERT: K 261 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.4937 (mmm) REVERT: K 397 MET cc_start: 0.5317 (tmt) cc_final: 0.4190 (ppp) outliers start: 94 outliers final: 51 residues processed: 363 average time/residue: 0.4535 time to fit residues: 196.8701 Evaluate side-chains 333 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 267 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain H residue 491 CYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Chi-restraints excluded: chain K residue 491 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 276 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 270 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 29 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN B 58 GLN B 353 GLN D 353 GLN H 58 GLN H 124 ASN H 201 ASN K 58 GLN K 257 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.192615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.166358 restraints weight = 25912.553| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.57 r_work: 0.3723 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25662 Z= 0.127 Angle : 0.547 9.929 34872 Z= 0.293 Chirality : 0.044 0.329 3762 Planarity : 0.005 0.061 4350 Dihedral : 15.143 176.830 3792 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.23 % Favored : 96.46 % Rotamer: Outliers : 3.40 % Allowed : 22.84 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 2940 helix: 0.99 (0.12), residues: 1746 sheet: -0.25 (0.38), residues: 204 loop : -0.87 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 227 TYR 0.016 0.001 TYR A 447 PHE 0.020 0.001 PHE F 478 TRP 0.009 0.001 TRP B 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (25662) covalent geometry : angle 0.54688 / 0.29 (34872) hydrogen bonds : bond 0.04094 / 2.72 ( 1217) hydrogen bonds : angle 4.47431 / 3.14 ( 3573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 287 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7506 (tpp-160) REVERT: A 97 GLU cc_start: 0.7848 (mm-30) cc_final: 0.6957 (pm20) REVERT: A 188 SER cc_start: 0.8405 (t) cc_final: 0.8131 (p) REVERT: A 300 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7719 (tttp) REVERT: A 313 SER cc_start: 0.7580 (p) cc_final: 0.7255 (p) REVERT: A 488 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6768 (p0) REVERT: A 489 ASP cc_start: 0.7102 (p0) cc_final: 0.6865 (p0) REVERT: B 97 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7068 (mp0) REVERT: B 113 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: B 132 THR cc_start: 0.4988 (OUTLIER) cc_final: 0.4770 (p) REVERT: B 202 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 434 ASP cc_start: 0.7745 (m-30) cc_final: 0.7358 (m-30) REVERT: D 75 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.5282 (tpm170) REVERT: D 97 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7100 (mp0) REVERT: D 113 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: D 131 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.6119 (ttpt) REVERT: D 132 THR cc_start: 0.5077 (OUTLIER) cc_final: 0.4772 (p) REVERT: D 202 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8162 (mt-10) REVERT: D 313 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7499 (m) REVERT: D 349 TYR cc_start: 0.7803 (m-80) cc_final: 0.7553 (m-80) REVERT: D 434 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: F 97 GLU cc_start: 0.7650 (mm-30) cc_final: 0.6905 (pm20) REVERT: F 104 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: F 300 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7499 (tmtm) REVERT: F 309 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6235 (mptt) REVERT: F 397 MET cc_start: 0.4281 (tmm) cc_final: 0.3497 (pp-130) REVERT: F 446 ILE cc_start: 0.4985 (mm) cc_final: 0.4460 (mt) REVERT: H 97 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7157 (mp0) REVERT: H 135 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6432 (tp30) REVERT: H 202 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8017 (mt-10) REVERT: H 397 MET cc_start: 0.4961 (tmt) cc_final: 0.4049 (ppp) REVERT: H 434 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: K 62 CYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8630 (p) REVERT: K 75 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7256 (tpp-160) REVERT: K 97 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7137 (pm20) REVERT: K 123 MET cc_start: 0.7757 (mtp) cc_final: 0.7449 (mtm) REVERT: K 158 TYR cc_start: 0.7679 (t80) cc_final: 0.7242 (t80) REVERT: K 204 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7255 (t70) REVERT: K 261 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.4965 (mmm) REVERT: K 397 MET cc_start: 0.5288 (tmt) cc_final: 0.4150 (ppp) outliers start: 92 outliers final: 50 residues processed: 362 average time/residue: 0.4679 time to fit residues: 202.6451 Evaluate side-chains 342 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain H residue 491 CYS Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Chi-restraints excluded: chain K residue 491 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 154 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 287 optimal weight: 0.6980 chunk 217 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN H 58 GLN K 58 GLN K 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.192582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.166105 restraints weight = 25984.465| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.57 r_work: 0.3724 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25662 Z= 0.133 Angle : 0.559 9.859 34872 Z= 0.299 Chirality : 0.045 0.328 3762 Planarity : 0.005 0.057 4350 Dihedral : 15.057 176.579 3792 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.30 % Favored : 96.43 % Rotamer: Outliers : 2.77 % Allowed : 23.73 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 2940 helix: 1.06 (0.12), residues: 1728 sheet: -0.26 (0.38), residues: 204 loop : -0.79 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 134 TYR 0.019 0.001 TYR F 447 PHE 0.022 0.001 PHE F 478 TRP 0.009 0.001 TRP B 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (25662) covalent geometry : angle 0.55861 / 0.30 (34872) hydrogen bonds : bond 0.04104 / 2.72 ( 1217) hydrogen bonds : angle 4.46902 / 3.14 ( 3573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 289 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7556 (tpp-160) REVERT: A 97 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7008 (pm20) REVERT: A 188 SER cc_start: 0.8406 (t) cc_final: 0.8112 (p) REVERT: A 300 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7751 (tttp) REVERT: A 313 SER cc_start: 0.7561 (p) cc_final: 0.7231 (p) REVERT: A 488 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6684 (p0) REVERT: A 489 ASP cc_start: 0.7094 (p0) cc_final: 0.6851 (p0) REVERT: B 97 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7157 (mp0) REVERT: B 113 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: B 132 THR cc_start: 0.5089 (OUTLIER) cc_final: 0.4869 (p) REVERT: B 202 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8186 (mt-10) REVERT: D 75 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.5236 (tpm170) REVERT: D 97 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7101 (mp0) REVERT: D 113 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: D 131 LYS cc_start: 0.6322 (OUTLIER) cc_final: 0.5893 (ttpt) REVERT: D 132 THR cc_start: 0.5207 (OUTLIER) cc_final: 0.4908 (p) REVERT: D 158 TYR cc_start: 0.8276 (t80) cc_final: 0.7876 (t80) REVERT: D 313 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7458 (m) REVERT: D 349 TYR cc_start: 0.7851 (m-80) cc_final: 0.7595 (m-80) REVERT: D 434 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: F 97 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6873 (pm20) REVERT: F 104 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: F 300 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7552 (tmtm) REVERT: F 309 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6304 (mptt) REVERT: F 397 MET cc_start: 0.4323 (tmm) cc_final: 0.3649 (pp-130) REVERT: F 489 ASP cc_start: 0.6833 (p0) cc_final: 0.6577 (p0) REVERT: H 97 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7149 (mp0) REVERT: H 202 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8067 (mt-10) REVERT: H 397 MET cc_start: 0.4871 (tmt) cc_final: 0.4067 (ppp) REVERT: H 434 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: K 62 CYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8629 (p) REVERT: K 75 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7226 (tpp-160) REVERT: K 97 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7274 (mp0) REVERT: K 123 MET cc_start: 0.7751 (mtp) cc_final: 0.7432 (mtm) REVERT: K 261 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.4973 (mmm) REVERT: K 397 MET cc_start: 0.5272 (tmt) cc_final: 0.4139 (ppp) outliers start: 75 outliers final: 46 residues processed: 350 average time/residue: 0.4678 time to fit residues: 196.6375 Evaluate side-chains 334 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Chi-restraints excluded: chain K residue 491 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 0.0050 chunk 150 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 287 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 GLN B 353 GLN H 58 GLN K 58 GLN K 257 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.193343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167117 restraints weight = 25960.773| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.56 r_work: 0.3733 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25662 Z= 0.124 Angle : 0.554 9.879 34872 Z= 0.296 Chirality : 0.044 0.328 3762 Planarity : 0.005 0.059 4350 Dihedral : 14.927 176.356 3792 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.33 % Favored : 96.39 % Rotamer: Outliers : 2.77 % Allowed : 24.17 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 2940 helix: 1.12 (0.12), residues: 1728 sheet: -0.28 (0.38), residues: 204 loop : -0.78 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 54 TYR 0.016 0.001 TYR F 447 PHE 0.021 0.001 PHE F 478 TRP 0.008 0.001 TRP B 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (25662) covalent geometry : angle 0.55361 / 0.30 (34872) hydrogen bonds : bond 0.03974 / 2.64 ( 1217) hydrogen bonds : angle 4.43350 / 3.11 ( 3573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 294 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 75 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7559 (tpp-160) REVERT: A 97 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7006 (pm20) REVERT: A 188 SER cc_start: 0.8391 (t) cc_final: 0.8099 (p) REVERT: A 284 LEU cc_start: 0.4473 (OUTLIER) cc_final: 0.4087 (mt) REVERT: A 300 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7707 (tttp) REVERT: A 313 SER cc_start: 0.7581 (p) cc_final: 0.7247 (p) REVERT: A 488 ASN cc_start: 0.7006 (OUTLIER) cc_final: 0.6668 (p0) REVERT: A 489 ASP cc_start: 0.7006 (p0) cc_final: 0.6768 (p0) REVERT: B 97 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7118 (mp0) REVERT: B 113 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: B 202 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 75 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.5272 (tpm170) REVERT: D 97 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7092 (mp0) REVERT: D 113 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: D 158 TYR cc_start: 0.8261 (t80) cc_final: 0.7860 (t80) REVERT: D 202 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8168 (mt-10) REVERT: D 349 TYR cc_start: 0.7841 (m-80) cc_final: 0.7585 (m-80) REVERT: D 434 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: F 97 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6857 (pm20) REVERT: F 300 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7582 (tmtm) REVERT: F 309 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6305 (mptt) REVERT: F 397 MET cc_start: 0.4294 (tmm) cc_final: 0.3611 (pp-130) REVERT: F 489 ASP cc_start: 0.6954 (p0) cc_final: 0.6706 (p0) REVERT: H 97 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7164 (mp0) REVERT: H 124 ASN cc_start: 0.5702 (m110) cc_final: 0.5170 (p0) REVERT: H 202 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8035 (mt-10) REVERT: H 397 MET cc_start: 0.4918 (tmt) cc_final: 0.4077 (ppp) REVERT: H 407 MET cc_start: 0.7426 (tpp) cc_final: 0.6556 (tmm) REVERT: H 434 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: K 62 CYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8638 (p) REVERT: K 75 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7212 (tpp-160) REVERT: K 97 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7274 (mp0) REVERT: K 123 MET cc_start: 0.7849 (mtp) cc_final: 0.7511 (mtm) REVERT: K 132 THR cc_start: 0.5246 (OUTLIER) cc_final: 0.5030 (p) REVERT: K 158 TYR cc_start: 0.7683 (t80) cc_final: 0.7101 (t80) REVERT: K 202 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8158 (mt-10) REVERT: K 204 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7364 (t70) REVERT: K 261 MET cc_start: 0.5687 (OUTLIER) cc_final: 0.4989 (mmm) REVERT: K 397 MET cc_start: 0.5366 (tmt) cc_final: 0.4180 (ppp) REVERT: K 407 MET cc_start: 0.7570 (tpp) cc_final: 0.6649 (tmm) outliers start: 75 outliers final: 46 residues processed: 352 average time/residue: 0.4718 time to fit residues: 197.9036 Evaluate side-chains 339 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 278 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 GLN H 58 GLN K 58 GLN K 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.192318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.165836 restraints weight = 25986.950| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.57 r_work: 0.3723 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25662 Z= 0.140 Angle : 0.575 9.848 34872 Z= 0.306 Chirality : 0.045 0.325 3762 Planarity : 0.005 0.059 4350 Dihedral : 14.890 176.256 3792 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.27 % Favored : 96.46 % Rotamer: Outliers : 2.77 % Allowed : 24.24 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 2940 helix: 1.05 (0.12), residues: 1728 sheet: -0.29 (0.38), residues: 204 loop : -0.75 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 54 TYR 0.016 0.001 TYR F 447 PHE 0.022 0.001 PHE F 478 TRP 0.010 0.001 TRP B 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (25662) covalent geometry : angle 0.57513 / 0.31 (34872) hydrogen bonds : bond 0.04113 / 2.73 ( 1217) hydrogen bonds : angle 4.46460 / 3.12 ( 3573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6405.20 seconds wall clock time: 110 minutes 30.65 seconds (6630.65 seconds total)