Starting phenix.real_space_refine on Fri Feb 6 12:38:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdo_64990/02_2026/9vdo_64990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdo_64990/02_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_64990/02_2026/9vdo_64990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdo_64990/02_2026/9vdo_64990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vdo_64990/02_2026/9vdo_64990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdo_64990/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 4.61, 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: 1.53 Conformation dependent library (CDL) restraints added in 739.7 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: 0.49 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: 3.53 Time building geometry restraints manager: 2.17 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=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 1.492 1.623 -0.131 5.00e-02 4.00e+02 6.86e+00 bond pdb=" C3' DC G 5 " pdb=" O3' DC G 5 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.20e+00 bond pdb=" C3' DC I 5 " pdb=" O3' DC I 5 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.20e+00 bond pdb=" C3' DC C 5 " pdb=" O3' DC C 5 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.17e+00 bond pdb=" C3' DC E 5 " pdb=" O3' DC E 5 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.09e+00 ... (remaining 25657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 34079 2.43 - 4.85: 689 4.85 - 7.28: 87 7.28 - 9.70: 15 9.70 - 12.13: 2 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=" C GLU D 126 " pdb=" N ASP D 127 " pdb=" CA ASP D 127 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.22e+01 ... (remaining 34867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 14794 35.96 - 71.92: 525 71.92 - 107.88: 17 107.88 - 143.84: 0 143.84 - 179.80: 12 Dihedral angle restraints: 15348 sinusoidal: 6552 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 15345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2757 0.053 - 0.105: 797 0.105 - 0.158: 182 0.158 - 0.210: 19 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: 1.650 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.350 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.005 0.131 25662 Z= 0.208 Angle : 0.812 12.129 34872 Z= 0.458 Chirality : 0.051 0.263 3762 Planarity : 0.007 0.157 4350 Dihedral : 18.495 179.801 9684 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 covalent geometry : bond 0.00455 (25662) covalent geometry : angle 0.81190 (34872) hydrogen bonds : bond 0.16151 ( 1217) hydrogen bonds : angle 6.16326 ( 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 : 0.695 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: 0.4799 time to fit residues: 161.4970 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 : 1.044 ------------------------------------------------------------------------------- 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: 0.0570 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: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 295 ASN B 124 ASN D 124 ASN D 201 ASN F 257 HIS F 295 ASN H 201 ASN K 257 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.193479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.167079 restraints weight = 25915.154| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.56 r_work: 0.3721 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25662 Z= 0.162 Angle : 0.581 7.956 34872 Z= 0.320 Chirality : 0.044 0.173 3762 Planarity : 0.005 0.084 4350 Dihedral : 15.292 179.427 3758 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.24 % Rotamer: Outliers : 3.18 % Allowed : 20.77 % Favored : 76.05 % 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: -0.23 (0.14), residues: 2940 helix: 0.51 (0.12), residues: 1722 sheet: -0.24 (0.37), residues: 204 loop : -1.16 (0.16), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.015 0.002 TYR F 447 PHE 0.017 0.001 PHE H 140 TRP 0.018 0.002 TRP F 96 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00365 (25662) covalent geometry : angle 0.58133 (34872) hydrogen bonds : bond 0.05218 ( 1217) hydrogen bonds : angle 4.73255 ( 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 375 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 0.907 Fit side-chains REVERT: A 188 SER cc_start: 0.8372 (t) cc_final: 0.8171 (p) REVERT: A 261 MET cc_start: 0.5832 (mmm) cc_final: 0.5534 (mmm) REVERT: A 300 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7629 (tttp) REVERT: A 313 SER cc_start: 0.7422 (p) cc_final: 0.7122 (p) REVERT: A 397 MET cc_start: 0.4280 (tmm) cc_final: 0.3577 (pp-130) REVERT: B 113 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: B 265 LYS cc_start: 0.7406 (mttm) cc_final: 0.7194 (mptt) REVERT: B 374 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7694 (p) REVERT: D 113 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: D 188 SER cc_start: 0.8408 (t) cc_final: 0.8118 (p) REVERT: D 227 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6728 (mpp-170) REVERT: D 349 TYR cc_start: 0.7833 (m-80) cc_final: 0.7608 (m-80) REVERT: D 374 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7716 (p) REVERT: D 498 TYR cc_start: 0.7803 (m-80) cc_final: 0.7560 (m-80) REVERT: F 97 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6742 (pm20) REVERT: F 374 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7831 (p) REVERT: F 397 MET cc_start: 0.4323 (tmm) cc_final: 0.3313 (pp-130) REVERT: H 97 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6610 (pm20) REVERT: K 261 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.4951 (mmm) outliers start: 86 outliers final: 19 residues processed: 350 average time/residue: 0.4488 time to fit residues: 189.2646 Evaluate side-chains 289 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 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 374 VAL 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: 0.7980 chunk 51 optimal weight: 0.0030 chunk 156 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 212 optimal weight: 0.0870 chunk 261 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 overall best weight: 0.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 201 ASN D 58 GLN H 124 ASN H 197 GLN H 201 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 = 0.4113 r_free = 0.4113 target = 0.195213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.168984 restraints weight = 25975.266| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.57 r_work: 0.3750 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25662 Z= 0.123 Angle : 0.528 10.096 34872 Z= 0.289 Chirality : 0.042 0.198 3762 Planarity : 0.005 0.074 4350 Dihedral : 15.027 179.210 3750 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.93 % Favored : 96.87 % Rotamer: Outliers : 2.25 % Allowed : 22.06 % Favored : 75.68 % 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: 0.95 (0.12), residues: 1716 sheet: -0.31 (0.37), residues: 204 loop : -0.87 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.016 0.001 TYR H 158 PHE 0.017 0.001 PHE D 140 TRP 0.011 0.001 TRP F 96 HIS 0.008 0.001 HIS H 249 Details of bonding type rmsd covalent geometry : bond 0.00263 (25662) covalent geometry : angle 0.52844 (34872) hydrogen bonds : bond 0.04423 ( 1217) hydrogen bonds : angle 4.53339 ( 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 369 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 308 time to evaluate : 0.869 Fit side-chains REVERT: A 15 LEU cc_start: 0.8612 (mm) cc_final: 0.8384 (mt) REVERT: A 97 GLU cc_start: 0.7857 (mm-30) cc_final: 0.6909 (pm20) REVERT: A 188 SER cc_start: 0.8362 (t) cc_final: 0.8089 (p) REVERT: A 261 MET cc_start: 0.5626 (mmm) cc_final: 0.5281 (mmm) REVERT: A 300 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7702 (tttp) REVERT: A 313 SER cc_start: 0.7544 (p) cc_final: 0.7250 (p) REVERT: A 374 VAL cc_start: 0.7840 (m) cc_final: 0.7602 (p) REVERT: A 397 MET cc_start: 0.4294 (tmm) cc_final: 0.3426 (pp-130) REVERT: B 97 GLU cc_start: 0.7857 (mm-30) cc_final: 0.6982 (mp0) REVERT: B 113 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: B 202 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8224 (mt-10) REVERT: B 227 ARG cc_start: 0.6602 (mmp-170) cc_final: 0.6130 (mpp-170) REVERT: B 313 SER cc_start: 0.7765 (t) cc_final: 0.7137 (m) REVERT: B 374 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7698 (p) REVERT: B 442 ASP cc_start: 0.5997 (t0) cc_final: 0.5657 (t0) REVERT: D 97 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7117 (mp0) REVERT: D 113 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: D 188 SER cc_start: 0.8420 (t) cc_final: 0.8073 (p) REVERT: D 202 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8302 (mt-10) REVERT: D 313 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7523 (m) REVERT: D 498 TYR cc_start: 0.7757 (m-80) cc_final: 0.7489 (m-80) REVERT: F 97 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6833 (pm20) REVERT: F 192 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7289 (t70) REVERT: F 397 MET cc_start: 0.4377 (tmm) cc_final: 0.3393 (pp-130) REVERT: H 54 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7665 (ttp80) REVERT: H 97 GLU cc_start: 0.7749 (mm-30) cc_final: 0.6788 (pm20) REVERT: H 202 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8110 (mm-30) REVERT: H 261 MET cc_start: 0.5652 (mmm) cc_final: 0.4869 (mmm) REVERT: H 397 MET cc_start: 0.4990 (tmt) cc_final: 0.4106 (pp-130) REVERT: K 97 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7005 (pm20) REVERT: K 261 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.4875 (mmm) REVERT: K 397 MET cc_start: 0.4890 (OUTLIER) cc_final: 0.4065 (pp-130) REVERT: K 407 MET cc_start: 0.7408 (tpp) cc_final: 0.7148 (tpp) outliers start: 61 outliers final: 19 residues processed: 355 average time/residue: 0.4570 time to fit residues: 195.5095 Evaluate side-chains 303 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 176 LEU Chi-restraints excluded: chain B residue 374 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 313 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 421 ILE 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 397 MET 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: 5.9990 chunk 180 optimal weight: 0.8980 chunk 283 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 201 ASN D 58 GLN D 392 ASN F 201 ASN H 58 GLN H 124 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 = 0.4056 r_free = 0.4056 target = 0.189178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.161992 restraints weight = 26145.046| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.60 r_work: 0.3674 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25662 Z= 0.209 Angle : 0.607 9.578 34872 Z= 0.327 Chirality : 0.046 0.160 3762 Planarity : 0.005 0.071 4350 Dihedral : 15.159 179.665 3750 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 3.70 % Allowed : 21.36 % 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: 0.09 (0.15), residues: 2940 helix: 0.83 (0.12), residues: 1716 sheet: -0.36 (0.38), residues: 204 loop : -1.08 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 196 TYR 0.017 0.002 TYR F 447 PHE 0.014 0.002 PHE H 140 TRP 0.014 0.002 TRP B 96 HIS 0.005 0.001 HIS K 257 Details of bonding type rmsd covalent geometry : bond 0.00502 (25662) covalent geometry : angle 0.60653 (34872) hydrogen bonds : bond 0.04992 ( 1217) hydrogen bonds : angle 4.64974 ( 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 392 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 292 time to evaluate : 0.932 Fit side-chains REVERT: A 97 GLU cc_start: 0.7923 (mm-30) cc_final: 0.6979 (pm20) REVERT: A 132 THR cc_start: 0.5076 (OUTLIER) cc_final: 0.4795 (m) REVERT: A 188 SER cc_start: 0.8490 (t) cc_final: 0.8143 (p) REVERT: A 261 MET cc_start: 0.5753 (mmm) cc_final: 0.5464 (mmm) REVERT: A 300 LYS cc_start: 0.8292 (ttmm) cc_final: 0.7744 (tttp) REVERT: A 313 SER cc_start: 0.7569 (p) cc_final: 0.7281 (p) REVERT: A 397 MET cc_start: 0.4347 (tmm) cc_final: 0.3607 (pp-130) REVERT: B 97 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7114 (mp0) REVERT: B 113 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: B 192 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7580 (t70) REVERT: D 97 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7151 (mp0) REVERT: D 113 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: D 227 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6717 (mpp-170) REVERT: D 344 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8151 (m-40) REVERT: D 434 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: F 97 GLU cc_start: 0.7732 (mm-30) cc_final: 0.6913 (pm20) REVERT: F 300 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7516 (tmtm) REVERT: F 397 MET cc_start: 0.4478 (tmm) cc_final: 0.3771 (pp-130) REVERT: H 54 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7737 (ttp80) REVERT: H 97 GLU cc_start: 0.7833 (mm-30) cc_final: 0.6911 (pm20) REVERT: H 397 MET cc_start: 0.4976 (OUTLIER) cc_final: 0.4063 (ppp) REVERT: H 434 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6446 (m-30) REVERT: K 97 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7100 (pm20) REVERT: K 123 MET cc_start: 0.7738 (mtp) cc_final: 0.7460 (mtm) REVERT: K 261 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.4936 (mmm) REVERT: K 397 MET cc_start: 0.4992 (OUTLIER) cc_final: 0.4130 (ppp) REVERT: K 407 MET cc_start: 0.7499 (tpp) cc_final: 0.7168 (tpp) outliers start: 100 outliers final: 50 residues processed: 366 average time/residue: 0.4302 time to fit residues: 191.5749 Evaluate side-chains 322 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 51 THR 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 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 192 ASP Chi-restraints excluded: chain B residue 307 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 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 227 ARG Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain F residue 51 THR 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 H residue 51 THR 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 374 VAL 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 120 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 307 LEU Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 397 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 82 optimal weight: 0.8980 chunk 114 optimal weight: 0.0570 chunk 205 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 149 optimal weight: 0.1980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 353 GLN H 58 GLN H 124 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 = 0.4093 r_free = 0.4093 target = 0.193013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.166620 restraints weight = 25906.081| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.57 r_work: 0.3725 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25662 Z= 0.124 Angle : 0.529 10.206 34872 Z= 0.287 Chirality : 0.042 0.163 3762 Planarity : 0.005 0.062 4350 Dihedral : 14.926 179.820 3750 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.20 % Favored : 96.56 % Rotamer: Outliers : 3.18 % Allowed : 22.28 % Favored : 74.54 % 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: 0.34 (0.15), residues: 2940 helix: 0.98 (0.12), residues: 1740 sheet: -0.30 (0.38), residues: 204 loop : -0.90 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 134 TYR 0.014 0.001 TYR F 447 PHE 0.015 0.001 PHE F 478 TRP 0.009 0.001 TRP B 96 HIS 0.005 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00271 (25662) covalent geometry : angle 0.52911 (34872) hydrogen bonds : bond 0.04169 ( 1217) hydrogen bonds : angle 4.52917 ( 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 389 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 303 time to evaluate : 0.972 Fit side-chains REVERT: A 97 GLU cc_start: 0.7868 (mm-30) cc_final: 0.6999 (pm20) REVERT: A 132 THR cc_start: 0.5180 (OUTLIER) cc_final: 0.4874 (m) REVERT: A 188 SER cc_start: 0.8499 (t) cc_final: 0.8155 (p) REVERT: A 300 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7716 (tttp) REVERT: A 313 SER cc_start: 0.7537 (p) cc_final: 0.7233 (p) REVERT: A 397 MET cc_start: 0.4240 (tmm) cc_final: 0.3497 (pp-130) REVERT: A 488 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6784 (p0) REVERT: B 97 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7141 (mp0) REVERT: B 113 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: B 227 ARG cc_start: 0.6725 (mmp-170) cc_final: 0.6204 (mpp-170) REVERT: D 97 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7104 (mp0) REVERT: D 113 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: D 313 SER cc_start: 0.7707 (OUTLIER) cc_final: 0.7475 (m) REVERT: D 434 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: F 97 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6894 (pm20) REVERT: F 158 TYR cc_start: 0.8284 (t80) cc_final: 0.8067 (t80) REVERT: F 265 LYS cc_start: 0.7235 (mptt) cc_final: 0.7019 (mppt) REVERT: F 300 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7552 (tmtm) REVERT: F 397 MET cc_start: 0.4304 (tmm) cc_final: 0.3509 (pp-130) REVERT: F 489 ASP cc_start: 0.7013 (p0) cc_final: 0.6755 (p0) REVERT: H 97 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7122 (mp0) REVERT: H 135 GLU cc_start: 0.7093 (tp30) cc_final: 0.6841 (tp30) REVERT: H 202 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8019 (mt-10) REVERT: H 397 MET cc_start: 0.4956 (tmt) cc_final: 0.4134 (ppp) REVERT: K 97 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7162 (pm20) REVERT: K 123 MET cc_start: 0.7748 (mtp) cc_final: 0.7438 (mtm) REVERT: K 132 THR cc_start: 0.5363 (OUTLIER) cc_final: 0.5146 (p) REVERT: K 261 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.4929 (mmm) REVERT: K 397 MET cc_start: 0.4919 (OUTLIER) cc_final: 0.4085 (ppp) REVERT: K 407 MET cc_start: 0.7437 (tpp) cc_final: 0.7225 (tpp) outliers start: 86 outliers final: 33 residues processed: 370 average time/residue: 0.4677 time to fit residues: 207.3554 Evaluate side-chains 318 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP 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 488 ASN 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 B residue 376 ILE Chi-restraints excluded: chain B residue 425 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 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 113 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 313 SER 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 421 ILE 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 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 397 MET 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: 0.3980 chunk 235 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN B 353 GLN D 95 ASN D 353 GLN H 58 GLN H 95 ASN H 124 ASN K 58 GLN K 95 ASN K 257 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.187038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.159897 restraints weight = 26140.982| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.58 r_work: 0.3642 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 25662 Z= 0.271 Angle : 0.670 9.708 34872 Z= 0.359 Chirality : 0.048 0.168 3762 Planarity : 0.006 0.058 4350 Dihedral : 15.236 179.605 3750 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.67 % Favored : 96.12 % Rotamer: Outliers : 4.03 % Allowed : 22.47 % 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: -0.12 (0.15), residues: 2940 helix: 0.56 (0.12), residues: 1722 sheet: -0.29 (0.39), residues: 204 loop : -1.00 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 196 TYR 0.022 0.002 TYR A 447 PHE 0.020 0.002 PHE F 478 TRP 0.018 0.002 TRP B 96 HIS 0.006 0.001 HIS K 257 Details of bonding type rmsd covalent geometry : bond 0.00660 (25662) covalent geometry : angle 0.67027 (34872) hydrogen bonds : bond 0.05312 ( 1217) hydrogen bonds : angle 4.81438 ( 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 392 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 283 time to evaluate : 0.866 Fit side-chains REVERT: A 97 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7044 (pm20) REVERT: A 132 THR cc_start: 0.5080 (OUTLIER) cc_final: 0.4848 (m) REVERT: A 313 SER cc_start: 0.7623 (p) cc_final: 0.7324 (p) REVERT: A 434 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7004 (m-30) REVERT: B 97 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7203 (mp0) REVERT: B 113 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: B 434 ASP cc_start: 0.8006 (m-30) cc_final: 0.7574 (m-30) REVERT: B 442 ASP cc_start: 0.6236 (t0) cc_final: 0.6012 (t0) REVERT: D 97 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7197 (mp0) REVERT: D 113 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: D 192 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7744 (t70) REVERT: D 227 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6846 (mmm-85) REVERT: D 434 ASP cc_start: 0.7924 (m-30) cc_final: 0.7415 (m-30) REVERT: D 442 ASP cc_start: 0.6268 (t0) cc_final: 0.6000 (t0) REVERT: D 446 ILE cc_start: 0.5180 (mm) cc_final: 0.4651 (mt) REVERT: F 97 GLU cc_start: 0.7768 (mm-30) cc_final: 0.6986 (pm20) REVERT: F 265 LYS cc_start: 0.7343 (mptt) cc_final: 0.7139 (mptt) REVERT: F 434 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: H 97 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7181 (mp0) REVERT: H 135 GLU cc_start: 0.7160 (tp30) cc_final: 0.6923 (tp30) REVERT: H 158 TYR cc_start: 0.8315 (t80) cc_final: 0.8019 (t80) REVERT: H 397 MET cc_start: 0.5123 (tmt) cc_final: 0.4134 (ppp) REVERT: H 434 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: K 97 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7218 (pm20) REVERT: K 123 MET cc_start: 0.7846 (mtp) cc_final: 0.7549 (mtm) REVERT: K 132 THR cc_start: 0.5339 (OUTLIER) cc_final: 0.5087 (p) REVERT: K 261 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5071 (mmm) REVERT: K 397 MET cc_start: 0.5131 (OUTLIER) cc_final: 0.4154 (ppp) REVERT: K 407 MET cc_start: 0.7368 (tpp) cc_final: 0.7092 (tpp) REVERT: K 434 ASP cc_start: 0.8017 (m-30) cc_final: 0.7680 (m-30) outliers start: 109 outliers final: 59 residues processed: 368 average time/residue: 0.4587 time to fit residues: 203.4926 Evaluate side-chains 323 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 253 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 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 434 ASP Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 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 307 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 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 192 ASP Chi-restraints excluded: chain D residue 227 ARG 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 F residue 51 THR 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 F residue 376 ILE Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 374 VAL 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 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 272 LEU Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 397 MET 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: 0.8980 chunk 213 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN F 58 GLN F 197 GLN H 124 ASN K 204 HIS K 257 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.191616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.165290 restraints weight = 25939.068| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.56 r_work: 0.3693 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2021 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= 0.138 Angle : 0.557 10.288 34872 Z= 0.301 Chirality : 0.043 0.187 3762 Planarity : 0.005 0.058 4350 Dihedral : 15.008 179.906 3750 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.10 % Favored : 96.70 % Rotamer: Outliers : 3.36 % Allowed : 22.95 % Favored : 73.69 % 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: 0.27 (0.15), residues: 2940 helix: 0.87 (0.12), residues: 1722 sheet: -0.26 (0.39), residues: 204 loop : -0.80 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.015 0.001 TYR A 447 PHE 0.016 0.001 PHE F 478 TRP 0.010 0.001 TRP H 96 HIS 0.005 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00313 (25662) covalent geometry : angle 0.55675 (34872) hydrogen bonds : bond 0.04266 ( 1217) hydrogen bonds : angle 4.60026 ( 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 372 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 281 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7058 (pm20) REVERT: A 300 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7706 (tttp) REVERT: A 313 SER cc_start: 0.7521 (p) cc_final: 0.7063 (m) REVERT: A 348 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: B 97 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7154 (mp0) REVERT: B 113 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: B 132 THR cc_start: 0.4966 (OUTLIER) cc_final: 0.4626 (m) REVERT: B 202 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 434 ASP cc_start: 0.7751 (m-30) cc_final: 0.7353 (m-30) REVERT: D 75 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.5055 (tpm170) REVERT: D 97 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7164 (mp0) REVERT: D 113 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: D 434 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: D 442 ASP cc_start: 0.6213 (t0) cc_final: 0.6009 (t0) REVERT: D 446 ILE cc_start: 0.5125 (mm) cc_final: 0.4603 (mt) REVERT: F 75 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7500 (tpp-160) REVERT: F 97 GLU cc_start: 0.7710 (mm-30) cc_final: 0.6949 (pm20) REVERT: F 265 LYS cc_start: 0.7110 (mptt) cc_final: 0.6885 (mptt) REVERT: F 300 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7562 (tmtm) REVERT: F 397 MET cc_start: 0.4435 (tmm) cc_final: 0.3721 (pp-130) REVERT: F 434 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: F 446 ILE cc_start: 0.4763 (mm) cc_final: 0.4259 (mt) REVERT: F 489 ASP cc_start: 0.7026 (p0) cc_final: 0.6770 (p0) REVERT: H 97 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7175 (mp0) REVERT: H 158 TYR cc_start: 0.8271 (t80) cc_final: 0.8003 (t80) REVERT: H 202 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8100 (mt-10) REVERT: H 397 MET cc_start: 0.5056 (tmt) cc_final: 0.4094 (ppp) REVERT: H 403 CYS cc_start: 0.6781 (p) cc_final: 0.6530 (m) REVERT: K 75 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7546 (tpp-160) REVERT: K 97 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7182 (pm20) REVERT: K 123 MET cc_start: 0.7785 (mtp) cc_final: 0.7501 (mtm) REVERT: K 132 THR cc_start: 0.5286 (OUTLIER) cc_final: 0.5050 (p) REVERT: K 261 MET cc_start: 0.5765 (OUTLIER) cc_final: 0.5118 (mmm) REVERT: K 397 MET cc_start: 0.5017 (tmt) cc_final: 0.4115 (ppp) REVERT: K 407 MET cc_start: 0.7310 (tpp) cc_final: 0.6968 (tpp) REVERT: K 434 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7690 (m-30) outliers start: 91 outliers final: 46 residues processed: 356 average time/residue: 0.5194 time to fit residues: 220.3972 Evaluate side-chains 319 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 376 ILE 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 204 HIS 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 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 204 HIS 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 75 ARG Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 133 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 313 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 434 ASP 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 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 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 261 MET Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 374 VAL 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 434 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 276 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 192 optimal weight: 0.3980 chunk 270 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 353 GLN D 58 GLN F 58 GLN H 58 GLN H 124 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 = 0.4052 r_free = 0.4052 target = 0.189074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162462 restraints weight = 25918.423| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.55 r_work: 0.3673 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25662 Z= 0.204 Angle : 0.615 10.356 34872 Z= 0.329 Chirality : 0.045 0.172 3762 Planarity : 0.005 0.055 4350 Dihedral : 15.077 179.947 3750 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.99 % Rotamer: Outliers : 3.40 % Allowed : 23.02 % Favored : 73.58 % 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: 0.16 (0.15), residues: 2940 helix: 0.77 (0.12), residues: 1710 sheet: -0.33 (0.39), residues: 204 loop : -0.80 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 54 TYR 0.020 0.002 TYR F 447 PHE 0.019 0.002 PHE F 478 TRP 0.015 0.002 TRP B 96 HIS 0.005 0.001 HIS K 257 Details of bonding type rmsd covalent geometry : bond 0.00489 (25662) covalent geometry : angle 0.61464 (34872) hydrogen bonds : bond 0.04775 ( 1217) hydrogen bonds : angle 4.64782 ( 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 360 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 268 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7088 (pm20) REVERT: A 313 SER cc_start: 0.7520 (p) cc_final: 0.7224 (p) REVERT: A 348 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: B 97 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7159 (mp0) REVERT: B 113 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: B 284 LEU cc_start: 0.4414 (OUTLIER) cc_final: 0.4191 (mt) REVERT: B 434 ASP cc_start: 0.7762 (m-30) cc_final: 0.7350 (m-30) REVERT: D 97 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7155 (mp0) REVERT: D 113 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: D 131 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5985 (ttmt) REVERT: D 227 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6754 (mmm-85) REVERT: D 349 TYR cc_start: 0.7754 (m-80) cc_final: 0.7502 (m-80) REVERT: D 434 ASP cc_start: 0.7837 (m-30) cc_final: 0.7362 (m-30) REVERT: D 442 ASP cc_start: 0.6261 (t0) cc_final: 0.6009 (t0) REVERT: F 75 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7471 (tpp-160) REVERT: F 97 GLU cc_start: 0.7736 (mm-30) cc_final: 0.6957 (pm20) REVERT: F 434 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: F 489 ASP cc_start: 0.7087 (p0) cc_final: 0.6826 (p0) REVERT: H 97 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7159 (mp0) REVERT: H 158 TYR cc_start: 0.8296 (t80) cc_final: 0.8007 (t80) REVERT: H 397 MET cc_start: 0.5063 (tmt) cc_final: 0.4094 (ppp) REVERT: K 97 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7326 (mp0) REVERT: K 123 MET cc_start: 0.7926 (mtp) cc_final: 0.7585 (mtm) REVERT: K 261 MET cc_start: 0.5719 (OUTLIER) cc_final: 0.5054 (mmm) REVERT: K 397 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.4053 (ppp) REVERT: K 407 MET cc_start: 0.7279 (tpp) cc_final: 0.6908 (tpp) REVERT: K 434 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: K 446 ILE cc_start: 0.5014 (mm) cc_final: 0.4664 (mt) outliers start: 92 outliers final: 56 residues processed: 346 average time/residue: 0.4789 time to fit residues: 199.0117 Evaluate side-chains 316 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 249 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 376 ILE 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 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 284 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 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 227 ARG 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 F residue 75 ARG Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR 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 434 ASP Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 132 THR 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 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 491 CYS 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 251 ASP Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 397 MET Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Chi-restraints excluded: chain K residue 434 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 154 optimal weight: 0.7980 chunk 218 optimal weight: 0.0980 chunk 287 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 238 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 58 GLN F 58 GLN H 124 ASN K 257 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.192444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166262 restraints weight = 26014.943| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.55 r_work: 0.3715 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2160 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 10.378 34872 Z= 0.301 Chirality : 0.042 0.167 3762 Planarity : 0.005 0.057 4350 Dihedral : 14.881 179.982 3750 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.20 % Favored : 96.53 % Rotamer: Outliers : 2.92 % Allowed : 23.65 % Favored : 73.43 % 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: 0.37 (0.15), residues: 2940 helix: 0.94 (0.12), residues: 1728 sheet: -0.32 (0.40), residues: 204 loop : -0.72 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 54 TYR 0.016 0.001 TYR F 447 PHE 0.017 0.001 PHE F 478 TRP 0.009 0.001 TRP H 96 HIS 0.005 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00301 (25662) covalent geometry : angle 0.55851 (34872) hydrogen bonds : bond 0.04134 ( 1217) hydrogen bonds : angle 4.51835 ( 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 361 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 282 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7055 (pm20) REVERT: A 300 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7722 (tttp) REVERT: A 313 SER cc_start: 0.7569 (p) cc_final: 0.7103 (m) REVERT: A 348 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: A 489 ASP cc_start: 0.6944 (p0) cc_final: 0.6730 (p0) REVERT: B 97 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7166 (mp0) REVERT: B 113 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: B 202 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8217 (mt-10) REVERT: B 309 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.6725 (mptt) REVERT: D 97 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7165 (mp0) REVERT: D 113 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: D 434 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7251 (m-30) REVERT: F 97 GLU cc_start: 0.7694 (mm-30) cc_final: 0.6953 (pm20) REVERT: F 261 MET cc_start: 0.5873 (ttt) cc_final: 0.5666 (ttt) REVERT: F 397 MET cc_start: 0.4413 (tmm) cc_final: 0.3697 (pp-130) REVERT: F 434 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: F 489 ASP cc_start: 0.7131 (p0) cc_final: 0.6867 (p0) REVERT: H 97 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7201 (mp0) REVERT: H 124 ASN cc_start: 0.5761 (m110) cc_final: 0.5167 (p0) REVERT: H 158 TYR cc_start: 0.8249 (t80) cc_final: 0.7978 (t80) REVERT: H 202 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8051 (mt-10) REVERT: H 397 MET cc_start: 0.5102 (tmt) cc_final: 0.4122 (ppp) REVERT: H 407 MET cc_start: 0.7466 (tpp) cc_final: 0.6584 (tmm) REVERT: H 434 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6674 (m-30) REVERT: K 75 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7535 (tpp-160) REVERT: K 97 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7329 (mp0) REVERT: K 123 MET cc_start: 0.7902 (mtp) cc_final: 0.7570 (mtm) REVERT: K 158 TYR cc_start: 0.7714 (t80) cc_final: 0.7165 (t80) REVERT: K 261 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5159 (mmm) REVERT: K 382 ASP cc_start: 0.3227 (OUTLIER) cc_final: 0.2982 (p0) REVERT: K 397 MET cc_start: 0.5001 (tmt) cc_final: 0.4123 (ppp) REVERT: K 407 MET cc_start: 0.7315 (tpp) cc_final: 0.6995 (tpp) REVERT: K 434 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: K 446 ILE cc_start: 0.5054 (mm) cc_final: 0.4677 (mt) REVERT: K 498 TYR cc_start: 0.7994 (m-80) cc_final: 0.7747 (m-80) outliers start: 79 outliers final: 48 residues processed: 348 average time/residue: 0.5024 time to fit residues: 208.5580 Evaluate side-chains 329 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 425 VAL 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 204 HIS Chi-restraints excluded: chain B residue 309 LYS 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 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 376 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 133 ILE 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 F residue 376 ILE Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 132 THR 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 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 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 204 HIS Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Chi-restraints excluded: chain K residue 434 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 287 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 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: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN F 58 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 = 0.4083 r_free = 0.4083 target = 0.192216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.165955 restraints weight = 25966.603| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.55 r_work: 0.3714 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25662 Z= 0.145 Angle : 0.569 10.197 34872 Z= 0.307 Chirality : 0.043 0.167 3762 Planarity : 0.005 0.055 4350 Dihedral : 14.813 179.942 3750 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.40 % Favored : 96.33 % Rotamer: Outliers : 2.73 % Allowed : 23.98 % Favored : 73.28 % 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: 0.91 (0.12), residues: 1728 sheet: -0.32 (0.40), residues: 204 loop : -0.75 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.020 0.001 TYR D 447 PHE 0.019 0.001 PHE A 478 TRP 0.009 0.001 TRP H 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00338 (25662) covalent geometry : angle 0.56899 (34872) hydrogen bonds : bond 0.04237 ( 1217) hydrogen bonds : angle 4.54022 ( 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 358 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 284 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7046 (pm20) REVERT: A 300 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7667 (tttp) REVERT: A 313 SER cc_start: 0.7585 (p) cc_final: 0.7083 (m) REVERT: A 348 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: A 489 ASP cc_start: 0.6931 (p0) cc_final: 0.6729 (p0) REVERT: B 97 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7188 (mp0) REVERT: B 113 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: B 202 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 309 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6710 (mptt) REVERT: D 97 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7184 (mp0) REVERT: D 113 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: D 349 TYR cc_start: 0.7790 (m-80) cc_final: 0.7533 (m-80) REVERT: D 434 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: F 97 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6927 (pm20) REVERT: F 261 MET cc_start: 0.5886 (ttt) cc_final: 0.5668 (ttt) REVERT: F 397 MET cc_start: 0.4405 (tmm) cc_final: 0.3679 (pp-130) REVERT: F 434 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: F 489 ASP cc_start: 0.7123 (p0) cc_final: 0.6843 (p0) REVERT: H 97 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7163 (mp0) REVERT: H 124 ASN cc_start: 0.5763 (m110) cc_final: 0.5111 (p0) REVERT: H 158 TYR cc_start: 0.8242 (t80) cc_final: 0.7947 (t80) REVERT: H 202 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8156 (mt-10) REVERT: H 397 MET cc_start: 0.5050 (tmt) cc_final: 0.4119 (ppp) REVERT: H 407 MET cc_start: 0.7533 (tpp) cc_final: 0.6691 (tmm) REVERT: H 434 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: K 97 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7310 (mp0) REVERT: K 158 TYR cc_start: 0.7696 (t80) cc_final: 0.7146 (t80) REVERT: K 261 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.5139 (mmm) REVERT: K 382 ASP cc_start: 0.3251 (OUTLIER) cc_final: 0.2995 (p0) REVERT: K 397 MET cc_start: 0.4999 (tmt) cc_final: 0.4077 (ppp) REVERT: K 434 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: K 446 ILE cc_start: 0.5058 (mm) cc_final: 0.4691 (mt) REVERT: K 498 TYR cc_start: 0.7964 (m-80) cc_final: 0.7731 (m-80) outliers start: 74 outliers final: 54 residues processed: 348 average time/residue: 0.5374 time to fit residues: 222.9198 Evaluate side-chains 330 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 425 VAL 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 204 HIS Chi-restraints excluded: chain B residue 309 LYS 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 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 113 ASP Chi-restraints excluded: chain F residue 133 ILE 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 F residue 376 ILE Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 204 HIS 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 120 ILE Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 146 VAL 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 272 LEU Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Chi-restraints excluded: chain K residue 434 ASP 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 185 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 288 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 258 optimal weight: 0.7980 chunk 192 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN F 58 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 = 0.4091 r_free = 0.4091 target = 0.193076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.166899 restraints weight = 25909.291| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.55 r_work: 0.3728 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 25662 Z= 0.137 Angle : 0.565 10.242 34872 Z= 0.305 Chirality : 0.043 0.166 3762 Planarity : 0.005 0.056 4350 Dihedral : 14.685 179.408 3750 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.22 % Rotamer: Outliers : 2.55 % Allowed : 24.24 % Favored : 73.21 % 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: 0.37 (0.15), residues: 2940 helix: 0.92 (0.12), residues: 1734 sheet: -0.34 (0.39), residues: 204 loop : -0.70 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.018 0.001 TYR D 447 PHE 0.019 0.001 PHE A 478 TRP 0.008 0.001 TRP H 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd covalent geometry : bond 0.00317 (25662) covalent geometry : angle 0.56462 (34872) hydrogen bonds : bond 0.04103 ( 1217) hydrogen bonds : angle 4.52969 ( 3573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6652.61 seconds wall clock time: 114 minutes 52.33 seconds (6892.33 seconds total)