Starting phenix.real_space_refine on Sun Jul 5 04:11:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdo_64990/07_2026/9vdo_64990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdo_64990/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9vdo_64990/07_2026/9vdo_64990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdo_64990/07_2026/9vdo_64990.map" model { file = "/net/cci-nas-00/data/ceres_data/9vdo_64990/07_2026/9vdo_64990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdo_64990/07_2026/9vdo_64990.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 12 7.51 5 P 48 5.49 5 S 132 5.16 5 C 15834 2.51 5 N 4152 2.21 5 O 4848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25026 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "B" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "F" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "H" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "K" Number of atoms: 4042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4042 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 5.28, per 1000 atoms: 0.21 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: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.586A pdb=" N ALA A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.666A pdb=" N ASN A 95 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 160 through 168 removed outlier: 4.227A pdb=" N TRP A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.824A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.663A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.690A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.563A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 Processing helix chain 'A' and resid 366 through 375 Proline residue: A 370 - end of helix removed outlier: 3.722A pdb=" N GLY A 373 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 402 removed outlier: 3.587A pdb=" N ASN A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 422 through 433 Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.820A pdb=" N ASP A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.559A pdb=" N ALA B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.686A pdb=" N ASN B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.524A pdb=" N PHE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 4.247A pdb=" N TRP B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.787A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.667A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.685A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.535A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 Processing helix chain 'B' and resid 366 through 370 Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.895A pdb=" N LEU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 401 removed outlier: 3.569A pdb=" N ASN B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.778A pdb=" N ASP B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 81 through 95 removed outlier: 3.684A pdb=" N ASN D 95 " --> pdb=" O HIS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 127 through 140 Processing helix chain 'D' and resid 160 through 168 removed outlier: 4.248A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.786A pdb=" N LYS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.662A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.705A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.535A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 365 Processing helix chain 'D' and resid 366 through 370 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.893A pdb=" N LEU D 375 " --> pdb=" O TYR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 402 removed outlier: 3.513A pdb=" N ASN D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.802A pdb=" N ASP D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 40 through 50 removed outlier: 3.597A pdb=" N ALA F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.615A pdb=" N ASN F 95 " --> pdb=" O HIS F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 127 through 140 removed outlier: 3.550A pdb=" N PHE F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 removed outlier: 4.191A pdb=" N TRP F 164 " --> pdb=" O HIS F 160 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.818A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 230 removed outlier: 3.670A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 266 removed outlier: 4.016A pdb=" N TYR F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 3.701A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 329 removed outlier: 3.514A pdb=" N VAL F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 343 removed outlier: 3.585A pdb=" N VAL F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 365 Processing helix chain 'F' and resid 366 through 370 Proline residue: F 370 - end of helix Processing helix chain 'F' and resid 371 through 376 removed outlier: 3.899A pdb=" N LEU F 375 " --> pdb=" O TYR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 402 removed outlier: 3.597A pdb=" N ASN F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 417 Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 447 through 462 removed outlier: 3.803A pdb=" N ASP F 462 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 469 Processing helix chain 'F' and resid 470 through 480 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 81 through 95 removed outlier: 3.678A pdb=" N ASN H 95 " --> pdb=" O HIS H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 100 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 126 through 140 removed outlier: 4.264A pdb=" N THR H 130 " --> pdb=" O GLU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 removed outlier: 4.278A pdb=" N TRP H 164 " --> pdb=" O HIS H 160 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL H 166 " --> pdb=" O ILE H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 176 Processing helix chain 'H' and resid 186 through 199 removed outlier: 3.798A pdb=" N LYS H 199 " --> pdb=" O GLN H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 230 removed outlier: 3.713A pdb=" N SER H 214 " --> pdb=" O PRO H 210 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA H 223 " --> pdb=" O ILE H 219 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL H 224 " --> pdb=" O ILE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 265 Processing helix chain 'H' and resid 286 through 295 removed outlier: 3.724A pdb=" N SER H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 329 Processing helix chain 'H' and resid 333 through 343 removed outlier: 3.546A pdb=" N VAL H 342 " --> pdb=" O ALA H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 365 Processing helix chain 'H' and resid 366 through 370 Proline residue: H 370 - end of helix Processing helix chain 'H' and resid 371 through 376 removed outlier: 3.927A pdb=" N LEU H 375 " --> pdb=" O TYR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 402 removed outlier: 3.537A pdb=" N ASN H 389 " --> pdb=" O ASP H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 417 Processing helix chain 'H' and resid 422 through 433 Processing helix chain 'H' and resid 434 through 445 Processing helix chain 'H' and resid 447 through 462 removed outlier: 3.803A pdb=" N ASP H 462 " --> pdb=" O ILE H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 469 Processing helix chain 'H' and resid 470 through 480 Processing helix chain 'H' and resid 490 through 498 Processing helix chain 'K' and resid 6 through 17 Processing helix chain 'K' and resid 40 through 50 Processing helix chain 'K' and resid 81 through 95 removed outlier: 3.686A pdb=" N ASN K 95 " --> pdb=" O HIS K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 100 Processing helix chain 'K' and resid 101 through 103 No H-bonds generated for 'chain 'K' and resid 101 through 103' Processing helix chain 'K' and resid 127 through 140 removed outlier: 3.504A pdb=" N PHE K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 168 removed outlier: 4.215A pdb=" N TRP K 164 " --> pdb=" O HIS K 160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL K 166 " --> pdb=" O ILE K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 176 Processing helix chain 'K' and resid 186 through 199 removed outlier: 3.782A pdb=" N LYS K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 230 removed outlier: 3.710A pdb=" N SER K 214 " --> pdb=" O PRO K 210 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA K 223 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL K 224 " --> pdb=" O ILE K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 265 Processing helix chain 'K' and resid 286 through 295 removed outlier: 3.719A pdb=" N SER K 290 " --> pdb=" O ASP K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 329 Processing helix chain 'K' and resid 333 through 343 removed outlier: 3.544A pdb=" N VAL K 342 " --> pdb=" O ALA K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 365 Processing helix chain 'K' and resid 366 through 370 Proline residue: K 370 - end of helix Processing helix chain 'K' and resid 371 through 376 removed outlier: 3.929A pdb=" N LEU K 375 " --> pdb=" O TYR K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 401 removed outlier: 3.560A pdb=" N ASN K 389 " --> pdb=" O ASP K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 417 Processing helix chain 'K' and resid 422 through 433 Processing helix chain 'K' and resid 434 through 445 Processing helix chain 'K' and resid 447 through 462 removed outlier: 3.791A pdb=" N ASP K 462 " --> pdb=" O ILE K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 469 Processing helix chain 'K' and resid 470 through 480 Processing helix chain 'K' and resid 490 through 498 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 238 removed outlier: 11.188A pdb=" N LYS A 145 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N THR A 275 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ASN A 147 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS A 273 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 149 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 238 removed outlier: 11.178A pdb=" N LYS B 145 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N THR B 275 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N ASN B 147 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS B 273 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP B 149 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 63 through 68 Processing sheet with id=AA6, first strand: chain 'D' and resid 235 through 238 removed outlier: 11.248A pdb=" N LYS D 145 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N THR D 275 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ASN D 147 " --> pdb=" O HIS D 273 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N HIS D 273 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP D 149 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 63 through 68 Processing sheet with id=AA8, first strand: chain 'F' and resid 235 through 238 removed outlier: 11.185A pdb=" N LYS F 145 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N THR F 275 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASN F 147 " --> pdb=" O HIS F 273 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N HIS F 273 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP F 149 " --> pdb=" O ASN F 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 63 through 68 Processing sheet with id=AB1, first strand: chain 'H' and resid 235 through 238 removed outlier: 11.163A pdb=" N LYS H 145 " --> pdb=" O THR H 275 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N THR H 275 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ASN H 147 " --> pdb=" O HIS H 273 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS H 273 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP H 149 " --> pdb=" O ASN H 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 63 through 68 Processing sheet with id=AB3, first strand: chain 'K' and resid 235 through 238 removed outlier: 11.166A pdb=" N LYS K 145 " --> pdb=" O THR K 275 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N THR K 275 " --> pdb=" O LYS K 145 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASN K 147 " --> pdb=" O HIS K 273 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N HIS K 273 " --> pdb=" O ASN K 147 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP K 149 " --> pdb=" O ASN K 271 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7980 1.34 - 1.46: 6044 1.46 - 1.58: 11377 1.58 - 1.70: 75 1.70 - 1.82: 186 Bond restraints: 25662 Sorted by residual: bond pdb=" O3B DCP F 601 " pdb=" PG DCP F 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" O3B DCP K 601 " pdb=" PG DCP K 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O3B DCP H 601 " pdb=" PG DCP H 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" O3B DCP D 601 " pdb=" PG DCP D 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" O3B DCP B 601 " pdb=" PG DCP B 601 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.38e+01 ... (remaining 25657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 34244 2.80 - 5.60: 543 5.60 - 8.39: 70 8.39 - 11.19: 8 11.19 - 13.99: 7 Bond angle restraints: 34872 Sorted by residual: angle pdb=" CA PRO D 41 " pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 112.00 99.87 12.13 1.40e+00 5.10e-01 7.51e+01 angle pdb=" C GLU K 126 " pdb=" N ASP K 127 " pdb=" CA ASP K 127 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" CA LYS K 460 " pdb=" CB LYS K 460 " pdb=" CG LYS K 460 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" CA LYS B 460 " pdb=" CB LYS B 460 " pdb=" CG LYS B 460 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 angle pdb=" 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: 14839 35.96 - 71.92: 522 71.92 - 107.88: 17 107.88 - 143.84: 0 143.84 - 179.80: 12 Dihedral angle restraints: 15390 sinusoidal: 6594 harmonic: 8796 Sorted by residual: dihedral pdb=" CA GLY D 152 " pdb=" C GLY D 152 " pdb=" N CYS D 153 " pdb=" CA CYS D 153 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLY H 152 " pdb=" C GLY H 152 " pdb=" N CYS H 153 " pdb=" CA CYS H 153 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLY F 152 " pdb=" C GLY F 152 " pdb=" N CYS F 153 " pdb=" CA CYS F 153 " ideal model delta harmonic sigma weight residual -180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 15387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2747 0.053 - 0.105: 790 0.105 - 0.158: 191 0.158 - 0.210: 27 0.210 - 0.263: 7 Chirality restraints: 3762 Sorted by residual: chirality pdb=" CG LEU A 10 " pdb=" CB LEU A 10 " pdb=" CD1 LEU A 10 " pdb=" CD2 LEU A 10 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU F 10 " pdb=" CB LEU F 10 " pdb=" CD1 LEU F 10 " pdb=" CD2 LEU F 10 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 3759 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 40 " 0.110 5.00e-02 4.00e+02 1.57e-01 3.94e+01 pdb=" N PRO D 41 " -0.271 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 96 " -0.015 2.00e-02 2.50e+03 1.58e-02 6.22e+00 pdb=" CG TRP A 96 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 96 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 96 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 96 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 96 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 96 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 126 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLU H 126 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU H 126 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP H 127 " -0.015 2.00e-02 2.50e+03 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 716 2.69 - 3.24: 24679 3.24 - 3.80: 41818 3.80 - 4.35: 57952 4.35 - 4.90: 93987 Nonbonded interactions: 219152 Sorted by model distance: nonbonded pdb=" O ILE A 150 " pdb="MN MN A 603 " model vdw 2.141 3.060 nonbonded pdb=" O ILE B 150 " pdb="MN MN B 603 " model vdw 2.142 3.060 nonbonded pdb=" O ILE K 150 " pdb="MN MN K 603 " model vdw 2.143 3.060 nonbonded pdb=" O ILE D 150 " pdb="MN MN D 603 " model vdw 2.144 3.060 nonbonded pdb=" O ILE F 150 " pdb="MN MN F 603 " model vdw 2.146 3.060 ... (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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 22.420 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 25662 Z= 0.300 Angle : 0.873 13.991 34872 Z= 0.484 Chirality : 0.052 0.263 3762 Planarity : 0.007 0.157 4350 Dihedral : 18.482 179.801 9726 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.11 % Rotamer: Outliers : 0.37 % Allowed : 22.17 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 2940 helix: -0.40 (0.11), residues: 1680 sheet: -0.10 (0.36), residues: 204 loop : -1.20 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 477 TYR 0.030 0.002 TYR B 11 PHE 0.034 0.002 PHE B 140 TRP 0.043 0.003 TRP A 96 HIS 0.008 0.002 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.30 (25662) covalent geometry : angle 0.87261 / 0.48 (34872) hydrogen bonds : bond 0.16151 / 10.63 ( 1217) hydrogen bonds : angle 6.16326 / 4.28 ( 3573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 276 time to evaluate : 0.771 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: 0.5037 time to fit residues: 169.4353 Evaluate side-chains 252 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain H residue 11 TYR Chi-restraints excluded: chain K residue 11 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 295 ASN D 201 ASN F 295 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 = 0.4103 r_free = 0.4103 target = 0.194236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167580 restraints weight = 25847.059| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.57 r_work: 0.3723 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1028 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= 0.170 Angle : 0.614 6.944 34872 Z= 0.335 Chirality : 0.046 0.285 3762 Planarity : 0.005 0.083 4350 Dihedral : 15.987 176.837 3800 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.62 % Favored : 97.18 % Rotamer: Outliers : 3.14 % Allowed : 21.14 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 2940 helix: 0.51 (0.12), residues: 1722 sheet: -0.24 (0.37), residues: 204 loop : -1.21 (0.16), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 75 TYR 0.017 0.002 TYR A 245 PHE 0.021 0.001 PHE H 140 TRP 0.019 0.002 TRP F 96 HIS 0.005 0.001 HIS F 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (25662) covalent geometry : angle 0.61442 / 0.34 (34872) hydrogen bonds : bond 0.05272 / 3.51 ( 1217) hydrogen bonds : angle 4.83230 / 3.39 ( 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 374 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 289 time to evaluate : 0.851 Fit side-chains REVERT: A 188 SER cc_start: 0.8409 (t) cc_final: 0.8150 (p) REVERT: A 261 MET cc_start: 0.5766 (mmm) cc_final: 0.5466 (mmm) REVERT: A 313 SER cc_start: 0.7400 (p) cc_final: 0.7095 (p) REVERT: A 397 MET cc_start: 0.4132 (tmm) cc_final: 0.3556 (pp-130) REVERT: B 113 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: B 374 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7735 (p) REVERT: D 113 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: D 188 SER cc_start: 0.8370 (t) cc_final: 0.8058 (p) REVERT: D 227 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6741 (mpp-170) REVERT: D 349 TYR cc_start: 0.7859 (m-80) cc_final: 0.7634 (m-80) REVERT: D 374 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7744 (p) REVERT: D 498 TYR cc_start: 0.7810 (m-80) cc_final: 0.7538 (m-80) REVERT: F 97 GLU cc_start: 0.7699 (mm-30) cc_final: 0.6720 (pm20) REVERT: F 374 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7830 (p) REVERT: F 397 MET cc_start: 0.4391 (tmm) cc_final: 0.3472 (pp-130) REVERT: H 97 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6698 (pm20) REVERT: H 202 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8101 (mt-10) REVERT: K 261 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.4968 (mmm) outliers start: 85 outliers final: 22 residues processed: 349 average time/residue: 0.4558 time to fit residues: 192.0892 Evaluate side-chains 294 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 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 H residue 434 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 374 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 99 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 156 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 212 optimal weight: 0.4980 chunk 261 optimal weight: 0.2980 chunk 160 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN A 201 ASN D 58 GLN F 257 HIS H 124 ASN H 201 ASN K 257 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.195627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169437 restraints weight = 25790.914| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.56 r_work: 0.3749 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25662 Z= 0.125 Angle : 0.546 9.387 34872 Z= 0.297 Chirality : 0.044 0.301 3762 Planarity : 0.005 0.075 4350 Dihedral : 15.811 176.356 3792 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.86 % Favored : 96.94 % Rotamer: Outliers : 2.48 % Allowed : 22.14 % Favored : 75.39 % 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: 0.14 (0.15), residues: 2940 helix: 0.85 (0.12), residues: 1728 sheet: -0.28 (0.37), residues: 204 loop : -1.08 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 75 TYR 0.014 0.001 TYR F 447 PHE 0.017 0.001 PHE H 140 TRP 0.011 0.001 TRP F 96 HIS 0.012 0.001 HIS H 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (25662) covalent geometry : angle 0.54569 / 0.30 (34872) hydrogen bonds : bond 0.04577 / 3.06 ( 1217) hydrogen bonds : angle 4.62202 / 3.24 ( 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 367 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 75 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7300 (tpp-160) REVERT: A 97 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6838 (pm20) REVERT: A 188 SER cc_start: 0.8385 (t) cc_final: 0.8119 (p) REVERT: A 261 MET cc_start: 0.5706 (mmm) cc_final: 0.5367 (mmm) REVERT: A 300 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7729 (tttp) REVERT: A 313 SER cc_start: 0.7451 (p) cc_final: 0.7126 (p) REVERT: A 374 VAL cc_start: 0.7852 (m) cc_final: 0.7592 (p) REVERT: A 397 MET cc_start: 0.4368 (tmm) cc_final: 0.3612 (pp-130) REVERT: B 113 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: B 227 ARG cc_start: 0.6640 (mmp-170) cc_final: 0.6380 (mmm-85) REVERT: B 374 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7709 (p) REVERT: B 442 ASP cc_start: 0.6081 (t0) cc_final: 0.5839 (t0) REVERT: D 113 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: D 158 TYR cc_start: 0.8144 (t80) cc_final: 0.7813 (t80) REVERT: D 188 SER cc_start: 0.8362 (t) cc_final: 0.8049 (p) REVERT: D 202 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8198 (mt-10) REVERT: D 374 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7765 (p) REVERT: D 442 ASP cc_start: 0.6049 (t0) cc_final: 0.5840 (t0) REVERT: D 498 TYR cc_start: 0.7791 (m-80) cc_final: 0.7514 (m-80) REVERT: F 75 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7131 (tpp-160) REVERT: F 97 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6828 (pm20) REVERT: F 374 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7826 (p) REVERT: F 397 MET cc_start: 0.4310 (tmm) cc_final: 0.3323 (pp-130) REVERT: H 54 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7671 (ttp80) REVERT: H 97 GLU cc_start: 0.7682 (mm-30) cc_final: 0.6746 (pm20) REVERT: H 202 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8047 (mt-10) REVERT: H 261 MET cc_start: 0.5747 (mmm) cc_final: 0.5241 (mmm) REVERT: H 397 MET cc_start: 0.4978 (tmt) cc_final: 0.4250 (ppp) REVERT: K 75 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7090 (tpp-160) REVERT: K 123 MET cc_start: 0.7479 (mtp) cc_final: 0.7166 (mtm) REVERT: K 261 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5015 (mmm) REVERT: K 397 MET cc_start: 0.5183 (tmt) cc_final: 0.4215 (ppp) REVERT: K 407 MET cc_start: 0.7516 (tpp) cc_final: 0.7202 (tpp) outliers start: 67 outliers final: 21 residues processed: 356 average time/residue: 0.4849 time to fit residues: 207.2627 Evaluate side-chains 295 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 421 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 43 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 283 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN B 124 ASN B 201 ASN D 58 GLN D 197 GLN D 392 ASN F 201 ASN H 58 GLN H 124 ASN K 201 ASN K 257 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.191416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.164335 restraints weight = 25810.014| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.58 r_work: 0.3691 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25662 Z= 0.193 Angle : 0.599 9.460 34872 Z= 0.322 Chirality : 0.047 0.300 3762 Planarity : 0.005 0.065 4350 Dihedral : 15.738 176.462 3792 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.03 % Favored : 96.77 % Rotamer: Outliers : 3.03 % Allowed : 22.10 % Favored : 74.87 % 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: 0.84 (0.12), residues: 1722 sheet: -0.24 (0.37), residues: 204 loop : -1.14 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 75 TYR 0.016 0.002 TYR F 447 PHE 0.015 0.002 PHE H 140 TRP 0.013 0.002 TRP B 96 HIS 0.005 0.001 HIS K 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (25662) covalent geometry : angle 0.59877 / 0.32 (34872) hydrogen bonds : bond 0.04918 / 3.26 ( 1217) hydrogen bonds : angle 4.66922 / 3.28 ( 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 361 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 279 time to evaluate : 0.936 Fit side-chains REVERT: A 15 LEU cc_start: 0.8585 (mm) cc_final: 0.8372 (mt) REVERT: A 97 GLU cc_start: 0.7887 (mm-30) cc_final: 0.6917 (pm20) REVERT: A 132 THR cc_start: 0.5121 (OUTLIER) cc_final: 0.4846 (m) REVERT: A 188 SER cc_start: 0.8376 (t) cc_final: 0.8052 (p) REVERT: A 261 MET cc_start: 0.5684 (mmm) cc_final: 0.5350 (mmm) REVERT: A 300 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7651 (tttp) REVERT: A 313 SER cc_start: 0.7363 (p) cc_final: 0.7041 (p) REVERT: A 397 MET cc_start: 0.4397 (tmm) cc_final: 0.3410 (pp-130) REVERT: B 113 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: B 227 ARG cc_start: 0.6824 (mmp-170) cc_final: 0.6197 (mpp-170) REVERT: B 442 ASP cc_start: 0.6371 (t0) cc_final: 0.6129 (t0) REVERT: D 97 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7223 (mp0) REVERT: D 113 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: D 227 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6649 (mpp-170) REVERT: D 349 TYR cc_start: 0.7809 (m-80) cc_final: 0.7585 (m-80) REVERT: D 498 TYR cc_start: 0.7858 (m-80) cc_final: 0.7575 (m-80) REVERT: F 75 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7245 (tpp-160) REVERT: F 97 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6861 (pm20) REVERT: F 397 MET cc_start: 0.4273 (tmm) cc_final: 0.3584 (pp-130) REVERT: F 489 ASP cc_start: 0.7024 (p0) cc_final: 0.6795 (p0) REVERT: H 54 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7683 (ttp80) REVERT: H 97 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6858 (pm20) REVERT: H 261 MET cc_start: 0.5808 (mmm) cc_final: 0.4982 (mmm) REVERT: H 397 MET cc_start: 0.4962 (OUTLIER) cc_final: 0.4079 (ppp) REVERT: H 407 MET cc_start: 0.7448 (tpp) cc_final: 0.7141 (tpp) REVERT: K 75 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7210 (tpp-160) REVERT: K 97 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7033 (pm20) REVERT: K 123 MET cc_start: 0.7694 (mtp) cc_final: 0.7396 (mtm) REVERT: K 261 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.4935 (mmm) REVERT: K 397 MET cc_start: 0.5250 (tmt) cc_final: 0.4099 (ppp) outliers start: 82 outliers final: 43 residues processed: 341 average time/residue: 0.4455 time to fit residues: 184.3266 Evaluate side-chains 304 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 155 THR 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 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 358 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain H residue 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 397 MET Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 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 421 ILE Chi-restraints excluded: chain K residue 425 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 82 optimal weight: 0.8980 chunk 114 optimal weight: 0.0470 chunk 205 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 225 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 201 ASN 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 = 0.193359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.167096 restraints weight = 25679.464| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.55 r_work: 0.3728 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25662 Z= 0.126 Angle : 0.539 9.602 34872 Z= 0.290 Chirality : 0.044 0.303 3762 Planarity : 0.005 0.059 4350 Dihedral : 15.646 176.980 3792 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.10 % Favored : 96.70 % Rotamer: Outliers : 3.10 % Allowed : 22.47 % Favored : 74.43 % 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: 0.38 (0.15), residues: 2940 helix: 1.02 (0.12), residues: 1722 sheet: -0.23 (0.38), residues: 204 loop : -0.89 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 75 TYR 0.014 0.001 TYR F 447 PHE 0.014 0.001 PHE D 140 TRP 0.009 0.001 TRP F 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (25662) covalent geometry : angle 0.53880 / 0.29 (34872) hydrogen bonds : bond 0.04285 / 2.85 ( 1217) hydrogen bonds : angle 4.57066 / 3.21 ( 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 384 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 300 time to evaluate : 0.933 Fit side-chains REVERT: A 15 LEU cc_start: 0.8556 (mm) cc_final: 0.8339 (mt) REVERT: A 97 GLU cc_start: 0.7861 (mm-30) cc_final: 0.6954 (pm20) REVERT: A 132 THR cc_start: 0.5120 (OUTLIER) cc_final: 0.4854 (m) REVERT: A 188 SER cc_start: 0.8455 (t) cc_final: 0.8107 (p) REVERT: A 261 MET cc_start: 0.5583 (mmm) cc_final: 0.5296 (mmm) REVERT: A 300 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7715 (tttp) REVERT: A 313 SER cc_start: 0.7370 (p) cc_final: 0.7030 (p) REVERT: A 397 MET cc_start: 0.4399 (tmm) cc_final: 0.3565 (pp-130) REVERT: B 97 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7033 (mp0) REVERT: B 113 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: B 227 ARG cc_start: 0.6727 (mmp-170) cc_final: 0.6405 (mmm-85) REVERT: D 97 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7102 (mp0) REVERT: D 113 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: D 265 LYS cc_start: 0.7227 (mttt) cc_final: 0.6871 (mptt) REVERT: D 313 SER cc_start: 0.7746 (OUTLIER) cc_final: 0.7486 (m) REVERT: D 498 TYR cc_start: 0.7796 (m-80) cc_final: 0.7523 (m-80) REVERT: F 97 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6872 (pm20) REVERT: F 265 LYS cc_start: 0.7065 (mmtm) cc_final: 0.6860 (mptt) REVERT: F 348 GLU cc_start: 0.8634 (pm20) cc_final: 0.8394 (pm20) REVERT: F 374 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7747 (p) REVERT: F 397 MET cc_start: 0.4299 (tmm) cc_final: 0.3550 (pp-130) REVERT: H 97 GLU cc_start: 0.7814 (mm-30) cc_final: 0.6959 (pm20) REVERT: H 135 GLU cc_start: 0.7083 (tp30) cc_final: 0.6845 (tp30) REVERT: H 202 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8004 (mt-10) REVERT: H 397 MET cc_start: 0.4884 (tmt) cc_final: 0.4052 (ppp) REVERT: K 75 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7000 (tpp-160) REVERT: K 97 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7126 (pm20) REVERT: K 123 MET cc_start: 0.7686 (mtp) cc_final: 0.7368 (mtm) REVERT: K 132 THR cc_start: 0.5364 (OUTLIER) cc_final: 0.5142 (p) REVERT: K 158 TYR cc_start: 0.7661 (t80) cc_final: 0.7321 (t80) REVERT: K 261 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.4853 (mmm) REVERT: K 397 MET cc_start: 0.5228 (tmt) cc_final: 0.4073 (ppp) REVERT: K 407 MET cc_start: 0.7485 (tpp) cc_final: 0.7011 (tpp) outliers start: 84 outliers final: 33 residues processed: 368 average time/residue: 0.4648 time to fit residues: 205.5050 Evaluate side-chains 314 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 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 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 40 THR Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 374 VAL 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 376 ILE Chi-restraints excluded: chain H residue 421 ILE 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 132 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 376 ILE 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: 0.7980 chunk 235 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN B 353 GLN D 95 ASN D 124 ASN D 353 GLN F 95 ASN F 197 GLN F 201 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.185732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158765 restraints weight = 25997.484| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.56 r_work: 0.3632 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 25662 Z= 0.302 Angle : 0.717 9.212 34872 Z= 0.380 Chirality : 0.052 0.296 3762 Planarity : 0.007 0.067 4350 Dihedral : 15.644 177.892 3792 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.27 % Favored : 96.46 % Rotamer: Outliers : 4.03 % Allowed : 21.84 % Favored : 74.13 % 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: -0.25 (0.14), residues: 2940 helix: 0.44 (0.12), residues: 1722 sheet: -0.24 (0.38), residues: 204 loop : -1.08 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 75 TYR 0.023 0.003 TYR A 447 PHE 0.017 0.002 PHE H 34 TRP 0.019 0.002 TRP B 96 HIS 0.007 0.002 HIS K 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.30 (25662) covalent geometry : angle 0.71680 / 0.38 (34872) hydrogen bonds : bond 0.05583 / 3.70 ( 1217) hydrogen bonds : angle 4.91041 / 3.46 ( 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 388 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 279 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7037 (pm20) REVERT: A 132 THR cc_start: 0.5105 (OUTLIER) cc_final: 0.4880 (m) REVERT: A 313 SER cc_start: 0.7538 (p) cc_final: 0.7215 (p) REVERT: B 97 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7205 (mp0) REVERT: B 113 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: B 344 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8184 (m-40) REVERT: D 97 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7244 (mp0) REVERT: D 113 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: D 227 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6819 (mmm-85) REVERT: D 344 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8229 (m-40) REVERT: D 349 TYR cc_start: 0.7823 (m-80) cc_final: 0.7610 (m-80) REVERT: D 442 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.6112 (t0) REVERT: F 97 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7011 (pm20) REVERT: F 265 LYS cc_start: 0.7464 (mmtm) cc_final: 0.7154 (mptt) REVERT: F 348 GLU cc_start: 0.8608 (pm20) cc_final: 0.8403 (pm20) REVERT: H 97 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7137 (mp0) REVERT: H 135 GLU cc_start: 0.7224 (tp30) cc_final: 0.6976 (tp30) REVERT: H 158 TYR cc_start: 0.8290 (t80) cc_final: 0.8026 (t80) REVERT: H 283 THR cc_start: 0.6279 (m) cc_final: 0.6068 (p) REVERT: H 397 MET cc_start: 0.5144 (OUTLIER) cc_final: 0.4185 (ppp) REVERT: H 434 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: K 97 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7168 (pm20) REVERT: K 123 MET cc_start: 0.7845 (mtp) cc_final: 0.7563 (mtm) REVERT: K 132 THR cc_start: 0.5577 (OUTLIER) cc_final: 0.5316 (p) REVERT: K 261 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5087 (mmm) REVERT: K 397 MET cc_start: 0.5403 (tmt) cc_final: 0.4250 (ppp) REVERT: K 407 MET cc_start: 0.7627 (tpp) cc_final: 0.7259 (tpp) REVERT: K 434 ASP cc_start: 0.7973 (m-30) cc_final: 0.7674 (m-30) outliers start: 109 outliers final: 58 residues processed: 360 average time/residue: 0.4560 time to fit residues: 197.7417 Evaluate side-chains 323 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 254 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 437 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 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 344 ASN 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 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 344 ASN 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 442 ASP 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 307 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 442 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 51 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 358 LEU Chi-restraints excluded: chain H residue 374 VAL Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 397 MET Chi-restraints excluded: chain H residue 421 ILE Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 434 ASP Chi-restraints excluded: chain H residue 491 CYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 75 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 GLN H 124 ASN K 204 HIS K 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.191057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.164601 restraints weight = 25674.984| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.55 r_work: 0.3689 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25662 Z= 0.150 Angle : 0.583 9.518 34872 Z= 0.313 Chirality : 0.046 0.296 3762 Planarity : 0.005 0.060 4350 Dihedral : 15.527 178.830 3792 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.13 % Favored : 96.60 % Rotamer: Outliers : 3.07 % Allowed : 23.02 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 2940 helix: 0.76 (0.12), residues: 1722 sheet: -0.22 (0.39), residues: 204 loop : -1.05 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 75 TYR 0.016 0.002 TYR A 447 PHE 0.014 0.001 PHE F 478 TRP 0.012 0.001 TRP B 96 HIS 0.005 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (25662) covalent geometry : angle 0.58325 / 0.31 (34872) hydrogen bonds : bond 0.04507 / 2.99 ( 1217) hydrogen bonds : angle 4.70438 / 3.31 ( 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 360 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 277 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7013 (pm20) REVERT: A 300 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7714 (tttp) REVERT: A 313 SER cc_start: 0.7379 (p) cc_final: 0.6917 (m) REVERT: B 97 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7112 (mp0) REVERT: B 113 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: B 434 ASP cc_start: 0.7910 (m-30) cc_final: 0.7448 (m-30) REVERT: D 97 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7141 (mp0) REVERT: D 113 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: D 132 THR cc_start: 0.5208 (OUTLIER) cc_final: 0.4842 (m) REVERT: D 227 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6666 (mpp-170) REVERT: D 313 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7485 (m) REVERT: D 349 TYR cc_start: 0.7799 (m-80) cc_final: 0.7555 (m-80) REVERT: F 97 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6941 (pm20) REVERT: F 348 GLU cc_start: 0.8641 (pm20) cc_final: 0.8398 (pm20) REVERT: F 397 MET cc_start: 0.4485 (tmm) cc_final: 0.3628 (pp-130) REVERT: F 489 ASP cc_start: 0.6889 (p0) cc_final: 0.6654 (p0) REVERT: H 97 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7206 (mp0) REVERT: H 113 ASP cc_start: 0.7982 (m-30) cc_final: 0.7517 (m-30) REVERT: H 135 GLU cc_start: 0.7038 (tp30) cc_final: 0.6838 (tp30) REVERT: H 158 TYR cc_start: 0.8235 (t80) cc_final: 0.7977 (t80) REVERT: H 202 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8118 (mt-10) REVERT: H 397 MET cc_start: 0.5073 (tmt) cc_final: 0.4109 (ppp) REVERT: K 75 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7342 (tpp-160) REVERT: K 97 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7172 (pm20) REVERT: K 123 MET cc_start: 0.7726 (mtp) cc_final: 0.7456 (mtm) REVERT: K 132 THR cc_start: 0.5448 (OUTLIER) cc_final: 0.5212 (p) REVERT: K 261 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.4972 (mmm) REVERT: K 397 MET cc_start: 0.5280 (tmt) cc_final: 0.4119 (ppp) REVERT: K 407 MET cc_start: 0.7475 (tpp) cc_final: 0.7238 (tpp) REVERT: K 434 ASP cc_start: 0.7875 (m-30) cc_final: 0.7563 (m-30) outliers start: 83 outliers final: 47 residues processed: 347 average time/residue: 0.4807 time to fit residues: 200.6810 Evaluate side-chains 316 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 376 ILE Chi-restraints excluded: chain A residue 425 VAL 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 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 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 132 THR Chi-restraints excluded: chain D residue 133 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 204 HIS 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 113 ASP Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 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 491 CYS Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 261 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 276 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 158 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 253 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN B 58 GLN F 58 GLN H 58 GLN H 124 ASN K 58 GLN K 257 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.192905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.166792 restraints weight = 25575.413| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.53 r_work: 0.3715 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25662 Z= 0.133 Angle : 0.558 10.145 34872 Z= 0.299 Chirality : 0.044 0.301 3762 Planarity : 0.005 0.056 4350 Dihedral : 15.298 178.386 3792 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.54 % Favored : 96.16 % Rotamer: Outliers : 2.92 % Allowed : 23.28 % Favored : 73.80 % 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: 0.93 (0.12), residues: 1728 sheet: -0.16 (0.39), residues: 204 loop : -0.82 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 75 TYR 0.015 0.001 TYR A 447 PHE 0.017 0.001 PHE F 478 TRP 0.010 0.001 TRP K 96 HIS 0.005 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (25662) covalent geometry : angle 0.55815 / 0.30 (34872) hydrogen bonds : bond 0.04240 / 2.82 ( 1217) hydrogen bonds : angle 4.58473 / 3.22 ( 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 368 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 289 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7840 (mm-30) cc_final: 0.6987 (pm20) REVERT: A 300 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7742 (tttp) REVERT: A 313 SER cc_start: 0.7419 (p) cc_final: 0.6960 (m) REVERT: A 397 MET cc_start: 0.4365 (tmm) cc_final: 0.3399 (pp-130) REVERT: B 97 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7206 (mp0) REVERT: B 113 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: B 132 THR cc_start: 0.4938 (OUTLIER) cc_final: 0.4734 (p) REVERT: B 202 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 434 ASP cc_start: 0.7880 (m-30) cc_final: 0.7534 (m-30) REVERT: D 75 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.5455 (tpm170) REVERT: D 97 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7156 (mp0) REVERT: D 113 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: D 284 LEU cc_start: 0.4472 (OUTLIER) cc_final: 0.4090 (mt) REVERT: D 313 SER cc_start: 0.7783 (p) cc_final: 0.7538 (m) REVERT: D 349 TYR cc_start: 0.7826 (m-80) cc_final: 0.7587 (m-80) REVERT: F 97 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6935 (pm20) REVERT: F 348 GLU cc_start: 0.8602 (pm20) cc_final: 0.8346 (pm20) REVERT: F 397 MET cc_start: 0.4427 (tmm) cc_final: 0.3663 (pp-130) REVERT: F 489 ASP cc_start: 0.6912 (p0) cc_final: 0.6667 (p0) REVERT: H 97 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7203 (mp0) REVERT: H 135 GLU cc_start: 0.7078 (tp30) cc_final: 0.6867 (tp30) REVERT: H 202 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8119 (mt-10) REVERT: H 397 MET cc_start: 0.5130 (tmt) cc_final: 0.4198 (ppp) REVERT: H 407 MET cc_start: 0.7611 (tpp) cc_final: 0.7187 (tpp) REVERT: K 97 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7192 (pm20) REVERT: K 123 MET cc_start: 0.7746 (mtp) cc_final: 0.7455 (mtm) REVERT: K 158 TYR cc_start: 0.7706 (t80) cc_final: 0.7168 (t80) REVERT: K 261 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.5041 (mmm) REVERT: K 397 MET cc_start: 0.5320 (tmt) cc_final: 0.4176 (ppp) outliers start: 79 outliers final: 46 residues processed: 357 average time/residue: 0.4674 time to fit residues: 200.8402 Evaluate side-chains 320 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 425 VAL 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 132 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 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 284 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 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 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 157 ILE 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 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 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 154 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 287 optimal weight: 0.7980 chunk 217 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 238 optimal weight: 0.0870 chunk 237 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 124 ASN H 58 GLN K 58 GLN K 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.192732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.166703 restraints weight = 25756.378| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.54 r_work: 0.3734 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25662 Z= 0.127 Angle : 0.560 10.042 34872 Z= 0.299 Chirality : 0.044 0.302 3762 Planarity : 0.005 0.076 4350 Dihedral : 15.133 179.166 3792 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.99 % Favored : 96.70 % Rotamer: Outliers : 2.70 % Allowed : 23.58 % Favored : 73.73 % 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: 0.46 (0.15), residues: 2940 helix: 1.03 (0.12), residues: 1728 sheet: -0.14 (0.39), residues: 204 loop : -0.76 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 75 TYR 0.019 0.001 TYR F 447 PHE 0.019 0.001 PHE F 478 TRP 0.008 0.001 TRP D 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (25662) covalent geometry : angle 0.56018 / 0.30 (34872) hydrogen bonds : bond 0.04080 / 2.71 ( 1217) hydrogen bonds : angle 4.53911 / 3.19 ( 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 363 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 290 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 97 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7032 (pm20) REVERT: A 300 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7693 (tttp) REVERT: A 313 SER cc_start: 0.7561 (p) cc_final: 0.7074 (m) REVERT: A 397 MET cc_start: 0.4304 (tmm) cc_final: 0.3415 (pp-130) REVERT: A 489 ASP cc_start: 0.6998 (p0) cc_final: 0.6755 (p0) REVERT: B 97 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7170 (mp0) REVERT: B 106 GLU cc_start: 0.8057 (mp0) cc_final: 0.7773 (mm-30) REVERT: B 113 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: B 132 THR cc_start: 0.5057 (OUTLIER) cc_final: 0.4847 (p) REVERT: B 202 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 309 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7306 (mptt) REVERT: B 434 ASP cc_start: 0.7792 (m-30) cc_final: 0.7445 (m-30) REVERT: D 75 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.5417 (tpm170) REVERT: D 97 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7163 (mp0) REVERT: D 113 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: D 313 SER cc_start: 0.7722 (p) cc_final: 0.7474 (m) REVERT: D 442 ASP cc_start: 0.5941 (t0) cc_final: 0.5666 (t0) REVERT: F 97 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6886 (pm20) REVERT: F 348 GLU cc_start: 0.8585 (pm20) cc_final: 0.8333 (pm20) REVERT: F 397 MET cc_start: 0.4335 (tmm) cc_final: 0.3573 (pp-130) REVERT: F 434 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: F 489 ASP cc_start: 0.6948 (p0) cc_final: 0.6721 (p0) REVERT: H 97 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7192 (mp0) REVERT: H 124 ASN cc_start: 0.5695 (m110) cc_final: 0.5151 (p0) REVERT: H 202 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8015 (mt-10) REVERT: H 397 MET cc_start: 0.5054 (tmt) cc_final: 0.4130 (ppp) REVERT: H 407 MET cc_start: 0.7474 (tpp) cc_final: 0.7239 (tpp) REVERT: K 97 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7302 (mp0) REVERT: K 123 MET cc_start: 0.7752 (mtp) cc_final: 0.7450 (mtm) REVERT: K 158 TYR cc_start: 0.7782 (t80) cc_final: 0.7307 (t80) REVERT: K 261 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.5046 (mmm) REVERT: K 397 MET cc_start: 0.5341 (tmt) cc_final: 0.4264 (ppp) REVERT: K 407 MET cc_start: 0.7525 (tpp) cc_final: 0.7143 (tpp) outliers start: 73 outliers final: 45 residues processed: 350 average time/residue: 0.4913 time to fit residues: 206.0140 Evaluate side-chains 322 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain 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 157 ILE Chi-restraints excluded: chain B residue 176 LEU 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 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 425 VAL Chi-restraints excluded: chain F residue 40 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 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 132 THR Chi-restraints excluded: chain H residue 146 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 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 261 MET Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 259 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 58 GLN H 58 GLN K 58 GLN K 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.192757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.166661 restraints weight = 25702.909| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.54 r_work: 0.3730 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25662 Z= 0.134 Angle : 0.569 10.108 34872 Z= 0.304 Chirality : 0.045 0.302 3762 Planarity : 0.005 0.087 4350 Dihedral : 15.045 178.210 3792 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.40 % Favored : 96.29 % Rotamer: Outliers : 2.25 % Allowed : 23.98 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 2940 helix: 1.04 (0.12), residues: 1722 sheet: -0.15 (0.39), residues: 204 loop : -0.79 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 75 TYR 0.016 0.001 TYR F 447 PHE 0.020 0.001 PHE F 478 TRP 0.008 0.001 TRP D 96 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25662) covalent geometry : angle 0.56874 / 0.30 (34872) hydrogen bonds : bond 0.04122 / 2.73 ( 1217) hydrogen bonds : angle 4.54976 / 3.19 ( 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 343 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 282 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 97 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7013 (pm20) REVERT: A 300 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7661 (tttp) REVERT: A 489 ASP cc_start: 0.6920 (p0) cc_final: 0.6708 (p0) REVERT: B 97 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7159 (mp0) REVERT: B 106 GLU cc_start: 0.8074 (mp0) cc_final: 0.7790 (mm-30) REVERT: B 113 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: B 132 THR cc_start: 0.5061 (OUTLIER) cc_final: 0.4851 (p) REVERT: B 309 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7157 (mptt) REVERT: B 434 ASP cc_start: 0.7739 (m-30) cc_final: 0.7383 (m-30) REVERT: D 75 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.5426 (tpm170) REVERT: D 97 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7144 (mp0) REVERT: D 113 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: D 349 TYR cc_start: 0.7831 (m-80) cc_final: 0.7573 (m-80) REVERT: D 442 ASP cc_start: 0.5912 (t0) cc_final: 0.5631 (t0) REVERT: F 97 GLU cc_start: 0.7598 (mm-30) cc_final: 0.6852 (pm20) REVERT: F 348 GLU cc_start: 0.8602 (pm20) cc_final: 0.8353 (pm20) REVERT: F 397 MET cc_start: 0.4309 (tmm) cc_final: 0.3616 (pp-130) REVERT: F 434 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: F 489 ASP cc_start: 0.6939 (p0) cc_final: 0.6707 (p0) REVERT: H 97 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7183 (mp0) REVERT: H 124 ASN cc_start: 0.5684 (m110) cc_final: 0.5144 (p0) REVERT: H 202 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8020 (mt-10) REVERT: H 397 MET cc_start: 0.4910 (tmt) cc_final: 0.4034 (ppp) REVERT: H 407 MET cc_start: 0.7439 (tpp) cc_final: 0.7206 (tpp) REVERT: K 97 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7299 (mp0) REVERT: K 158 TYR cc_start: 0.7784 (t80) cc_final: 0.7243 (t80) REVERT: K 261 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.5031 (mmm) REVERT: K 397 MET cc_start: 0.5241 (tmt) cc_final: 0.4123 (ppp) outliers start: 61 outliers final: 45 residues processed: 332 average time/residue: 0.4788 time to fit residues: 190.4526 Evaluate side-chains 320 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 425 VAL 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 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 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 308 ASN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 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 132 THR Chi-restraints excluded: chain H residue 146 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 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 313 SER Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 376 ILE Chi-restraints excluded: chain K residue 421 ILE Chi-restraints excluded: chain K residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN D 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 = 0.4088 r_free = 0.4088 target = 0.192398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.166259 restraints weight = 25689.292| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.54 r_work: 0.3728 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25662 Z= 0.140 Angle : 0.575 9.694 34872 Z= 0.307 Chirality : 0.045 0.301 3762 Planarity : 0.005 0.082 4350 Dihedral : 14.958 177.741 3792 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.47 % Favored : 96.22 % Rotamer: Outliers : 2.25 % Allowed : 24.28 % Favored : 73.47 % 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: 0.48 (0.15), residues: 2940 helix: 1.02 (0.12), residues: 1716 sheet: -0.15 (0.39), residues: 204 loop : -0.70 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 75 TYR 0.017 0.001 TYR F 447 PHE 0.019 0.001 PHE A 478 TRP 0.009 0.001 TRP D 96 HIS 0.004 0.001 HIS H 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (25662) covalent geometry : angle 0.57517 / 0.31 (34872) hydrogen bonds : bond 0.04133 / 2.73 ( 1217) hydrogen bonds : angle 4.57691 / 3.22 ( 3573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6761.41 seconds wall clock time: 117 minutes 3.10 seconds (7023.10 seconds total)