Starting phenix.real_space_refine on Fri Jul 3 05:19:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o51_70120/07_2026/9o51_70120_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o51_70120/07_2026/9o51_70120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o51_70120/07_2026/9o51_70120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o51_70120/07_2026/9o51_70120.map" model { file = "/net/cci-nas-00/data/ceres_data/9o51_70120/07_2026/9o51_70120_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o51_70120/07_2026/9o51_70120_neut.cif" } resolution = 3.4 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= 0.051 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 Ca 4 9.91 5 K 2 8.98 5 S 88 5.16 5 C 7952 2.51 5 N 2064 2.21 5 O 2192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s 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: 12302 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2673 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2673 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2673 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2673 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 55} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 55} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 55} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 55} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.90, per 1000 atoms: 0.24 Number of scatterers: 12302 At special positions: 0 Unit cell: (122.525, 122.525, 92.95, 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) Ca 4 19.99 K 2 19.00 S 88 16.00 O 2192 8.00 N 2064 7.00 C 7952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 332 " - pdb=" SG CYS D 370 " distance=2.03 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: 0.73 Conformation dependent library (CDL) restraints added in 500.8 milliseconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 77.5% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 120 through 159 removed outlier: 3.524A pdb=" N SER A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 201 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.500A pdb=" N ILE A 207 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.626A pdb=" N ILE A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.936A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.588A pdb=" N THR A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 333 removed outlier: 3.600A pdb=" N VAL A 313 " --> pdb=" O CYS A 309 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.547A pdb=" N TRP A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 389 removed outlier: 3.875A pdb=" N THR A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 389 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 438 Processing helix chain 'A' and resid 442 through 475 removed outlier: 3.534A pdb=" N ARG A 447 " --> pdb=" O HIS A 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 159 removed outlier: 3.525A pdb=" N SER B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 201 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.501A pdb=" N ILE B 207 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.626A pdb=" N ILE B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.937A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 309 removed outlier: 3.588A pdb=" N THR B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 333 removed outlier: 3.599A pdb=" N VAL B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.547A pdb=" N TRP B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 389 removed outlier: 3.875A pdb=" N THR B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 389 " --> pdb=" O CYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 438 Processing helix chain 'B' and resid 442 through 475 removed outlier: 3.534A pdb=" N ARG B 447 " --> pdb=" O HIS B 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 159 removed outlier: 3.524A pdb=" N SER C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 201 Processing helix chain 'C' and resid 204 through 208 removed outlier: 3.501A pdb=" N ILE C 207 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.625A pdb=" N ILE C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 266 through 277 removed outlier: 3.935A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.588A pdb=" N THR C 307 " --> pdb=" O LYS C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 333 removed outlier: 3.599A pdb=" N VAL C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 removed outlier: 3.547A pdb=" N TRP C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 389 removed outlier: 3.875A pdb=" N THR C 386 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 389 " --> pdb=" O CYS C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 438 Processing helix chain 'C' and resid 442 through 475 removed outlier: 3.534A pdb=" N ARG C 447 " --> pdb=" O HIS C 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 159 removed outlier: 3.524A pdb=" N SER D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 201 Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.501A pdb=" N ILE D 207 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.626A pdb=" N ILE D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.937A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 309 removed outlier: 3.588A pdb=" N THR D 307 " --> pdb=" O LYS D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 333 removed outlier: 3.600A pdb=" N VAL D 313 " --> pdb=" O CYS D 309 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.547A pdb=" N TRP D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 389 removed outlier: 3.875A pdb=" N THR D 386 " --> pdb=" O GLY D 382 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 389 " --> pdb=" O CYS D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 438 Processing helix chain 'D' and resid 442 through 475 removed outlier: 3.534A pdb=" N ARG D 447 " --> pdb=" O HIS D 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 120 through 130 Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'G' and resid 83 through 94 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'H' and resid 83 through 94 Processing helix chain 'H' and resid 102 through 109 Processing helix chain 'H' and resid 120 through 130 Processing helix chain 'H' and resid 138 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 240 Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 240 Processing sheet with id=AA3, first strand: chain 'C' and resid 234 through 240 Processing sheet with id=AA4, first strand: chain 'D' and resid 234 through 240 933 hydrogen bonds defined for protein. 2763 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: 1.81 Time building geometry restraints manager: 1.09 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: 3936 1.34 - 1.46: 3034 1.46 - 1.58: 5422 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 12536 Sorted by residual: bond pdb=" N HIS C 336 " pdb=" CA HIS C 336 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.10e-02 8.26e+03 5.08e+00 bond pdb=" N HIS D 336 " pdb=" CA HIS D 336 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.10e-02 8.26e+03 4.87e+00 bond pdb=" N HIS B 336 " pdb=" CA HIS B 336 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.10e-02 8.26e+03 4.76e+00 bond pdb=" N HIS A 336 " pdb=" CA HIS A 336 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.10e-02 8.26e+03 4.74e+00 bond pdb=" CG HIS C 336 " pdb=" CD2 HIS C 336 " ideal model delta sigma weight residual 1.354 1.330 0.024 1.10e-02 8.26e+03 4.60e+00 ... (remaining 12531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 16529 0.97 - 1.95: 415 1.95 - 2.92: 58 2.92 - 3.89: 22 3.89 - 4.87: 8 Bond angle restraints: 17032 Sorted by residual: angle pdb=" N VAL D 393 " pdb=" CA VAL D 393 " pdb=" C VAL D 393 " ideal model delta sigma weight residual 113.07 108.20 4.87 1.36e+00 5.41e-01 1.28e+01 angle pdb=" N VAL B 393 " pdb=" CA VAL B 393 " pdb=" C VAL B 393 " ideal model delta sigma weight residual 113.07 108.22 4.85 1.36e+00 5.41e-01 1.27e+01 angle pdb=" N VAL C 393 " pdb=" CA VAL C 393 " pdb=" C VAL C 393 " ideal model delta sigma weight residual 113.07 108.23 4.84 1.36e+00 5.41e-01 1.27e+01 angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 113.07 108.23 4.84 1.36e+00 5.41e-01 1.26e+01 angle pdb=" C MET C 364 " pdb=" N VAL C 365 " pdb=" CA VAL C 365 " ideal model delta sigma weight residual 122.59 120.24 2.35 7.20e-01 1.93e+00 1.06e+01 ... (remaining 17027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.95: 6299 12.95 - 25.90: 754 25.90 - 38.86: 239 38.86 - 51.81: 52 51.81 - 64.76: 20 Dihedral angle restraints: 7364 sinusoidal: 2680 harmonic: 4684 Sorted by residual: dihedral pdb=" CB CYS A 332 " pdb=" SG CYS A 332 " pdb=" SG CYS A 370 " pdb=" CB CYS A 370 " ideal model delta sinusoidal sigma weight residual 93.00 61.08 31.92 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CB CYS B 332 " pdb=" SG CYS B 332 " pdb=" SG CYS B 370 " pdb=" CB CYS B 370 " ideal model delta sinusoidal sigma weight residual 93.00 61.09 31.91 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CB CYS D 332 " pdb=" SG CYS D 332 " pdb=" SG CYS D 370 " pdb=" CB CYS D 370 " ideal model delta sinusoidal sigma weight residual 93.00 61.09 31.91 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 7361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1330 0.026 - 0.052: 435 0.052 - 0.078: 202 0.078 - 0.104: 51 0.104 - 0.130: 14 Chirality restraints: 2032 Sorted by residual: chirality pdb=" CA ILE D 229 " pdb=" N ILE D 229 " pdb=" C ILE D 229 " pdb=" CB ILE D 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE C 229 " pdb=" N ILE C 229 " pdb=" C ILE C 229 " pdb=" CB ILE C 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2029 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 227 " -0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO D 228 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 228 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 228 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 227 " 0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO A 228 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 227 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO C 228 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " -0.016 5.00e-02 4.00e+02 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.92: 4877 2.92 - 3.48: 14989 3.48 - 4.03: 21605 4.03 - 4.59: 32643 4.59 - 5.14: 43576 Nonbonded interactions: 117690 Sorted by model distance: nonbonded pdb=" O TYR F 100 " pdb="CA CA F 201 " model vdw 2.368 3.250 nonbonded pdb=" O TYR E 100 " pdb="CA CA E 201 " model vdw 2.368 3.250 nonbonded pdb=" O TYR G 100 " pdb="CA CA G 201 " model vdw 2.369 3.250 nonbonded pdb=" O TYR H 100 " pdb="CA CA H 201 " model vdw 2.369 3.250 nonbonded pdb=" N SER G 102 " pdb="CA CA G 201 " model vdw 2.437 3.330 ... (remaining 117685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 120 through 475) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.080 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.002 0.025 12540 Z= 0.109 Angle : 0.400 4.866 17040 Z= 0.258 Chirality : 0.033 0.130 2032 Planarity : 0.002 0.028 2108 Dihedral : 13.020 64.761 4304 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1556 helix: 1.01 (0.15), residues: 1192 sheet: 1.96 (0.72), residues: 64 loop : -0.32 (0.40), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 240 TYR 0.007 0.001 TYR B 188 PHE 0.004 0.001 PHE G 142 TRP 0.006 0.001 TRP D 431 HIS 0.002 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.11 (12536) covalent geometry : angle 0.39994 / 0.26 (17032) SS BOND : bond 0.00054 / 0.02 ( 4) SS BOND : angle 0.38345 / 0.23 ( 8) hydrogen bonds : bond 0.18715 / 12.53 ( 933) hydrogen bonds : angle 6.44100 / 4.71 ( 2763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 172 CYS cc_start: 0.8556 (m) cc_final: 0.8326 (m) REVERT: A 209 MET cc_start: 0.8565 (mmm) cc_final: 0.8082 (mpp) REVERT: A 340 ASP cc_start: 0.8665 (t70) cc_final: 0.8259 (t70) REVERT: A 425 ARG cc_start: 0.7732 (ttp-110) cc_final: 0.7230 (ttm-80) REVERT: B 204 ASP cc_start: 0.7804 (m-30) cc_final: 0.7502 (m-30) REVERT: B 209 MET cc_start: 0.8675 (mmm) cc_final: 0.8162 (mpp) REVERT: B 340 ASP cc_start: 0.8650 (t70) cc_final: 0.8245 (t70) REVERT: B 425 ARG cc_start: 0.7719 (ttp-110) cc_final: 0.7371 (ttm-80) REVERT: B 449 GLN cc_start: 0.8466 (tp40) cc_final: 0.7582 (tm-30) REVERT: C 209 MET cc_start: 0.8680 (mmm) cc_final: 0.8121 (mpp) REVERT: C 340 ASP cc_start: 0.8643 (t70) cc_final: 0.8239 (t70) REVERT: C 425 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7401 (ttm-80) REVERT: D 200 ASN cc_start: 0.8215 (m-40) cc_final: 0.7810 (m110) REVERT: D 340 ASP cc_start: 0.8657 (t70) cc_final: 0.8258 (t70) REVERT: D 425 ARG cc_start: 0.7729 (ttp-110) cc_final: 0.7366 (ttm-80) REVERT: E 125 MET cc_start: 0.5812 (ptm) cc_final: 0.5562 (ptm) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1034 time to fit residues: 50.2283 Evaluate side-chains 299 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 HIS B 407 HIS C 407 HIS D 407 HIS D 472 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.190917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139996 restraints weight = 14364.451| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.70 r_work: 0.3427 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12540 Z= 0.135 Angle : 0.442 8.438 17040 Z= 0.245 Chirality : 0.035 0.130 2032 Planarity : 0.004 0.057 2108 Dihedral : 3.231 13.540 1716 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.37 % Allowed : 9.57 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.71 (0.22), residues: 1556 helix: 2.24 (0.15), residues: 1200 sheet: 2.38 (0.74), residues: 64 loop : -0.23 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 470 TYR 0.019 0.001 TYR C 434 PHE 0.021 0.001 PHE B 409 TRP 0.010 0.001 TRP C 431 HIS 0.008 0.001 HIS D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (12536) covalent geometry : angle 0.44205 / 0.25 (17032) SS BOND : bond 0.00098 / 0.04 ( 4) SS BOND : angle 0.32938 / 0.20 ( 8) hydrogen bonds : bond 0.05035 / 3.37 ( 933) hydrogen bonds : angle 3.69565 / 2.66 ( 2763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 287 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7871 (tt0) cc_final: 0.7567 (tt0) REVERT: A 340 ASP cc_start: 0.8766 (t70) cc_final: 0.8304 (t70) REVERT: A 377 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8042 (tt) REVERT: A 422 SER cc_start: 0.8668 (m) cc_final: 0.8451 (t) REVERT: A 425 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7202 (ttm-80) REVERT: A 446 ARG cc_start: 0.7481 (mtm110) cc_final: 0.6974 (mtm110) REVERT: A 460 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7881 (mtm110) REVERT: A 470 ARG cc_start: 0.7293 (mtm-85) cc_final: 0.6969 (mtm-85) REVERT: B 209 MET cc_start: 0.8796 (mmm) cc_final: 0.8238 (mpp) REVERT: B 340 ASP cc_start: 0.8777 (t70) cc_final: 0.8274 (t70) REVERT: B 377 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7911 (mt) REVERT: B 411 MET cc_start: 0.8371 (mmt) cc_final: 0.8009 (mmt) REVERT: B 425 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7368 (ttm-80) REVERT: B 449 GLN cc_start: 0.8348 (tp40) cc_final: 0.7471 (tm-30) REVERT: B 470 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.7066 (mtm-85) REVERT: C 204 ASP cc_start: 0.7594 (m-30) cc_final: 0.6857 (t0) REVERT: C 340 ASP cc_start: 0.8730 (t70) cc_final: 0.8265 (t70) REVERT: C 377 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8043 (tt) REVERT: C 422 SER cc_start: 0.8560 (m) cc_final: 0.8285 (t) REVERT: C 425 ARG cc_start: 0.7671 (ttp-110) cc_final: 0.7408 (ttm-80) REVERT: C 463 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8002 (ttm170) REVERT: D 337 ASP cc_start: 0.8561 (t70) cc_final: 0.8350 (t70) REVERT: D 340 ASP cc_start: 0.8754 (t70) cc_final: 0.8268 (t70) REVERT: D 377 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8050 (tt) REVERT: D 411 MET cc_start: 0.8383 (mmt) cc_final: 0.8046 (mmt) REVERT: D 422 SER cc_start: 0.8589 (m) cc_final: 0.8313 (t) REVERT: D 425 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7169 (ttm-80) REVERT: D 460 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7806 (mtm-85) REVERT: E 125 MET cc_start: 0.5802 (ptm) cc_final: 0.5497 (ptm) REVERT: G 125 MET cc_start: 0.5049 (ptm) cc_final: 0.4824 (ptm) REVERT: H 125 MET cc_start: 0.5176 (ptm) cc_final: 0.4869 (ptm) outliers start: 17 outliers final: 9 residues processed: 298 average time/residue: 0.1201 time to fit residues: 49.8087 Evaluate side-chains 286 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 273 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 462 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 0.0010 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 HIS ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.190957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140407 restraints weight = 14528.924| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.74 r_work: 0.3436 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12540 Z= 0.105 Angle : 0.388 6.343 17040 Z= 0.216 Chirality : 0.034 0.130 2032 Planarity : 0.003 0.025 2108 Dihedral : 3.112 14.103 1716 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.45 % Allowed : 12.70 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.27 (0.22), residues: 1556 helix: 2.68 (0.15), residues: 1200 sheet: 2.23 (0.71), residues: 64 loop : -0.16 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 470 TYR 0.014 0.001 TYR A 434 PHE 0.018 0.001 PHE B 409 TRP 0.013 0.001 TRP C 431 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (12536) covalent geometry : angle 0.38840 / 0.22 (17032) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 0.25681 / 0.15 ( 8) hydrogen bonds : bond 0.03973 / 2.67 ( 933) hydrogen bonds : angle 3.30999 / 2.38 ( 2763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 304 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7757 (mpp) REVERT: A 340 ASP cc_start: 0.8403 (t70) cc_final: 0.7916 (t0) REVERT: A 377 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7910 (mt) REVERT: A 422 SER cc_start: 0.8692 (m) cc_final: 0.8456 (t) REVERT: A 425 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.7246 (ttm-80) REVERT: A 470 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.7110 (mtm-85) REVERT: B 340 ASP cc_start: 0.8387 (t70) cc_final: 0.7935 (t0) REVERT: B 377 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7932 (mt) REVERT: B 425 ARG cc_start: 0.7618 (ttp-110) cc_final: 0.7305 (ttm-80) REVERT: B 463 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8559 (ttm110) REVERT: B 470 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6969 (mtm-85) REVERT: C 340 ASP cc_start: 0.8766 (t70) cc_final: 0.8217 (t70) REVERT: C 341 VAL cc_start: 0.8924 (t) cc_final: 0.8713 (p) REVERT: C 377 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7894 (mt) REVERT: C 413 ILE cc_start: 0.8654 (mm) cc_final: 0.8417 (mt) REVERT: C 422 SER cc_start: 0.8615 (m) cc_final: 0.8340 (t) REVERT: C 425 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7392 (ttm-80) REVERT: C 460 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7987 (mtm-85) REVERT: C 463 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.7919 (ttm170) REVERT: C 470 ARG cc_start: 0.7273 (mtm110) cc_final: 0.6824 (mtm-85) REVERT: D 340 ASP cc_start: 0.8451 (t70) cc_final: 0.7932 (t0) REVERT: D 377 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7896 (mt) REVERT: D 413 ILE cc_start: 0.8682 (mm) cc_final: 0.8467 (mt) REVERT: D 422 SER cc_start: 0.8642 (m) cc_final: 0.8382 (t) REVERT: D 425 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7291 (ttm-80) REVERT: D 460 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7716 (mtm-85) REVERT: H 125 MET cc_start: 0.5166 (ptm) cc_final: 0.4883 (ptm) outliers start: 18 outliers final: 10 residues processed: 310 average time/residue: 0.1142 time to fit residues: 49.6946 Evaluate side-chains 301 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 286 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 462 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 130 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.186386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136477 restraints weight = 14403.044| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.87 r_work: 0.3282 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12540 Z= 0.111 Angle : 0.385 5.516 17040 Z= 0.212 Chirality : 0.034 0.130 2032 Planarity : 0.003 0.026 2108 Dihedral : 3.064 13.332 1716 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.85 % Allowed : 14.31 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.44 (0.21), residues: 1556 helix: 2.86 (0.15), residues: 1192 sheet: 1.90 (0.68), residues: 64 loop : -0.18 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 470 TYR 0.011 0.001 TYR A 434 PHE 0.015 0.001 PHE B 409 TRP 0.013 0.001 TRP C 431 HIS 0.004 0.001 HIS D 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (12536) covalent geometry : angle 0.38448 / 0.21 (17032) SS BOND : bond 0.00263 / 0.12 ( 4) SS BOND : angle 0.49669 / 0.29 ( 8) hydrogen bonds : bond 0.03642 / 2.45 ( 933) hydrogen bonds : angle 3.19835 / 2.30 ( 2763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 290 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7844 (mpp) REVERT: A 340 ASP cc_start: 0.8482 (t70) cc_final: 0.7911 (t0) REVERT: A 377 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7854 (mt) REVERT: A 413 ILE cc_start: 0.8387 (mm) cc_final: 0.8159 (mp) REVERT: A 422 SER cc_start: 0.8697 (m) cc_final: 0.8440 (t) REVERT: A 425 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7231 (ttm-80) REVERT: A 470 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6963 (mtm-85) REVERT: B 340 ASP cc_start: 0.8608 (t70) cc_final: 0.8080 (t0) REVERT: B 377 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7853 (mt) REVERT: B 425 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7256 (ttm-80) REVERT: B 470 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.7012 (mtm-85) REVERT: C 340 ASP cc_start: 0.8728 (t70) cc_final: 0.8251 (t70) REVERT: C 377 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7838 (mt) REVERT: C 413 ILE cc_start: 0.8586 (mm) cc_final: 0.8295 (mp) REVERT: C 422 SER cc_start: 0.8642 (m) cc_final: 0.8360 (t) REVERT: C 425 ARG cc_start: 0.7652 (ttp-110) cc_final: 0.7372 (ttm-80) REVERT: C 463 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.7873 (ttm170) REVERT: C 470 ARG cc_start: 0.7152 (mtm110) cc_final: 0.6773 (mtm-85) REVERT: D 340 ASP cc_start: 0.8451 (t70) cc_final: 0.7948 (t0) REVERT: D 377 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7854 (mt) REVERT: D 413 ILE cc_start: 0.8573 (mm) cc_final: 0.8287 (mp) REVERT: D 422 SER cc_start: 0.8628 (m) cc_final: 0.8369 (t) REVERT: D 425 ARG cc_start: 0.7697 (ttp-110) cc_final: 0.7304 (ttm-80) REVERT: D 460 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7492 (mtm110) REVERT: D 463 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7992 (ttm170) REVERT: D 470 ARG cc_start: 0.6922 (mtm-85) cc_final: 0.6717 (mtm-85) REVERT: H 125 MET cc_start: 0.5102 (ptm) cc_final: 0.4852 (ptm) outliers start: 23 outliers final: 14 residues processed: 299 average time/residue: 0.1072 time to fit residues: 45.1526 Evaluate side-chains 295 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 462 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.190230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139754 restraints weight = 14479.017| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.89 r_work: 0.3363 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12540 Z= 0.130 Angle : 0.398 5.286 17040 Z= 0.218 Chirality : 0.035 0.131 2032 Planarity : 0.003 0.026 2108 Dihedral : 3.092 12.119 1716 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.17 % Allowed : 14.95 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.48 (0.22), residues: 1556 helix: 2.91 (0.14), residues: 1192 sheet: 1.69 (0.67), residues: 64 loop : -0.19 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 470 TYR 0.011 0.001 TYR D 188 PHE 0.014 0.001 PHE B 409 TRP 0.013 0.001 TRP C 431 HIS 0.003 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12536) covalent geometry : angle 0.39837 / 0.22 (17032) SS BOND : bond 0.00359 / 0.17 ( 4) SS BOND : angle 0.35463 / 0.23 ( 8) hydrogen bonds : bond 0.03611 / 2.42 ( 933) hydrogen bonds : angle 3.16382 / 2.27 ( 2763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7852 (mpp) REVERT: A 340 ASP cc_start: 0.8587 (t70) cc_final: 0.8045 (t0) REVERT: A 377 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7906 (mt) REVERT: A 413 ILE cc_start: 0.8462 (mm) cc_final: 0.8221 (mp) REVERT: A 422 SER cc_start: 0.8722 (m) cc_final: 0.8473 (t) REVERT: A 425 ARG cc_start: 0.7548 (ttp-110) cc_final: 0.7178 (ttm-80) REVERT: A 460 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7757 (mtm110) REVERT: A 470 ARG cc_start: 0.7224 (mtm-85) cc_final: 0.6951 (mtm-85) REVERT: B 340 ASP cc_start: 0.8701 (t70) cc_final: 0.8129 (t0) REVERT: B 377 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7893 (mt) REVERT: B 425 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.7207 (ttm-80) REVERT: B 463 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8546 (ttm110) REVERT: B 470 ARG cc_start: 0.7390 (mtm-85) cc_final: 0.7130 (mtm-85) REVERT: C 340 ASP cc_start: 0.8723 (t70) cc_final: 0.8027 (t0) REVERT: C 377 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7925 (mt) REVERT: C 413 ILE cc_start: 0.8609 (mm) cc_final: 0.8312 (mp) REVERT: C 422 SER cc_start: 0.8653 (m) cc_final: 0.8402 (t) REVERT: C 425 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.7323 (ttm-80) REVERT: C 470 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6819 (mtm-85) REVERT: D 340 ASP cc_start: 0.8701 (t70) cc_final: 0.8192 (t0) REVERT: D 377 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8045 (tt) REVERT: D 422 SER cc_start: 0.8629 (m) cc_final: 0.8395 (t) REVERT: D 425 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.7238 (ttm-80) REVERT: D 470 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6665 (mtm-85) outliers start: 27 outliers final: 18 residues processed: 291 average time/residue: 0.1179 time to fit residues: 48.1332 Evaluate side-chains 301 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 462 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 57 optimal weight: 0.0470 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.190985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139894 restraints weight = 14407.208| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.84 r_work: 0.3406 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12540 Z= 0.115 Angle : 0.390 5.928 17040 Z= 0.212 Chirality : 0.035 0.130 2032 Planarity : 0.002 0.026 2108 Dihedral : 3.045 11.816 1716 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.65 % Allowed : 15.59 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.54 (0.21), residues: 1556 helix: 2.98 (0.14), residues: 1196 sheet: 1.59 (0.66), residues: 64 loop : -0.32 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 470 TYR 0.010 0.001 TYR C 233 PHE 0.010 0.001 PHE D 196 TRP 0.013 0.001 TRP C 431 HIS 0.003 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12536) covalent geometry : angle 0.39013 / 0.21 (17032) SS BOND : bond 0.00205 / 0.09 ( 4) SS BOND : angle 0.26747 / 0.16 ( 8) hydrogen bonds : bond 0.03433 / 2.30 ( 933) hydrogen bonds : angle 3.10711 / 2.23 ( 2763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7871 (mpp) REVERT: A 340 ASP cc_start: 0.8589 (t70) cc_final: 0.8013 (t0) REVERT: A 377 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7861 (mt) REVERT: A 413 ILE cc_start: 0.8459 (mm) cc_final: 0.8237 (mp) REVERT: A 422 SER cc_start: 0.8788 (m) cc_final: 0.8544 (t) REVERT: A 425 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.7168 (ttm-80) REVERT: A 470 ARG cc_start: 0.7207 (mtm-85) cc_final: 0.6983 (mtm-85) REVERT: B 340 ASP cc_start: 0.8700 (t70) cc_final: 0.8184 (t70) REVERT: B 377 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7916 (mt) REVERT: B 425 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7204 (ttm-80) REVERT: B 470 ARG cc_start: 0.7349 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: C 340 ASP cc_start: 0.8722 (t70) cc_final: 0.8017 (t0) REVERT: C 377 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7911 (mt) REVERT: C 413 ILE cc_start: 0.8592 (mm) cc_final: 0.8321 (mp) REVERT: C 422 SER cc_start: 0.8671 (m) cc_final: 0.8434 (t) REVERT: C 425 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.7299 (ttm-80) REVERT: C 463 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8353 (ttm170) REVERT: C 470 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6861 (mtm-85) REVERT: D 204 ASP cc_start: 0.7088 (m-30) cc_final: 0.6754 (t0) REVERT: D 340 ASP cc_start: 0.8746 (t70) cc_final: 0.8221 (t0) REVERT: D 377 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7920 (mt) REVERT: D 403 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8327 (mp0) REVERT: D 422 SER cc_start: 0.8691 (m) cc_final: 0.8451 (t) REVERT: D 425 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7267 (ttm-80) REVERT: D 463 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8266 (ttm110) REVERT: D 470 ARG cc_start: 0.6908 (mtm-85) cc_final: 0.6675 (mtm-85) outliers start: 33 outliers final: 21 residues processed: 291 average time/residue: 0.1104 time to fit residues: 44.9316 Evaluate side-chains 290 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 264 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 462 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.190929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139820 restraints weight = 14326.346| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.80 r_work: 0.3407 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12540 Z= 0.113 Angle : 0.387 5.702 17040 Z= 0.210 Chirality : 0.035 0.130 2032 Planarity : 0.002 0.026 2108 Dihedral : 3.026 11.369 1716 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.25 % Allowed : 16.96 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.66 (0.21), residues: 1556 helix: 3.07 (0.14), residues: 1196 sheet: 1.57 (0.66), residues: 64 loop : -0.32 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 470 TYR 0.010 0.001 TYR C 233 PHE 0.014 0.001 PHE B 409 TRP 0.013 0.001 TRP C 431 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12536) covalent geometry : angle 0.38688 / 0.21 (17032) SS BOND : bond 0.00212 / 0.10 ( 4) SS BOND : angle 0.27597 / 0.16 ( 8) hydrogen bonds : bond 0.03364 / 2.25 ( 933) hydrogen bonds : angle 3.07674 / 2.21 ( 2763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: A 340 ASP cc_start: 0.8618 (t70) cc_final: 0.8064 (t0) REVERT: A 377 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7893 (mt) REVERT: A 413 ILE cc_start: 0.8470 (mm) cc_final: 0.8245 (mp) REVERT: A 422 SER cc_start: 0.8821 (m) cc_final: 0.8592 (t) REVERT: A 425 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7182 (ttm-80) REVERT: B 340 ASP cc_start: 0.8712 (t70) cc_final: 0.8193 (t70) REVERT: B 377 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7935 (mt) REVERT: B 425 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7176 (ttm-80) REVERT: C 204 ASP cc_start: 0.7394 (m-30) cc_final: 0.7129 (t0) REVERT: C 340 ASP cc_start: 0.8733 (t70) cc_final: 0.8001 (t0) REVERT: C 377 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 413 ILE cc_start: 0.8586 (mm) cc_final: 0.8326 (mp) REVERT: C 419 MET cc_start: 0.8275 (ttt) cc_final: 0.8072 (ttt) REVERT: C 422 SER cc_start: 0.8703 (m) cc_final: 0.8475 (t) REVERT: C 425 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.7275 (ttm-80) REVERT: C 434 TYR cc_start: 0.7913 (t80) cc_final: 0.7694 (t80) REVERT: C 463 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8396 (ttm170) REVERT: C 470 ARG cc_start: 0.7205 (mtm110) cc_final: 0.6812 (mtm-85) REVERT: D 204 ASP cc_start: 0.7111 (m-30) cc_final: 0.6754 (t0) REVERT: D 340 ASP cc_start: 0.8769 (t70) cc_final: 0.8258 (t70) REVERT: D 377 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7945 (mt) REVERT: D 403 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8273 (mp0) REVERT: D 422 SER cc_start: 0.8745 (m) cc_final: 0.8513 (t) REVERT: D 425 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.7276 (ttm-80) REVERT: D 463 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8329 (ttm110) outliers start: 28 outliers final: 19 residues processed: 288 average time/residue: 0.1087 time to fit residues: 44.0842 Evaluate side-chains 291 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 60 optimal weight: 0.0040 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.189570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138281 restraints weight = 14458.793| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.71 r_work: 0.3400 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12540 Z= 0.141 Angle : 0.427 6.922 17040 Z= 0.227 Chirality : 0.036 0.131 2032 Planarity : 0.003 0.029 2108 Dihedral : 3.060 11.187 1716 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.57 % Allowed : 17.93 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.61 (0.21), residues: 1556 helix: 3.04 (0.14), residues: 1196 sheet: 1.51 (0.67), residues: 64 loop : -0.34 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 470 TYR 0.011 0.001 TYR D 188 PHE 0.012 0.001 PHE D 196 TRP 0.013 0.001 TRP C 431 HIS 0.003 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (12536) covalent geometry : angle 0.42692 / 0.23 (17032) SS BOND : bond 0.00399 / 0.18 ( 4) SS BOND : angle 0.44942 / 0.27 ( 8) hydrogen bonds : bond 0.03495 / 2.34 ( 933) hydrogen bonds : angle 3.13781 / 2.25 ( 2763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7962 (mpp) REVERT: A 340 ASP cc_start: 0.8621 (t70) cc_final: 0.8087 (t0) REVERT: A 377 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8049 (tt) REVERT: A 413 ILE cc_start: 0.8512 (mm) cc_final: 0.8269 (mp) REVERT: A 422 SER cc_start: 0.8814 (m) cc_final: 0.8574 (t) REVERT: A 425 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7164 (ttm-80) REVERT: A 470 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.7016 (mtm-85) REVERT: B 340 ASP cc_start: 0.8698 (t70) cc_final: 0.8170 (t70) REVERT: B 377 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8078 (tt) REVERT: B 425 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7137 (ttm-80) REVERT: B 470 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.7010 (mtm-85) REVERT: C 340 ASP cc_start: 0.8621 (t70) cc_final: 0.7907 (t0) REVERT: C 377 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8065 (tt) REVERT: C 419 MET cc_start: 0.8251 (ttt) cc_final: 0.8050 (ttt) REVERT: C 422 SER cc_start: 0.8732 (m) cc_final: 0.8492 (t) REVERT: C 425 ARG cc_start: 0.7656 (ttp-110) cc_final: 0.7259 (ttm-80) REVERT: C 434 TYR cc_start: 0.7972 (t80) cc_final: 0.7749 (t80) REVERT: C 463 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8402 (ttm170) REVERT: C 470 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6855 (mtm-85) REVERT: D 204 ASP cc_start: 0.7180 (m-30) cc_final: 0.6820 (t0) REVERT: D 340 ASP cc_start: 0.8741 (t70) cc_final: 0.8213 (t70) REVERT: D 377 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8055 (tt) REVERT: D 422 SER cc_start: 0.8746 (m) cc_final: 0.8515 (t) REVERT: D 425 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7227 (ttm-80) REVERT: D 463 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8342 (ttm110) REVERT: D 470 ARG cc_start: 0.7078 (mtm-85) cc_final: 0.6782 (mtm-85) outliers start: 32 outliers final: 23 residues processed: 287 average time/residue: 0.1066 time to fit residues: 43.2909 Evaluate side-chains 298 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain G residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 118 optimal weight: 0.0070 chunk 82 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.191339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138884 restraints weight = 14397.190| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.65 r_work: 0.3445 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12540 Z= 0.106 Angle : 0.396 6.669 17040 Z= 0.212 Chirality : 0.034 0.130 2032 Planarity : 0.003 0.027 2108 Dihedral : 3.004 11.272 1716 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.25 % Allowed : 18.65 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.79 (0.21), residues: 1556 helix: 3.19 (0.14), residues: 1196 sheet: 1.56 (0.66), residues: 64 loop : -0.36 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 470 TYR 0.010 0.001 TYR A 233 PHE 0.012 0.001 PHE D 196 TRP 0.013 0.001 TRP C 431 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (12536) covalent geometry : angle 0.39561 / 0.21 (17032) SS BOND : bond 0.00186 / 0.08 ( 4) SS BOND : angle 0.27790 / 0.16 ( 8) hydrogen bonds : bond 0.03280 / 2.20 ( 933) hydrogen bonds : angle 3.05759 / 2.20 ( 2763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7895 (mpp) REVERT: A 340 ASP cc_start: 0.8563 (t70) cc_final: 0.8022 (t0) REVERT: A 377 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7868 (mt) REVERT: A 413 ILE cc_start: 0.8437 (mm) cc_final: 0.8201 (mp) REVERT: A 470 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6911 (mtm-85) REVERT: B 340 ASP cc_start: 0.8674 (t70) cc_final: 0.8152 (t70) REVERT: B 377 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7892 (mt) REVERT: B 425 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7079 (ttm-80) REVERT: B 470 ARG cc_start: 0.7216 (mtm-85) cc_final: 0.6934 (mtm-85) REVERT: C 340 ASP cc_start: 0.8600 (t70) cc_final: 0.7868 (t0) REVERT: C 377 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7891 (mt) REVERT: C 422 SER cc_start: 0.8693 (m) cc_final: 0.8490 (t) REVERT: C 425 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.7195 (ttm-80) REVERT: C 434 TYR cc_start: 0.7995 (t80) cc_final: 0.7724 (t80) REVERT: C 463 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8374 (ttm170) REVERT: C 470 ARG cc_start: 0.7204 (mtm110) cc_final: 0.6802 (mtm-85) REVERT: D 340 ASP cc_start: 0.8704 (t70) cc_final: 0.8183 (t70) REVERT: D 377 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7906 (mt) REVERT: D 403 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8279 (mp0) REVERT: D 422 SER cc_start: 0.8718 (m) cc_final: 0.8496 (t) REVERT: D 425 ARG cc_start: 0.7624 (ttp-110) cc_final: 0.7214 (ttm-80) REVERT: D 463 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8355 (ttm110) REVERT: D 470 ARG cc_start: 0.7047 (mtm-85) cc_final: 0.6746 (mtm-85) outliers start: 28 outliers final: 21 residues processed: 285 average time/residue: 0.1080 time to fit residues: 43.0997 Evaluate side-chains 292 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.185548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135016 restraints weight = 14427.106| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.86 r_work: 0.3331 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12540 Z= 0.116 Angle : 0.409 6.485 17040 Z= 0.218 Chirality : 0.035 0.130 2032 Planarity : 0.003 0.027 2108 Dihedral : 3.016 11.174 1716 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.17 % Allowed : 18.89 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.81 (0.21), residues: 1556 helix: 3.20 (0.14), residues: 1196 sheet: 1.55 (0.66), residues: 64 loop : -0.37 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 470 TYR 0.010 0.001 TYR D 188 PHE 0.013 0.001 PHE D 196 TRP 0.012 0.001 TRP C 431 HIS 0.002 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12536) covalent geometry : angle 0.40945 / 0.22 (17032) SS BOND : bond 0.00239 / 0.11 ( 4) SS BOND : angle 0.29618 / 0.17 ( 8) hydrogen bonds : bond 0.03294 / 2.20 ( 933) hydrogen bonds : angle 3.06570 / 2.20 ( 2763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7939 (mpp) REVERT: A 340 ASP cc_start: 0.8613 (t70) cc_final: 0.8083 (t0) REVERT: A 377 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7855 (mt) REVERT: A 413 ILE cc_start: 0.8437 (mm) cc_final: 0.8188 (mp) REVERT: A 470 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6931 (mtm-85) REVERT: B 340 ASP cc_start: 0.8709 (t70) cc_final: 0.8201 (t70) REVERT: B 377 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7863 (mt) REVERT: B 425 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.7106 (ttm-80) REVERT: B 470 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6892 (mtm-85) REVERT: C 340 ASP cc_start: 0.8630 (t70) cc_final: 0.7928 (t0) REVERT: C 377 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7862 (mt) REVERT: C 422 SER cc_start: 0.8712 (m) cc_final: 0.8510 (t) REVERT: C 425 ARG cc_start: 0.7653 (ttp-110) cc_final: 0.7269 (ttm-80) REVERT: C 434 TYR cc_start: 0.8045 (t80) cc_final: 0.7805 (t80) REVERT: C 470 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6811 (mtm-85) REVERT: D 204 ASP cc_start: 0.7236 (m-30) cc_final: 0.6845 (t0) REVERT: D 340 ASP cc_start: 0.8714 (t70) cc_final: 0.8190 (t70) REVERT: D 377 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7850 (mt) REVERT: D 403 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8253 (mp0) REVERT: D 463 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8405 (ttm110) REVERT: D 470 ARG cc_start: 0.7038 (mtm-85) cc_final: 0.6737 (mtm-85) outliers start: 27 outliers final: 19 residues processed: 274 average time/residue: 0.1162 time to fit residues: 44.9252 Evaluate side-chains 286 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 205 TRP Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 137 optimal weight: 0.1980 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 127 optimal weight: 0.0670 chunk 138 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.186048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134326 restraints weight = 14224.160| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.70 r_work: 0.3361 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12540 Z= 0.107 Angle : 0.398 6.501 17040 Z= 0.212 Chirality : 0.034 0.130 2032 Planarity : 0.003 0.027 2108 Dihedral : 2.997 11.242 1716 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.33 % Allowed : 18.49 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.84 (0.21), residues: 1556 helix: 3.21 (0.14), residues: 1204 sheet: 1.39 (0.65), residues: 64 loop : -0.33 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 470 TYR 0.010 0.001 TYR C 233 PHE 0.013 0.001 PHE D 196 TRP 0.012 0.001 TRP C 431 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (12536) covalent geometry : angle 0.39846 / 0.21 (17032) SS BOND : bond 0.00159 / 0.07 ( 4) SS BOND : angle 0.25278 / 0.15 ( 8) hydrogen bonds : bond 0.03221 / 2.16 ( 933) hydrogen bonds : angle 3.03729 / 2.19 ( 2763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.19 seconds wall clock time: 52 minutes 53.47 seconds (3173.47 seconds total)