Starting phenix.real_space_refine on Wed Sep 17 23:45:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o51_70120/09_2025/9o51_70120_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o51_70120/09_2025/9o51_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 { model { file = "/net/cci-nas-00/data/ceres_data/9o51_70120/09_2025/9o51_70120_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o51_70120/09_2025/9o51_70120_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o51_70120/09_2025/9o51_70120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o51_70120/09_2025/9o51_70120.map" } 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-2.0-5805/lib/python3.9/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, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.97, 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: 0.97 Conformation dependent library (CDL) restraints added in 420.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.32 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: 1.56 Time building geometry restraints manager: 1.19 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 2.510 nonbonded pdb=" O TYR E 100 " pdb="CA CA E 201 " model vdw 2.368 2.510 nonbonded pdb=" O TYR G 100 " pdb="CA CA G 201 " model vdw 2.369 2.510 nonbonded pdb=" O TYR H 100 " pdb="CA CA H 201 " model vdw 2.369 2.510 nonbonded pdb=" N SER G 102 " pdb="CA CA G 201 " model vdw 2.437 2.590 ... (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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 aren 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 covalent geometry : bond 0.00177 (12536) covalent geometry : angle 0.39994 (17032) SS BOND : bond 0.00054 ( 4) SS BOND : angle 0.38345 ( 8) hydrogen bonds : bond 0.18715 ( 933) hydrogen bonds : angle 6.44100 ( 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 : 0.372 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: 0.7232 (ttm-80) REVERT: B 204 ASP cc_start: 0.7805 (m-30) cc_final: 0.7503 (m-30) REVERT: B 209 MET cc_start: 0.8675 (mmm) cc_final: 0.8163 (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: 0.7372 (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: 0.8122 (mpp) REVERT: C 340 ASP cc_start: 0.8643 (t70) cc_final: 0.8239 (t70) REVERT: C 425 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7401 (ttm-80) REVERT: D 200 ASN cc_start: 0.8215 (m-40) cc_final: 0.7809 (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: 0.1148 time to fit residues: 55.2053 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 : 0.386 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.191178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142713 restraints weight = 14393.542| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.83 r_work: 0.3399 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12540 Z= 0.131 Angle : 0.440 8.245 17040 Z= 0.244 Chirality : 0.035 0.130 2032 Planarity : 0.004 0.046 2108 Dihedral : 3.204 13.365 1716 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.29 % Allowed : 9.73 % Favored : 88.99 % 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 aren not related in a simple way. whole: 2.73 (0.22), residues: 1556 helix: 2.26 (0.15), residues: 1200 sheet: 2.41 (0.75), residues: 64 loop : -0.23 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 470 TYR 0.017 0.001 TYR C 434 PHE 0.021 0.001 PHE B 409 TRP 0.009 0.001 TRP C 431 HIS 0.007 0.001 HIS D 436 Details of bonding type rmsd covalent geometry : bond 0.00280 (12536) covalent geometry : angle 0.43960 (17032) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.30064 ( 8) hydrogen bonds : bond 0.05171 ( 933) hydrogen bonds : angle 3.73795 ( 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 309 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 293 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 GLU cc_start: 0.7941 (tt0) cc_final: 0.7632 (tt0) REVERT: A 340 ASP cc_start: 0.8788 (t70) cc_final: 0.8326 (t70) REVERT: A 377 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8064 (tt) REVERT: A 422 SER cc_start: 0.8688 (m) cc_final: 0.8475 (t) REVERT: A 425 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7238 (ttm-80) REVERT: A 446 ARG cc_start: 0.7497 (mtm110) cc_final: 0.6993 (mtm110) REVERT: A 460 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7861 (mtm-85) REVERT: A 470 ARG cc_start: 0.7379 (mtm110) cc_final: 0.6870 (mtm-85) REVERT: B 209 MET cc_start: 0.8809 (mmm) cc_final: 0.8245 (mpp) REVERT: B 340 ASP cc_start: 0.8789 (t70) cc_final: 0.8275 (t70) REVERT: B 377 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7931 (mt) REVERT: B 411 MET cc_start: 0.8419 (mmt) cc_final: 0.8057 (mmt) REVERT: B 425 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7401 (ttm-80) REVERT: B 449 GLN cc_start: 0.8380 (tp40) cc_final: 0.7500 (tm-30) REVERT: B 463 ARG cc_start: 0.8889 (ttp80) cc_final: 0.8586 (ttm110) REVERT: C 204 ASP cc_start: 0.7614 (m-30) cc_final: 0.6879 (t0) REVERT: C 340 ASP cc_start: 0.8746 (t70) cc_final: 0.8277 (t70) REVERT: C 377 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8056 (tt) REVERT: C 422 SER cc_start: 0.8589 (m) cc_final: 0.8309 (t) REVERT: C 425 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7451 (ttm-80) REVERT: C 463 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8032 (ttm170) REVERT: D 337 ASP cc_start: 0.8577 (t70) cc_final: 0.8365 (t70) REVERT: D 340 ASP cc_start: 0.8772 (t70) cc_final: 0.8281 (t70) REVERT: D 377 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8060 (tt) REVERT: D 411 MET cc_start: 0.8445 (mmt) cc_final: 0.8115 (mmt) REVERT: D 422 SER cc_start: 0.8641 (m) cc_final: 0.8369 (t) REVERT: D 425 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7179 (ttm-80) REVERT: D 460 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7812 (mtm-85) REVERT: E 125 MET cc_start: 0.5811 (ptm) cc_final: 0.5508 (ptm) REVERT: G 125 MET cc_start: 0.5082 (ptm) cc_final: 0.4858 (ptm) REVERT: H 125 MET cc_start: 0.5189 (ptm) cc_final: 0.4882 (ptm) outliers start: 16 outliers final: 9 residues processed: 303 average time/residue: 0.1173 time to fit residues: 49.3505 Evaluate side-chains 293 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 280 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN B 227 HIS B 472 GLN C 227 HIS C 472 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.187084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.138518 restraints weight = 14632.911| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.85 r_work: 0.3355 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12540 Z= 0.183 Angle : 0.459 6.753 17040 Z= 0.252 Chirality : 0.037 0.133 2032 Planarity : 0.003 0.057 2108 Dihedral : 3.275 11.817 1716 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.77 % Allowed : 13.75 % Favored : 84.49 % 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 aren not related in a simple way. whole: 2.91 (0.22), residues: 1556 helix: 2.41 (0.15), residues: 1196 sheet: 2.40 (0.73), residues: 64 loop : -0.25 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 470 TYR 0.014 0.001 TYR C 188 PHE 0.017 0.001 PHE B 409 TRP 0.013 0.001 TRP C 431 HIS 0.005 0.001 HIS D 336 Details of bonding type rmsd covalent geometry : bond 0.00434 (12536) covalent geometry : angle 0.45874 (17032) SS BOND : bond 0.00590 ( 4) SS BOND : angle 0.75196 ( 8) hydrogen bonds : bond 0.04424 ( 933) hydrogen bonds : angle 3.53475 ( 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 288 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7838 (mpp) REVERT: A 340 ASP cc_start: 0.8546 (t70) cc_final: 0.8026 (t0) REVERT: A 377 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8069 (tt) REVERT: A 422 SER cc_start: 0.8801 (m) cc_final: 0.8547 (t) REVERT: A 425 ARG cc_start: 0.7662 (ttp-110) cc_final: 0.7249 (ttm-80) REVERT: A 460 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7921 (mtm110) REVERT: A 470 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7016 (mtm-85) REVERT: B 209 MET cc_start: 0.8916 (mmm) cc_final: 0.8622 (mpp) REVERT: B 340 ASP cc_start: 0.8532 (t70) cc_final: 0.8064 (t0) REVERT: B 377 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 411 MET cc_start: 0.8445 (mmt) cc_final: 0.8074 (mmt) REVERT: B 425 ARG cc_start: 0.7737 (ttp-110) cc_final: 0.7404 (ttm-80) REVERT: B 470 ARG cc_start: 0.7047 (mtm-85) cc_final: 0.6709 (mtm-85) REVERT: C 340 ASP cc_start: 0.8773 (t70) cc_final: 0.8007 (t0) REVERT: C 377 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8053 (tt) REVERT: C 422 SER cc_start: 0.8741 (m) cc_final: 0.8459 (t) REVERT: C 425 ARG cc_start: 0.7681 (ttp-110) cc_final: 0.7433 (ttm-80) REVERT: C 460 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8063 (mtm-85) REVERT: C 463 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8037 (ttm170) REVERT: C 470 ARG cc_start: 0.7385 (mtm110) cc_final: 0.6899 (mtm-85) REVERT: D 340 ASP cc_start: 0.8588 (t70) cc_final: 0.8050 (t0) REVERT: D 377 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8043 (tt) REVERT: D 422 SER cc_start: 0.8720 (m) cc_final: 0.8470 (t) REVERT: D 425 ARG cc_start: 0.7726 (ttp-110) cc_final: 0.7363 (ttm-80) REVERT: D 434 TYR cc_start: 0.7881 (t80) cc_final: 0.7604 (t80) REVERT: D 460 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7847 (mtm-85) REVERT: D 470 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6886 (mtm-85) outliers start: 22 outliers final: 13 residues processed: 280 average time/residue: 0.1184 time to fit residues: 46.0143 Evaluate side-chains 274 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 312 THR 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 312 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 400 THR 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: 0.4980 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139156 restraints weight = 14357.313| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.82 r_work: 0.3383 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12540 Z= 0.124 Angle : 0.395 5.704 17040 Z= 0.218 Chirality : 0.035 0.130 2032 Planarity : 0.003 0.037 2108 Dihedral : 3.175 12.553 1716 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.53 % Allowed : 15.68 % Favored : 82.80 % 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 aren not related in a simple way. whole: 3.25 (0.22), residues: 1556 helix: 2.72 (0.15), residues: 1188 sheet: 2.27 (0.72), residues: 64 loop : -0.34 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 446 TYR 0.010 0.001 TYR D 233 PHE 0.015 0.001 PHE B 409 TRP 0.014 0.001 TRP C 431 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00284 (12536) covalent geometry : angle 0.39478 (17032) SS BOND : bond 0.00326 ( 4) SS BOND : angle 0.44697 ( 8) hydrogen bonds : bond 0.03809 ( 933) hydrogen bonds : angle 3.30719 ( 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 302 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 283 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7870 (mpp) REVERT: A 340 ASP cc_start: 0.8446 (t70) cc_final: 0.7845 (t0) REVERT: A 377 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8011 (tt) REVERT: A 422 SER cc_start: 0.8768 (m) cc_final: 0.8526 (t) REVERT: A 425 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7262 (ttm-80) REVERT: A 460 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7604 (mtm-85) REVERT: A 470 ARG cc_start: 0.7372 (mtm110) cc_final: 0.6997 (mtm-85) REVERT: B 340 ASP cc_start: 0.8543 (t70) cc_final: 0.7983 (t0) REVERT: B 377 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8041 (tt) REVERT: B 411 MET cc_start: 0.8349 (mmt) cc_final: 0.8114 (mmt) REVERT: B 425 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7326 (ttm-80) REVERT: B 463 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8574 (ttm110) REVERT: B 470 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6854 (mtm-85) REVERT: C 340 ASP cc_start: 0.8652 (t70) cc_final: 0.7984 (t0) REVERT: C 377 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8028 (tt) REVERT: C 413 ILE cc_start: 0.8695 (mm) cc_final: 0.8446 (mt) REVERT: C 422 SER cc_start: 0.8716 (m) cc_final: 0.8462 (t) REVERT: C 425 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7379 (ttm-80) REVERT: C 470 ARG cc_start: 0.7274 (mtm110) cc_final: 0.6883 (mtm-85) REVERT: D 340 ASP cc_start: 0.8574 (t70) cc_final: 0.8012 (t0) REVERT: D 377 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7995 (tt) REVERT: D 422 SER cc_start: 0.8675 (m) cc_final: 0.8446 (t) REVERT: D 425 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7300 (ttm-80) REVERT: D 434 TYR cc_start: 0.7927 (t80) cc_final: 0.7678 (t80) REVERT: D 460 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7573 (mtm110) REVERT: D 463 ARG cc_start: 0.8565 (ttp80) cc_final: 0.8220 (ttm170) REVERT: D 470 ARG cc_start: 0.7013 (mtm-85) cc_final: 0.6778 (mtm-85) outliers start: 19 outliers final: 11 residues processed: 289 average time/residue: 0.1180 time to fit residues: 47.5007 Evaluate side-chains 286 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 270 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 377 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 214 ILE 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 214 ILE 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: 0.9990 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 153 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140819 restraints weight = 14483.208| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.88 r_work: 0.3383 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2685 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= 0.119 Angle : 0.393 5.459 17040 Z= 0.215 Chirality : 0.035 0.131 2032 Planarity : 0.003 0.035 2108 Dihedral : 3.113 12.279 1716 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.65 % Allowed : 15.43 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.22), residues: 1556 helix: 2.83 (0.15), residues: 1192 sheet: 2.14 (0.71), residues: 64 loop : -0.45 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.012 0.001 TYR D 233 PHE 0.010 0.001 PHE D 459 TRP 0.014 0.001 TRP C 431 HIS 0.003 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00274 (12536) covalent geometry : angle 0.39268 (17032) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.20271 ( 8) hydrogen bonds : bond 0.03584 ( 933) hydrogen bonds : angle 3.18730 ( 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 312 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7868 (mpp) REVERT: A 340 ASP cc_start: 0.8503 (t70) cc_final: 0.7979 (t0) REVERT: A 377 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7882 (mt) REVERT: A 422 SER cc_start: 0.8796 (m) cc_final: 0.8556 (t) REVERT: A 425 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7232 (ttm-80) REVERT: A 470 ARG cc_start: 0.7390 (mtm110) cc_final: 0.6987 (mtm-85) REVERT: B 340 ASP cc_start: 0.8658 (t70) cc_final: 0.8098 (t0) REVERT: B 377 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7925 (mt) REVERT: B 425 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.7246 (ttm-80) REVERT: B 463 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8569 (ttm110) REVERT: B 470 ARG cc_start: 0.7161 (mtm-85) cc_final: 0.6916 (mtm-85) REVERT: C 340 ASP cc_start: 0.8750 (t70) cc_final: 0.8070 (t0) REVERT: C 341 VAL cc_start: 0.8989 (t) cc_final: 0.8724 (p) REVERT: C 377 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7917 (mt) REVERT: C 413 ILE cc_start: 0.8659 (mm) cc_final: 0.8363 (mp) REVERT: C 419 MET cc_start: 0.8316 (ttt) cc_final: 0.8098 (ttt) REVERT: C 422 SER cc_start: 0.8717 (m) cc_final: 0.8479 (t) REVERT: C 425 ARG cc_start: 0.7678 (ttp-110) cc_final: 0.7368 (ttm-80) REVERT: C 463 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8460 (ttm170) REVERT: C 470 ARG cc_start: 0.7234 (mtm110) cc_final: 0.6896 (mtm-85) REVERT: D 340 ASP cc_start: 0.8708 (t70) cc_final: 0.8167 (t0) REVERT: D 377 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8021 (tt) REVERT: D 422 SER cc_start: 0.8733 (m) cc_final: 0.8487 (t) REVERT: D 425 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7313 (ttm-80) REVERT: D 470 ARG cc_start: 0.7018 (mtm-85) cc_final: 0.6783 (mtm-85) outliers start: 33 outliers final: 21 residues processed: 294 average time/residue: 0.1133 time to fit residues: 46.4010 Evaluate side-chains 300 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 204 ASP 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 A residue 471 GLU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 16 optimal weight: 0.0670 chunk 38 optimal weight: 0.0070 chunk 30 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.193301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142381 restraints weight = 14396.333| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.90 r_work: 0.3390 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2864 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= 0.089 Angle : 0.366 5.285 17040 Z= 0.202 Chirality : 0.034 0.129 2032 Planarity : 0.003 0.029 2108 Dihedral : 3.011 12.890 1716 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.85 % Allowed : 17.52 % Favored : 80.63 % 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 aren not related in a simple way. whole: 3.56 (0.21), residues: 1556 helix: 2.98 (0.14), residues: 1196 sheet: 2.03 (0.69), residues: 64 loop : -0.40 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.011 0.001 TYR D 233 PHE 0.015 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 covalent geometry : bond 0.00185 (12536) covalent geometry : angle 0.36559 (17032) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.38445 ( 8) hydrogen bonds : bond 0.03286 ( 933) hydrogen bonds : angle 3.05113 ( 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 306 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7919 (mpp) REVERT: A 340 ASP cc_start: 0.8553 (t70) cc_final: 0.8018 (t0) REVERT: A 377 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7912 (mt) REVERT: A 403 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8274 (mp0) REVERT: A 422 SER cc_start: 0.8790 (m) cc_final: 0.8574 (t) REVERT: A 470 ARG cc_start: 0.7352 (mtm110) cc_final: 0.6953 (mtm-85) REVERT: B 340 ASP cc_start: 0.8656 (t70) cc_final: 0.8079 (t0) REVERT: B 377 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7911 (mt) REVERT: B 411 MET cc_start: 0.8312 (mmt) cc_final: 0.8112 (mmt) REVERT: B 425 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.7176 (ttm-80) REVERT: B 470 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6863 (mtm-85) REVERT: C 340 ASP cc_start: 0.8690 (t70) cc_final: 0.8019 (t0) REVERT: C 377 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 413 ILE cc_start: 0.8570 (mm) cc_final: 0.8290 (mp) REVERT: C 422 SER cc_start: 0.8696 (m) cc_final: 0.8478 (t) REVERT: C 425 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7337 (ttm-80) REVERT: C 463 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8402 (ttm170) REVERT: C 470 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6837 (mtm-85) REVERT: D 340 ASP cc_start: 0.8732 (t70) cc_final: 0.8213 (t70) REVERT: D 377 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7914 (mt) REVERT: D 403 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8333 (mp0) REVERT: D 422 SER cc_start: 0.8716 (m) cc_final: 0.8493 (t) REVERT: D 425 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7280 (ttm-80) REVERT: D 460 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7592 (mtm110) REVERT: D 463 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8341 (ttm110) outliers start: 23 outliers final: 17 residues processed: 293 average time/residue: 0.1165 time to fit residues: 47.4781 Evaluate side-chains 299 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 277 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 377 LEU Chi-restraints excluded: chain A residue 471 GLU 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 377 LEU Chi-restraints excluded: chain B residue 471 GLU 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 D residue 192 GLU Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 377 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.0020 chunk 154 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.192404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141833 restraints weight = 14418.485| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.86 r_work: 0.3373 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2961 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= 0.108 Angle : 0.386 6.342 17040 Z= 0.209 Chirality : 0.035 0.130 2032 Planarity : 0.003 0.028 2108 Dihedral : 2.987 12.046 1716 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.25 % Allowed : 17.93 % Favored : 79.82 % 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 aren not related in a simple way. whole: 3.68 (0.21), residues: 1556 helix: 3.08 (0.14), residues: 1196 sheet: 1.99 (0.70), residues: 64 loop : -0.37 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 470 TYR 0.011 0.001 TYR D 233 PHE 0.010 0.001 PHE D 196 TRP 0.013 0.001 TRP C 431 HIS 0.003 0.001 HIS D 436 Details of bonding type rmsd covalent geometry : bond 0.00243 (12536) covalent geometry : angle 0.38620 (17032) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.23097 ( 8) hydrogen bonds : bond 0.03317 ( 933) hydrogen bonds : angle 3.05754 ( 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 302 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7939 (mpp) REVERT: A 340 ASP cc_start: 0.8612 (t70) cc_final: 0.8092 (t0) REVERT: A 377 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7906 (mt) REVERT: A 403 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8245 (mp0) REVERT: A 470 ARG cc_start: 0.7393 (mtm110) cc_final: 0.7012 (mtm-85) REVERT: B 340 ASP cc_start: 0.8689 (t70) cc_final: 0.8146 (t0) REVERT: B 377 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7924 (mt) REVERT: B 411 MET cc_start: 0.8338 (mmt) cc_final: 0.8110 (mmt) REVERT: B 425 ARG cc_start: 0.7548 (ttp-110) cc_final: 0.7160 (ttm-80) REVERT: C 340 ASP cc_start: 0.8676 (t70) cc_final: 0.7957 (t0) REVERT: C 377 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7923 (mt) REVERT: C 413 ILE cc_start: 0.8570 (mm) cc_final: 0.8309 (mp) REVERT: C 422 SER cc_start: 0.8719 (m) cc_final: 0.8497 (t) REVERT: C 425 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7302 (ttm-80) REVERT: C 463 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8422 (ttm170) REVERT: C 470 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6799 (mtm-85) REVERT: D 204 ASP cc_start: 0.7096 (m-30) cc_final: 0.6773 (t0) REVERT: D 340 ASP cc_start: 0.8756 (t70) cc_final: 0.8239 (t70) REVERT: D 377 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7919 (mt) REVERT: D 403 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8308 (mp0) REVERT: D 422 SER cc_start: 0.8752 (m) cc_final: 0.8532 (t) REVERT: D 425 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7273 (ttm-80) REVERT: D 460 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7616 (mtm110) REVERT: D 463 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8320 (ttm110) REVERT: D 470 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6817 (mtm-85) outliers start: 28 outliers final: 19 residues processed: 288 average time/residue: 0.1127 time to fit residues: 45.4026 Evaluate side-chains 296 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 377 LEU Chi-restraints excluded: chain A residue 471 GLU 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 377 LEU Chi-restraints excluded: chain B residue 471 GLU 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 342 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 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: 0.8980 chunk 147 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.189224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138832 restraints weight = 14526.394| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.82 r_work: 0.3360 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12540 Z= 0.161 Angle : 0.442 7.584 17040 Z= 0.234 Chirality : 0.036 0.131 2032 Planarity : 0.003 0.030 2108 Dihedral : 3.072 11.613 1716 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.41 % Allowed : 18.65 % 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 aren not related in a simple way. whole: 3.57 (0.21), residues: 1556 helix: 2.99 (0.14), residues: 1196 sheet: 1.99 (0.68), residues: 64 loop : -0.36 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 470 TYR 0.012 0.001 TYR D 188 PHE 0.013 0.001 PHE B 409 TRP 0.014 0.001 TRP C 431 HIS 0.003 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00383 (12536) covalent geometry : angle 0.44158 (17032) SS BOND : bond 0.00478 ( 4) SS BOND : angle 0.55411 ( 8) hydrogen bonds : bond 0.03602 ( 933) hydrogen bonds : angle 3.18225 ( 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: 30 poor density : 274 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7307 (m-30) cc_final: 0.7045 (t0) REVERT: A 209 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7982 (mpp) REVERT: A 340 ASP cc_start: 0.8631 (t70) cc_final: 0.8155 (t0) REVERT: A 377 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 403 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8215 (mp0) REVERT: A 425 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7382 (ttm-80) REVERT: A 470 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7062 (mtm-85) REVERT: B 340 ASP cc_start: 0.8719 (t70) cc_final: 0.8203 (t70) REVERT: B 377 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8091 (tt) REVERT: B 411 MET cc_start: 0.8408 (mmt) cc_final: 0.8176 (mmt) REVERT: C 340 ASP cc_start: 0.8702 (t70) cc_final: 0.8005 (t0) REVERT: C 377 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8049 (tt) REVERT: C 422 SER cc_start: 0.8792 (m) cc_final: 0.8574 (t) REVERT: C 425 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7320 (ttm-80) REVERT: C 470 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6878 (mtm-85) REVERT: D 204 ASP cc_start: 0.7194 (m-30) cc_final: 0.6833 (t0) REVERT: D 340 ASP cc_start: 0.8756 (t70) cc_final: 0.8249 (t70) REVERT: D 377 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8033 (tt) REVERT: D 403 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8311 (mp0) REVERT: D 422 SER cc_start: 0.8799 (m) cc_final: 0.8561 (t) REVERT: D 425 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7277 (ttm-80) REVERT: D 463 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8422 (ttm110) REVERT: D 470 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6828 (mtm-85) outliers start: 30 outliers final: 22 residues processed: 288 average time/residue: 0.1143 time to fit residues: 45.9239 Evaluate side-chains 299 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 377 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 198 VAL 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 C residue 179 ILE 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 342 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.190770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139453 restraints weight = 14429.476| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.80 r_work: 0.3369 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3115 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 : 0.404 6.707 17040 Z= 0.216 Chirality : 0.035 0.130 2032 Planarity : 0.003 0.032 2108 Dihedral : 3.015 12.330 1716 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.33 % Allowed : 19.13 % Favored : 78.54 % 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 aren not related in a simple way. whole: 3.71 (0.21), residues: 1556 helix: 3.11 (0.14), residues: 1196 sheet: 1.96 (0.68), residues: 64 loop : -0.41 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 470 TYR 0.011 0.001 TYR D 233 PHE 0.012 0.001 PHE D 196 TRP 0.014 0.001 TRP C 431 HIS 0.002 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00266 (12536) covalent geometry : angle 0.40388 (17032) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.26317 ( 8) hydrogen bonds : bond 0.03367 ( 933) hydrogen bonds : angle 3.09798 ( 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 297 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7332 (m-30) cc_final: 0.7045 (t0) REVERT: A 209 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7900 (mpp) REVERT: A 340 ASP cc_start: 0.8532 (t70) cc_final: 0.8082 (t0) REVERT: A 377 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7878 (mt) REVERT: A 403 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8178 (mp0) REVERT: A 425 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7303 (ttm-80) REVERT: A 470 ARG cc_start: 0.7398 (mtm110) cc_final: 0.7032 (mtm-85) REVERT: B 340 ASP cc_start: 0.8700 (t70) cc_final: 0.8205 (t70) REVERT: B 377 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7885 (mt) REVERT: B 411 MET cc_start: 0.8375 (mmt) cc_final: 0.8124 (mmt) REVERT: B 425 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7264 (ttm-80) REVERT: C 340 ASP cc_start: 0.8701 (t70) cc_final: 0.7998 (t0) REVERT: C 377 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7878 (mt) REVERT: C 422 SER cc_start: 0.8744 (m) cc_final: 0.8520 (t) REVERT: C 425 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.7255 (ttm-80) REVERT: C 470 ARG cc_start: 0.7218 (mtm110) cc_final: 0.6796 (mtm-85) REVERT: D 204 ASP cc_start: 0.7248 (m-30) cc_final: 0.6937 (t0) REVERT: D 340 ASP cc_start: 0.8729 (t70) cc_final: 0.8213 (t70) REVERT: D 377 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7874 (mt) REVERT: D 403 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8253 (mp0) REVERT: D 422 SER cc_start: 0.8741 (m) cc_final: 0.8511 (t) REVERT: D 425 ARG cc_start: 0.7623 (ttp-110) cc_final: 0.7208 (ttm-80) REVERT: D 463 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8408 (ttm110) REVERT: D 470 ARG cc_start: 0.7080 (mtm-85) cc_final: 0.6757 (mtm-85) outliers start: 29 outliers final: 22 residues processed: 280 average time/residue: 0.1126 time to fit residues: 44.1903 Evaluate side-chains 294 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 377 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 198 VAL 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 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 342 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4148 r_free = 0.4148 target = 0.189583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138517 restraints weight = 14450.645| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.77 r_work: 0.3379 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3160 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= 0.138 Angle : 0.426 6.795 17040 Z= 0.226 Chirality : 0.035 0.130 2032 Planarity : 0.003 0.040 2108 Dihedral : 3.057 12.192 1716 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.33 % Allowed : 19.13 % Favored : 78.54 % 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 aren not related in a simple way. whole: 3.69 (0.21), residues: 1556 helix: 3.08 (0.14), residues: 1196 sheet: 1.98 (0.68), residues: 64 loop : -0.38 (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 0.013 0.001 PHE D 196 TRP 0.014 0.001 TRP C 431 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00325 (12536) covalent geometry : angle 0.42573 (17032) SS BOND : bond 0.00349 ( 4) SS BOND : angle 0.41049 ( 8) hydrogen bonds : bond 0.03458 ( 933) hydrogen bonds : angle 3.13420 ( 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 296 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7388 (m-30) cc_final: 0.7086 (t0) REVERT: A 209 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7948 (mpp) REVERT: A 340 ASP cc_start: 0.8583 (t70) cc_final: 0.8124 (t0) REVERT: A 377 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8040 (tt) REVERT: A 403 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8183 (mp0) REVERT: A 470 ARG cc_start: 0.7451 (mtm110) cc_final: 0.7210 (mtm110) REVERT: B 340 ASP cc_start: 0.8751 (t70) cc_final: 0.8272 (t70) REVERT: B 377 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8064 (tt) REVERT: B 411 MET cc_start: 0.8435 (mmt) cc_final: 0.8183 (mmp) REVERT: B 425 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7309 (ttm-80) REVERT: C 340 ASP cc_start: 0.8728 (t70) cc_final: 0.8061 (t0) REVERT: C 377 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8032 (tt) REVERT: C 422 SER cc_start: 0.8818 (m) cc_final: 0.8562 (t) REVERT: C 425 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7274 (ttm-80) REVERT: C 470 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6816 (mtm-85) REVERT: D 204 ASP cc_start: 0.7227 (m-30) cc_final: 0.6907 (t0) REVERT: D 340 ASP cc_start: 0.8740 (t70) cc_final: 0.8231 (t70) REVERT: D 377 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8020 (tt) REVERT: D 403 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8251 (mp0) REVERT: D 422 SER cc_start: 0.8795 (m) cc_final: 0.8559 (t) REVERT: D 425 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7251 (ttm-80) REVERT: D 470 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6801 (mtm-85) outliers start: 29 outliers final: 22 residues processed: 280 average time/residue: 0.1157 time to fit residues: 45.4039 Evaluate side-chains 293 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 377 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 198 VAL 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 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 342 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 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: 0.9980 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 0.0030 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 127 optimal weight: 0.0970 chunk 138 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.3666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.4169 r_free = 0.4169 target = 0.192063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139947 restraints weight = 14178.176| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.70 r_work: 0.3170 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3276 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= 0.093 Angle : 0.394 6.927 17040 Z= 0.209 Chirality : 0.034 0.131 2032 Planarity : 0.003 0.034 2108 Dihedral : 2.993 12.269 1716 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.17 % Allowed : 19.45 % Favored : 78.38 % 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 aren not related in a simple way. whole: 3.91 (0.21), residues: 1556 helix: 3.26 (0.14), residues: 1196 sheet: 2.10 (0.68), residues: 64 loop : -0.38 (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 233 PHE 0.012 0.001 PHE D 196 TRP 0.013 0.001 TRP C 431 HIS 0.002 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00197 (12536) covalent geometry : angle 0.39381 (17032) SS BOND : bond 0.00020 ( 4) SS BOND : angle 0.33083 ( 8) hydrogen bonds : bond 0.03189 ( 933) hydrogen bonds : angle 3.03580 ( 2763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3287.20 seconds wall clock time: 56 minutes 49.63 seconds (3409.63 seconds total)