Starting phenix.real_space_refine on Fri Jul 3 21:52:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d1k_27133/07_2026/8d1k_27133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1k_27133/07_2026/8d1k_27133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d1k_27133/07_2026/8d1k_27133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1k_27133/07_2026/8d1k_27133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d1k_27133/07_2026/8d1k_27133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1k_27133/07_2026/8d1k_27133.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d1k_27133/07_2026/8d1k_27133.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d1k_27133/07_2026/8d1k_27133.cif" } resolution = 2.28 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= 0.002 sd= 0.129 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 5 9.91 5 P 5 5.49 5 S 80 5.16 5 C 10905 2.51 5 N 2550 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16305 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 178 Unusual residues: {' CA': 1, 'MC3': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 108 Unusual residues: {' CA': 1, 'MC3': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 3.99, per 1000 atoms: 0.24 Number of scatterers: 16305 At special positions: 0 Unit cell: (107.9, 104.58, 110.39, 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 5 19.99 S 80 16.00 P 5 15.00 O 2760 8.00 N 2550 7.00 C 10905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 711.7 milliseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 5 sheets defined 69.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.559A pdb=" N ALA D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.882A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.646A pdb=" N LYS D 262 " --> pdb=" O ASN D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.696A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.559A pdb=" N ALA B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.883A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.646A pdb=" N LYS B 262 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.697A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.559A pdb=" N ALA A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.883A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.646A pdb=" N LYS A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.696A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.560A pdb=" N ALA E 10 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.882A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.646A pdb=" N LYS E 262 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.695A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.559A pdb=" N ALA C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 70 Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.882A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.645A pdb=" N LYS C 262 " --> pdb=" O ASN C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.696A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.519A pdb=" N TYR D 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.519A pdb=" N TYR E 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.519A pdb=" N TYR B 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.519A pdb=" N TYR C 347 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.519A pdb=" N TYR A 347 " --> pdb=" O GLN E 376 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2775 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: 2.58 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2769 1.32 - 1.45: 4504 1.45 - 1.58: 9317 1.58 - 1.71: 10 1.71 - 1.84: 135 Bond restraints: 16735 Sorted by residual: bond pdb=" C ARG A 105 " pdb=" O ARG A 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.31e+01 bond pdb=" C ARG E 105 " pdb=" O ARG E 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.31e+01 bond pdb=" C ARG B 105 " pdb=" O ARG B 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.31e+01 bond pdb=" C ARG D 105 " pdb=" O ARG D 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.30e+01 bond pdb=" C ARG C 105 " pdb=" O ARG C 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.30e+01 ... (remaining 16730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 21849 2.74 - 5.48: 701 5.48 - 8.22: 5 8.22 - 10.96: 0 10.96 - 13.70: 5 Bond angle restraints: 22560 Sorted by residual: angle pdb=" N PRO A 77 " pdb=" CA PRO A 77 " pdb=" CB PRO A 77 " ideal model delta sigma weight residual 102.81 99.30 3.51 6.70e-01 2.23e+00 2.74e+01 angle pdb=" N PRO E 77 " pdb=" CA PRO E 77 " pdb=" CB PRO E 77 " ideal model delta sigma weight residual 102.81 99.31 3.50 6.70e-01 2.23e+00 2.73e+01 angle pdb=" N PRO D 77 " pdb=" CA PRO D 77 " pdb=" CB PRO D 77 " ideal model delta sigma weight residual 102.81 99.32 3.49 6.70e-01 2.23e+00 2.71e+01 angle pdb=" N PRO B 77 " pdb=" CA PRO B 77 " pdb=" CB PRO B 77 " ideal model delta sigma weight residual 102.81 99.32 3.49 6.70e-01 2.23e+00 2.71e+01 angle pdb=" N PRO C 77 " pdb=" CA PRO C 77 " pdb=" CB PRO C 77 " ideal model delta sigma weight residual 102.81 99.32 3.49 6.70e-01 2.23e+00 2.71e+01 ... (remaining 22555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 9035 23.97 - 47.93: 635 47.93 - 71.90: 175 71.90 - 95.86: 35 95.86 - 119.83: 5 Dihedral angle restraints: 9885 sinusoidal: 4320 harmonic: 5565 Sorted by residual: dihedral pdb=" C33 MC3 B 603 " pdb=" C31 MC3 B 603 " pdb=" C32 MC3 B 603 " pdb=" O2 MC3 B 603 " ideal model delta sinusoidal sigma weight residual 175.52 55.69 119.83 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C33 MC3 E 603 " pdb=" C31 MC3 E 603 " pdb=" C32 MC3 E 603 " pdb=" O2 MC3 E 603 " ideal model delta sinusoidal sigma weight residual 175.52 55.75 119.77 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C33 MC3 D 603 " pdb=" C31 MC3 D 603 " pdb=" C32 MC3 D 603 " pdb=" O2 MC3 D 603 " ideal model delta sinusoidal sigma weight residual 175.52 55.76 119.76 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 9882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 968 0.040 - 0.080: 693 0.080 - 0.120: 486 0.120 - 0.160: 179 0.160 - 0.200: 59 Chirality restraints: 2385 Sorted by residual: chirality pdb=" CA LEU A 176 " pdb=" N LEU A 176 " pdb=" C LEU A 176 " pdb=" CB LEU A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA LEU D 176 " pdb=" N LEU D 176 " pdb=" C LEU D 176 " pdb=" CB LEU D 176 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA LEU B 176 " pdb=" N LEU B 176 " pdb=" C LEU B 176 " pdb=" CB LEU B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 2382 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 97 " -0.036 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR D 97 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR D 97 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 97 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR D 97 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR D 97 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 97 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR D 97 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 97 " -0.036 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR C 97 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR C 97 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 97 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 97 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 97 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR C 97 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR C 97 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 97 " -0.035 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR E 97 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR E 97 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR E 97 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR E 97 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR E 97 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR E 97 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR E 97 " 0.026 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3731 2.81 - 3.33: 16688 3.33 - 3.85: 29050 3.85 - 4.38: 35427 4.38 - 4.90: 57205 Nonbonded interactions: 142101 Sorted by model distance: nonbonded pdb=" O ASN A 296 " pdb="CA CA A 602 " model vdw 2.287 2.510 nonbonded pdb=" O ASN C 296 " pdb="CA CA C 602 " model vdw 2.288 2.510 nonbonded pdb=" O ASN D 296 " pdb="CA CA D 601 " model vdw 2.288 2.510 nonbonded pdb=" O ASN B 296 " pdb="CA CA B 601 " model vdw 2.288 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 601 " model vdw 2.288 2.510 ... (remaining 142096 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 2 through 377 or resid 604 or (resid 605 and (name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or (resid 606 and (name C33 or name C34 or name C35 o \ r name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C \ 42 or name C43 or name C44)) or (resid 607 through 608 and (name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name \ C41 or name C42)))) selection = (chain 'B' and (resid 2 through 377 or (resid 604 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 605 and (name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)) or (resid 606 and (name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name C44)) or (resid 607 through 608 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2)))) selection = (chain 'C' and (resid 2 through 377 or (resid 604 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 605 and (name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)) or resid 606 or (resid 607 through 608 and (name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name C42)))) selection = (chain 'D' and (resid 2 through 377 or (resid 604 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 605 and (name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)) or (resid 606 and (name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name C44)) or (resid 607 through 608 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2)))) selection = (chain 'E' and (resid 2 through 377 or (resid 604 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 605 and (name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)) or (resid 606 and (name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name C44)) or (resid 607 through 608 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2)))) } 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.910 Find NCS groups from input model: 0.420 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: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 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 : 0.013 0.065 16735 Z= 0.915 Angle : 1.275 13.700 22560 Z= 0.940 Chirality : 0.074 0.200 2385 Planarity : 0.007 0.031 2770 Dihedral : 18.103 119.825 6295 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.65 % Allowed : 8.85 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1870 helix: 0.79 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : 0.46 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.003 ARG E 313 TYR 0.051 0.008 TYR D 97 PHE 0.028 0.006 PHE E 162 TRP 0.054 0.011 TRP A 309 HIS 0.007 0.003 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.01297 / 0.91 (16735) covalent geometry : angle 1.27536 / 0.94 (22560) hydrogen bonds : bond 0.14685 / 9.65 ( 965) hydrogen bonds : angle 5.48454 / 4.00 ( 2775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.661 Fit side-chains REVERT: D 262 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6338 (mppt) REVERT: D 264 TYR cc_start: 0.7597 (m-80) cc_final: 0.7144 (m-80) REVERT: D 360 MET cc_start: 0.9026 (mmm) cc_final: 0.8793 (mmm) REVERT: D 376 GLN cc_start: 0.6917 (mm-40) cc_final: 0.6656 (mm110) REVERT: B 119 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8293 (tt0) REVERT: B 376 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6645 (mm110) REVERT: A 119 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8254 (tt0) REVERT: A 360 MET cc_start: 0.9020 (mmm) cc_final: 0.8728 (mmm) REVERT: A 369 ASN cc_start: 0.7356 (m-40) cc_final: 0.7152 (m110) REVERT: A 373 MET cc_start: 0.8346 (mtp) cc_final: 0.8025 (mtm) REVERT: A 376 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6678 (mm110) REVERT: E 8 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8637 (mt0) REVERT: E 376 GLN cc_start: 0.6747 (mm-40) cc_final: 0.6453 (mm110) REVERT: C 373 MET cc_start: 0.8225 (mtp) cc_final: 0.7988 (mtm) REVERT: C 376 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6698 (mm110) outliers start: 45 outliers final: 11 residues processed: 235 average time/residue: 0.6648 time to fit residues: 172.5900 Evaluate side-chains 175 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 178 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0170 chunk 149 optimal weight: 0.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 208 GLN B 208 GLN B 369 ASN A 208 GLN E 208 GLN E 369 ASN C 208 GLN C 369 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.101335 restraints weight = 18809.843| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.32 r_work: 0.3087 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16735 Z= 0.130 Angle : 0.534 8.192 22560 Z= 0.283 Chirality : 0.038 0.161 2385 Planarity : 0.004 0.025 2770 Dihedral : 14.218 117.456 2620 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.47 % Allowed : 10.62 % Favored : 87.91 % 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 are not related in a simple way. whole: 1.41 (0.19), residues: 1870 helix: 1.25 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.50 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 47 TYR 0.020 0.002 TYR C 97 PHE 0.021 0.002 PHE A 276 TRP 0.020 0.002 TRP D 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (16735) covalent geometry : angle 0.53443 / 0.28 (22560) hydrogen bonds : bond 0.05995 / 3.99 ( 965) hydrogen bonds : angle 4.40985 / 3.23 ( 2775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.658 Fit side-chains REVERT: D 72 TYR cc_start: 0.7004 (m-10) cc_final: 0.6414 (m-80) REVERT: D 262 LYS cc_start: 0.7031 (mmtm) cc_final: 0.6788 (mppt) REVERT: D 376 GLN cc_start: 0.6711 (mm-40) cc_final: 0.6354 (mm110) REVERT: B 68 TYR cc_start: 0.6689 (t80) cc_final: 0.6402 (t80) REVERT: B 376 GLN cc_start: 0.6913 (mm-40) cc_final: 0.6510 (mm110) REVERT: A 72 TYR cc_start: 0.6978 (m-80) cc_final: 0.6621 (m-10) REVERT: A 353 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: A 360 MET cc_start: 0.8734 (mmm) cc_final: 0.8489 (mmm) REVERT: A 376 GLN cc_start: 0.6686 (mm-40) cc_final: 0.6301 (mm110) REVERT: E 51 ARG cc_start: 0.7738 (mmt90) cc_final: 0.7489 (mpt90) REVERT: E 56 GLU cc_start: 0.6753 (mp0) cc_final: 0.6070 (pt0) REVERT: E 68 TYR cc_start: 0.7001 (t80) cc_final: 0.6630 (t80) REVERT: E 72 TYR cc_start: 0.6774 (m-80) cc_final: 0.6537 (m-10) REVERT: E 259 ASN cc_start: 0.7104 (m-40) cc_final: 0.6789 (m110) REVERT: E 373 MET cc_start: 0.8012 (mtt) cc_final: 0.7718 (mtp) REVERT: C 72 TYR cc_start: 0.6876 (m-80) cc_final: 0.6610 (m-10) REVERT: C 376 GLN cc_start: 0.6742 (mm-40) cc_final: 0.6391 (mm110) outliers start: 25 outliers final: 13 residues processed: 208 average time/residue: 0.6538 time to fit residues: 149.8194 Evaluate side-chains 183 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 178 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 116 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 369 ASN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094826 restraints weight = 19096.719| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.32 r_work: 0.2993 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 16735 Z= 0.294 Angle : 0.674 9.095 22560 Z= 0.356 Chirality : 0.047 0.164 2385 Planarity : 0.005 0.054 2770 Dihedral : 14.191 117.842 2610 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.83 % Allowed : 10.91 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1870 helix: 1.01 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : 0.17 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 125 TYR 0.032 0.003 TYR D 97 PHE 0.038 0.002 PHE E 248 TRP 0.022 0.003 TRP E 309 HIS 0.007 0.002 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.29 (16735) covalent geometry : angle 0.67414 / 0.36 (22560) hydrogen bonds : bond 0.07713 / 5.15 ( 965) hydrogen bonds : angle 4.65000 / 3.40 ( 2775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.629 Fit side-chains REVERT: D 178 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.8672 (m-70) REVERT: B 8 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: B 194 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8588 (tttp) REVERT: B 203 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8593 (t70) REVERT: B 376 GLN cc_start: 0.6855 (mm-40) cc_final: 0.6475 (mm110) REVERT: A 51 ARG cc_start: 0.7513 (mmt180) cc_final: 0.7204 (mmt90) REVERT: A 68 TYR cc_start: 0.6770 (t80) cc_final: 0.6504 (t80) REVERT: A 72 TYR cc_start: 0.6935 (m-80) cc_final: 0.6638 (m-80) REVERT: A 360 MET cc_start: 0.8745 (mmm) cc_final: 0.8410 (mmm) REVERT: A 369 ASN cc_start: 0.7191 (m-40) cc_final: 0.6981 (m110) REVERT: A 376 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6499 (mm110) REVERT: E 72 TYR cc_start: 0.6963 (m-80) cc_final: 0.6669 (m-80) REVERT: E 203 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8594 (t70) REVERT: C 51 ARG cc_start: 0.7892 (mmt90) cc_final: 0.7578 (mmt90) REVERT: C 72 TYR cc_start: 0.6987 (m-80) cc_final: 0.6707 (m-80) REVERT: C 270 ASP cc_start: 0.7587 (t0) cc_final: 0.7367 (t0) REVERT: C 373 MET cc_start: 0.8088 (mtm) cc_final: 0.7863 (mtm) REVERT: C 376 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6368 (mm110) outliers start: 31 outliers final: 13 residues processed: 210 average time/residue: 0.5850 time to fit residues: 136.5040 Evaluate side-chains 183 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 26 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100806 restraints weight = 18907.122| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.32 r_work: 0.3082 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16735 Z= 0.123 Angle : 0.514 8.188 22560 Z= 0.270 Chirality : 0.037 0.158 2385 Planarity : 0.004 0.030 2770 Dihedral : 13.396 117.028 2610 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.95 % Allowed : 11.27 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.19), residues: 1870 helix: 1.12 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : -0.16 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.021 0.001 TYR C 97 PHE 0.020 0.001 PHE B 248 TRP 0.017 0.002 TRP E 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (16735) covalent geometry : angle 0.51423 / 0.27 (22560) hydrogen bonds : bond 0.05753 / 3.84 ( 965) hydrogen bonds : angle 4.35041 / 3.19 ( 2775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.627 Fit side-chains REVERT: D 72 TYR cc_start: 0.6932 (m-80) cc_final: 0.6297 (m-80) REVERT: D 353 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: D 373 MET cc_start: 0.7984 (mtm) cc_final: 0.7774 (mtm) REVERT: B 376 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6472 (mm110) REVERT: A 68 TYR cc_start: 0.6882 (t80) cc_final: 0.6668 (t80) REVERT: A 72 TYR cc_start: 0.6928 (m-80) cc_final: 0.6604 (m-80) REVERT: A 178 HIS cc_start: 0.8858 (OUTLIER) cc_final: 0.8607 (m-70) REVERT: A 360 MET cc_start: 0.8651 (mmm) cc_final: 0.8209 (mmm) REVERT: A 376 GLN cc_start: 0.6775 (mm-40) cc_final: 0.6415 (mm110) REVERT: E 40 LEU cc_start: 0.8109 (tp) cc_final: 0.7654 (mt) REVERT: E 72 TYR cc_start: 0.6995 (m-80) cc_final: 0.6723 (m-80) REVERT: E 203 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8409 (t70) REVERT: C 203 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8368 (t70) REVERT: C 270 ASP cc_start: 0.7672 (t70) cc_final: 0.7447 (t0) REVERT: C 376 GLN cc_start: 0.6744 (mm-40) cc_final: 0.6317 (mm110) outliers start: 33 outliers final: 12 residues processed: 205 average time/residue: 0.5872 time to fit residues: 133.4911 Evaluate side-chains 185 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 203 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 178 HIS B 369 ASN A 369 ASN E 178 HIS E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096441 restraints weight = 18991.085| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.31 r_work: 0.3017 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16735 Z= 0.224 Angle : 0.606 8.632 22560 Z= 0.318 Chirality : 0.043 0.158 2385 Planarity : 0.005 0.034 2770 Dihedral : 13.415 117.675 2606 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.30 % Allowed : 12.21 % Favored : 85.49 % 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 are not related in a simple way. whole: 1.01 (0.19), residues: 1870 helix: 1.12 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.06 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 125 TYR 0.030 0.002 TYR D 97 PHE 0.031 0.002 PHE E 248 TRP 0.019 0.002 TRP E 309 HIS 0.008 0.002 HIS D 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (16735) covalent geometry : angle 0.60554 / 0.32 (22560) hydrogen bonds : bond 0.06979 / 4.67 ( 965) hydrogen bonds : angle 4.52014 / 3.30 ( 2775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.545 Fit side-chains REVERT: D 72 TYR cc_start: 0.6941 (m-80) cc_final: 0.6289 (m-80) REVERT: D 270 ASP cc_start: 0.7531 (t70) cc_final: 0.7232 (t0) REVERT: D 353 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: B 194 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8581 (tttp) REVERT: A 51 ARG cc_start: 0.7666 (mmt180) cc_final: 0.7345 (mmt90) REVERT: A 72 TYR cc_start: 0.7003 (m-80) cc_final: 0.6753 (m-80) REVERT: A 178 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8622 (m-70) REVERT: E 72 TYR cc_start: 0.7020 (m-80) cc_final: 0.6760 (m-80) REVERT: E 203 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8544 (t70) REVERT: C 51 ARG cc_start: 0.7856 (mmt90) cc_final: 0.7487 (mmt90) REVERT: C 72 TYR cc_start: 0.6972 (m-80) cc_final: 0.6725 (m-80) REVERT: C 203 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (t70) REVERT: C 376 GLN cc_start: 0.6812 (mm-40) cc_final: 0.6395 (mm110) outliers start: 39 outliers final: 13 residues processed: 212 average time/residue: 0.5792 time to fit residues: 136.3486 Evaluate side-chains 190 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 94 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 369 ASN A 369 ASN E 178 HIS E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100492 restraints weight = 18906.194| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.31 r_work: 0.3077 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16735 Z= 0.130 Angle : 0.517 8.093 22560 Z= 0.271 Chirality : 0.038 0.157 2385 Planarity : 0.004 0.031 2770 Dihedral : 12.776 118.091 2606 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.77 % Allowed : 12.98 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 1870 helix: 1.15 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : -0.33 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.022 0.002 TYR E 97 PHE 0.020 0.001 PHE B 248 TRP 0.017 0.002 TRP E 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16735) covalent geometry : angle 0.51687 / 0.27 (22560) hydrogen bonds : bond 0.05794 / 3.87 ( 965) hydrogen bonds : angle 4.33173 / 3.18 ( 2775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.640 Fit side-chains REVERT: D 72 TYR cc_start: 0.6873 (m-80) cc_final: 0.6312 (m-80) REVERT: D 270 ASP cc_start: 0.7578 (t70) cc_final: 0.7279 (t0) REVERT: D 353 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: B 262 LYS cc_start: 0.7270 (mppt) cc_final: 0.6932 (mptt) REVERT: A 51 ARG cc_start: 0.7591 (mmt180) cc_final: 0.7265 (mmt90) REVERT: A 72 TYR cc_start: 0.6907 (m-80) cc_final: 0.6682 (m-80) REVERT: A 360 MET cc_start: 0.8547 (mmm) cc_final: 0.8226 (mmm) REVERT: E 72 TYR cc_start: 0.6995 (m-80) cc_final: 0.6728 (m-80) REVERT: E 203 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8430 (t70) REVERT: C 72 TYR cc_start: 0.6957 (m-80) cc_final: 0.6686 (m-80) REVERT: C 203 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8373 (t70) REVERT: C 270 ASP cc_start: 0.7512 (t0) cc_final: 0.7285 (t0) REVERT: C 376 GLN cc_start: 0.6742 (mm-40) cc_final: 0.6321 (mm110) outliers start: 30 outliers final: 14 residues processed: 205 average time/residue: 0.6254 time to fit residues: 142.1046 Evaluate side-chains 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 203 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 125 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 369 ASN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099785 restraints weight = 18840.151| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.31 r_work: 0.3067 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16735 Z= 0.142 Angle : 0.528 8.085 22560 Z= 0.277 Chirality : 0.038 0.159 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.447 118.671 2604 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.95 % Allowed : 13.39 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 1870 helix: 1.32 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.19 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 25 TYR 0.024 0.002 TYR D 97 PHE 0.023 0.002 PHE D 283 TRP 0.017 0.002 TRP E 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16735) covalent geometry : angle 0.52843 / 0.28 (22560) hydrogen bonds : bond 0.05978 / 3.99 ( 965) hydrogen bonds : angle 4.33556 / 3.18 ( 2775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.648 Fit side-chains REVERT: D 72 TYR cc_start: 0.6878 (m-80) cc_final: 0.6322 (m-80) REVERT: D 270 ASP cc_start: 0.7653 (t70) cc_final: 0.7387 (t0) REVERT: D 353 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: B 51 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7658 (mpt90) REVERT: B 262 LYS cc_start: 0.7331 (mppt) cc_final: 0.6906 (mptt) REVERT: B 376 GLN cc_start: 0.7187 (mt0) cc_final: 0.6942 (mm-40) REVERT: A 51 ARG cc_start: 0.7627 (mmt90) cc_final: 0.7286 (mmt90) REVERT: A 353 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7884 (pt0) REVERT: A 360 MET cc_start: 0.8584 (mmm) cc_final: 0.8252 (mmm) REVERT: E 72 TYR cc_start: 0.7017 (m-80) cc_final: 0.6774 (m-80) REVERT: E 203 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8437 (t70) REVERT: C 51 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7439 (mpt90) REVERT: C 72 TYR cc_start: 0.7013 (m-80) cc_final: 0.6727 (m-80) REVERT: C 203 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8429 (t70) REVERT: C 270 ASP cc_start: 0.7486 (t0) cc_final: 0.7210 (t0) REVERT: C 376 GLN cc_start: 0.6748 (mm-40) cc_final: 0.6319 (mm110) outliers start: 33 outliers final: 17 residues processed: 209 average time/residue: 0.5841 time to fit residues: 135.4439 Evaluate side-chains 198 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 142 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 369 ASN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099534 restraints weight = 18817.386| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.31 r_work: 0.3064 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16735 Z= 0.148 Angle : 0.536 8.191 22560 Z= 0.282 Chirality : 0.039 0.159 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.103 119.591 2604 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.77 % Allowed : 13.75 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 1870 helix: 1.32 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.19 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.024 0.002 TYR C 97 PHE 0.027 0.002 PHE C 283 TRP 0.017 0.002 TRP E 309 HIS 0.005 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (16735) covalent geometry : angle 0.53633 / 0.28 (22560) hydrogen bonds : bond 0.06064 / 4.05 ( 965) hydrogen bonds : angle 4.34281 / 3.18 ( 2775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.674 Fit side-chains REVERT: D 72 TYR cc_start: 0.6833 (m-80) cc_final: 0.6307 (m-80) REVERT: D 270 ASP cc_start: 0.7691 (t70) cc_final: 0.7439 (t0) REVERT: D 353 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: B 51 ARG cc_start: 0.7929 (mmt90) cc_final: 0.7626 (mpt90) REVERT: B 178 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8765 (m-70) REVERT: B 376 GLN cc_start: 0.7125 (mt0) cc_final: 0.6903 (mm-40) REVERT: A 51 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7303 (mmt90) REVERT: A 270 ASP cc_start: 0.7465 (t70) cc_final: 0.7200 (t0) REVERT: E 72 TYR cc_start: 0.7012 (m-80) cc_final: 0.6758 (m-80) REVERT: E 203 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8439 (t70) REVERT: C 51 ARG cc_start: 0.7869 (mmt90) cc_final: 0.7470 (mpt90) REVERT: C 72 TYR cc_start: 0.6912 (m-80) cc_final: 0.6626 (m-80) REVERT: C 203 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8445 (t70) REVERT: C 270 ASP cc_start: 0.7547 (t0) cc_final: 0.7253 (t0) outliers start: 30 outliers final: 16 residues processed: 205 average time/residue: 0.6082 time to fit residues: 138.5546 Evaluate side-chains 198 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 145 optimal weight: 0.9990 chunk 121 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 0.0470 chunk 82 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 369 ASN A 353 GLN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103177 restraints weight = 18845.129| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.32 r_work: 0.3117 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16735 Z= 0.113 Angle : 0.496 7.803 22560 Z= 0.259 Chirality : 0.037 0.159 2385 Planarity : 0.004 0.032 2770 Dihedral : 11.494 119.382 2602 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.36 % Allowed : 14.28 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 1870 helix: 1.46 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.08 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.022 0.001 TYR E 68 PHE 0.027 0.001 PHE D 283 TRP 0.015 0.001 TRP A 309 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (16735) covalent geometry : angle 0.49627 / 0.26 (22560) hydrogen bonds : bond 0.05325 / 3.55 ( 965) hydrogen bonds : angle 4.23559 / 3.11 ( 2775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.614 Fit side-chains REVERT: D 72 TYR cc_start: 0.6815 (m-80) cc_final: 0.6303 (m-80) REVERT: D 270 ASP cc_start: 0.7675 (t70) cc_final: 0.7430 (t0) REVERT: D 353 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: B 376 GLN cc_start: 0.7119 (mt0) cc_final: 0.6904 (mm-40) REVERT: A 51 ARG cc_start: 0.7541 (mmt90) cc_final: 0.7071 (mpt90) REVERT: A 270 ASP cc_start: 0.7492 (t70) cc_final: 0.7226 (t0) REVERT: A 353 GLN cc_start: 0.7861 (pt0) cc_final: 0.7625 (pm20) REVERT: E 72 TYR cc_start: 0.7121 (m-80) cc_final: 0.6812 (m-80) REVERT: C 51 ARG cc_start: 0.7826 (mmt90) cc_final: 0.7595 (mpt90) REVERT: C 72 TYR cc_start: 0.6868 (m-80) cc_final: 0.6604 (m-80) REVERT: C 270 ASP cc_start: 0.7306 (t0) cc_final: 0.7060 (t0) outliers start: 23 outliers final: 13 residues processed: 208 average time/residue: 0.6341 time to fit residues: 146.5483 Evaluate side-chains 196 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 78 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 HIS B 369 ASN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.100237 restraints weight = 18770.774| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.31 r_work: 0.3073 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16735 Z= 0.149 Angle : 0.540 8.335 22560 Z= 0.282 Chirality : 0.039 0.220 2385 Planarity : 0.004 0.034 2770 Dihedral : 11.475 119.262 2600 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.18 % Allowed : 14.22 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1870 helix: 1.37 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.17 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.023 0.002 TYR A 97 PHE 0.036 0.002 PHE C 283 TRP 0.016 0.002 TRP E 309 HIS 0.007 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (16735) covalent geometry : angle 0.54023 / 0.28 (22560) hydrogen bonds : bond 0.05962 / 3.98 ( 965) hydrogen bonds : angle 4.31971 / 3.17 ( 2775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.641 Fit side-chains REVERT: D 72 TYR cc_start: 0.6809 (m-80) cc_final: 0.6306 (m-80) REVERT: D 270 ASP cc_start: 0.7767 (t70) cc_final: 0.7560 (t0) REVERT: D 353 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: B 51 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7684 (mpt90) REVERT: B 376 GLN cc_start: 0.7144 (mt0) cc_final: 0.6920 (mm-40) REVERT: A 51 ARG cc_start: 0.7563 (mmt90) cc_final: 0.7251 (mmt90) REVERT: A 214 MET cc_start: 0.8488 (tpt) cc_final: 0.8232 (mmm) REVERT: A 270 ASP cc_start: 0.7589 (t70) cc_final: 0.7338 (t0) REVERT: E 72 TYR cc_start: 0.7085 (m-80) cc_final: 0.6810 (m-80) REVERT: C 51 ARG cc_start: 0.7804 (mmt90) cc_final: 0.7582 (mpt90) REVERT: C 72 TYR cc_start: 0.6857 (m-80) cc_final: 0.6588 (m-80) REVERT: C 270 ASP cc_start: 0.7458 (t0) cc_final: 0.7205 (t0) outliers start: 20 outliers final: 14 residues processed: 194 average time/residue: 0.5932 time to fit residues: 127.6107 Evaluate side-chains 189 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 149 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 0.0980 chunk 112 optimal weight: 0.0970 chunk 175 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 369 ASN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105121 restraints weight = 18831.148| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.32 r_work: 0.3146 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16735 Z= 0.106 Angle : 0.488 8.507 22560 Z= 0.254 Chirality : 0.037 0.158 2385 Planarity : 0.004 0.031 2770 Dihedral : 10.993 118.097 2600 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.65 % Allowed : 14.87 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 1870 helix: 1.47 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.07 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.023 0.001 TYR D 68 PHE 0.028 0.001 PHE C 283 TRP 0.014 0.001 TRP E 94 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (16735) covalent geometry : angle 0.48803 / 0.25 (22560) hydrogen bonds : bond 0.05100 / 3.40 ( 965) hydrogen bonds : angle 4.20430 / 3.09 ( 2775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5631.14 seconds wall clock time: 96 minutes 52.18 seconds (5812.18 seconds total)