Starting phenix.real_space_refine on Wed Mar 4 21:13:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1k_27133/03_2026/8d1k_27133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1k_27133/03_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_27133/03_2026/8d1k_27133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1k_27133/03_2026/8d1k_27133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d1k_27133/03_2026/8d1k_27133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1k_27133/03_2026/8d1k_27133.map" } 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-5986/lib/python3.9/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: 200 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: 200 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: 209 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: 191 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: 200 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: 3.24, per 1000 atoms: 0.20 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: 1.31 Conformation dependent library (CDL) restraints added in 510.0 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: 0.41 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: 2.16 Time building geometry restraints manager: 1.68 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: 9055 23.97 - 47.93: 655 47.93 - 71.90: 185 71.90 - 95.86: 35 95.86 - 119.83: 5 Dihedral angle restraints: 9935 sinusoidal: 4370 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 9932 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: 3.780 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.280 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 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 : 18.326 119.825 6345 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 covalent geometry : bond 0.01297 (16735) covalent geometry : angle 1.27536 (22560) hydrogen bonds : bond 0.14685 ( 965) hydrogen bonds : angle 5.48454 ( 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 : 0.632 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: 0.6863 time to fit residues: 176.9910 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 : 0.490 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3534 r_free = 0.3534 target = 0.126286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100783 restraints weight = 18799.932| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.32 r_work: 0.3079 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1248 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= 0.134 Angle : 0.536 8.031 22560 Z= 0.284 Chirality : 0.038 0.160 2385 Planarity : 0.004 0.025 2770 Dihedral : 14.946 116.777 2670 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.47 % Allowed : 10.91 % Favored : 87.61 % 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: 1.16 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : 0.27 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 47 TYR 0.021 0.002 TYR C 97 PHE 0.020 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 covalent geometry : bond 0.00272 (16735) covalent geometry : angle 0.53609 (22560) hydrogen bonds : bond 0.06097 ( 965) hydrogen bonds : angle 4.42501 ( 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 208 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.638 Fit side-chains REVERT: D 262 LYS cc_start: 0.7021 (mmtm) cc_final: 0.6763 (mppt) REVERT: D 376 GLN cc_start: 0.6714 (mm-40) cc_final: 0.6360 (mm110) REVERT: B 68 TYR cc_start: 0.6724 (t80) cc_final: 0.6477 (t80) REVERT: B 376 GLN cc_start: 0.6906 (mm-40) cc_final: 0.6549 (mm110) REVERT: A 72 TYR cc_start: 0.6967 (m-80) cc_final: 0.6672 (m-10) REVERT: A 353 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: A 360 MET cc_start: 0.8738 (mmm) cc_final: 0.8487 (mmm) REVERT: A 376 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6300 (mm110) REVERT: E 51 ARG cc_start: 0.7761 (mmt90) cc_final: 0.7521 (mpt90) REVERT: E 56 GLU cc_start: 0.6777 (mp0) cc_final: 0.6040 (pt0) REVERT: E 68 TYR cc_start: 0.6981 (t80) cc_final: 0.6598 (t80) REVERT: E 72 TYR cc_start: 0.6815 (m-80) cc_final: 0.6603 (m-10) REVERT: E 259 ASN cc_start: 0.7069 (m-40) cc_final: 0.6771 (m110) REVERT: E 373 MET cc_start: 0.8079 (mtt) cc_final: 0.7792 (mtp) REVERT: C 72 TYR cc_start: 0.6855 (m-80) cc_final: 0.6591 (m-80) REVERT: C 376 GLN cc_start: 0.6739 (mm-40) cc_final: 0.6390 (mm110) outliers start: 25 outliers final: 13 residues processed: 206 average time/residue: 0.6775 time to fit residues: 153.3127 Evaluate side-chains 184 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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: 3.9990 chunk 94 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3510 r_free = 0.3510 target = 0.124447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098830 restraints weight = 18971.812| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.32 r_work: 0.3052 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16735 Z= 0.156 Angle : 0.544 8.291 22560 Z= 0.288 Chirality : 0.039 0.157 2385 Planarity : 0.004 0.030 2770 Dihedral : 14.382 114.234 2660 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.77 % Allowed : 10.62 % Favored : 87.61 % 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: 1.13 (0.19), residues: 1870 helix: 1.16 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : 0.04 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.025 0.002 TYR C 97 PHE 0.025 0.002 PHE B 248 TRP 0.018 0.002 TRP E 309 HIS 0.005 0.002 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00340 (16735) covalent geometry : angle 0.54392 (22560) hydrogen bonds : bond 0.06324 ( 965) hydrogen bonds : angle 4.38980 ( 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 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.603 Fit side-chains REVERT: D 72 TYR cc_start: 0.7006 (m-10) cc_final: 0.6484 (m-80) REVERT: D 178 HIS cc_start: 0.8906 (OUTLIER) cc_final: 0.8607 (m-70) REVERT: B 194 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8545 (ttmp) REVERT: B 376 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6519 (mm110) REVERT: A 72 TYR cc_start: 0.6912 (m-80) cc_final: 0.6607 (m-10) REVERT: A 214 MET cc_start: 0.8569 (tpt) cc_final: 0.8314 (mmm) REVERT: A 360 MET cc_start: 0.8732 (mmm) cc_final: 0.8469 (mmm) REVERT: A 376 GLN cc_start: 0.6719 (mm-40) cc_final: 0.6328 (mm110) REVERT: E 8 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: E 68 TYR cc_start: 0.7001 (t80) cc_final: 0.6298 (t80) REVERT: E 203 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8425 (t70) REVERT: C 51 ARG cc_start: 0.7737 (mmt90) cc_final: 0.7312 (mmt90) REVERT: C 72 TYR cc_start: 0.6938 (m-80) cc_final: 0.6599 (m-80) REVERT: C 376 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6348 (mm110) outliers start: 30 outliers final: 13 residues processed: 211 average time/residue: 0.6618 time to fit residues: 153.5321 Evaluate side-chains 185 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 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 178 HIS 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 8 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 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: 10.0000 chunk 182 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3543 r_free = 0.3543 target = 0.127099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101784 restraints weight = 18867.840| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.32 r_work: 0.3097 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16735 Z= 0.119 Angle : 0.494 7.960 22560 Z= 0.261 Chirality : 0.037 0.156 2385 Planarity : 0.004 0.031 2770 Dihedral : 13.882 111.746 2660 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.71 % Allowed : 11.33 % Favored : 86.96 % 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: 1.33 (0.19), residues: 1870 helix: 1.33 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.13 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.020 0.001 TYR C 97 PHE 0.018 0.001 PHE B 248 TRP 0.015 0.001 TRP E 309 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00241 (16735) covalent geometry : angle 0.49432 (22560) hydrogen bonds : bond 0.05608 ( 965) hydrogen bonds : angle 4.27377 ( 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 215 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.546 Fit side-chains REVERT: D 72 TYR cc_start: 0.6833 (m-10) cc_final: 0.6459 (m-80) REVERT: D 353 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7832 (pt0) REVERT: B 40 LEU cc_start: 0.8212 (tp) cc_final: 0.7744 (mt) REVERT: B 376 GLN cc_start: 0.6905 (mm-40) cc_final: 0.6512 (mm110) REVERT: A 51 ARG cc_start: 0.7693 (mmt90) cc_final: 0.7375 (mmt90) REVERT: A 72 TYR cc_start: 0.6919 (m-80) cc_final: 0.6716 (m-80) REVERT: A 178 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8535 (m-70) REVERT: A 360 MET cc_start: 0.8617 (mmm) cc_final: 0.8307 (mmm) REVERT: A 376 GLN cc_start: 0.6568 (mm-40) cc_final: 0.6275 (mm110) REVERT: E 40 LEU cc_start: 0.8151 (tp) cc_final: 0.7720 (mt) REVERT: E 51 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7600 (mmt90) REVERT: E 68 TYR cc_start: 0.7122 (t80) cc_final: 0.6450 (t80) REVERT: E 203 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8421 (t70) REVERT: E 331 ARG cc_start: 0.8049 (ttp-110) cc_final: 0.7836 (ttp-110) REVERT: C 376 GLN cc_start: 0.6656 (mm-40) cc_final: 0.6333 (mm110) outliers start: 29 outliers final: 12 residues processed: 210 average time/residue: 0.6422 time to fit residues: 148.7306 Evaluate side-chains 188 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 HIS B 369 ASN A 353 GLN A 369 ASN E 178 HIS E 369 ASN E 376 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 = 0.3484 r_free = 0.3484 target = 0.122425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096804 restraints weight = 18930.276| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.32 r_work: 0.3022 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16735 Z= 0.210 Angle : 0.594 8.445 22560 Z= 0.313 Chirality : 0.042 0.158 2385 Planarity : 0.005 0.037 2770 Dihedral : 13.927 112.064 2656 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.89 % Allowed : 11.86 % Favored : 86.25 % 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: 1.05 (0.19), residues: 1870 helix: 1.11 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : -0.01 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 25 TYR 0.029 0.002 TYR C 97 PHE 0.030 0.002 PHE B 248 TRP 0.018 0.002 TRP E 309 HIS 0.007 0.002 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00480 (16735) covalent geometry : angle 0.59368 (22560) hydrogen bonds : bond 0.06894 ( 965) hydrogen bonds : angle 4.48699 ( 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 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.635 Fit side-chains REVERT: D 8 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: D 72 TYR cc_start: 0.6907 (m-10) cc_final: 0.6522 (m-80) REVERT: D 270 ASP cc_start: 0.7586 (t70) cc_final: 0.7312 (t0) REVERT: D 353 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: B 194 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8588 (tttp) REVERT: A 51 ARG cc_start: 0.7737 (mmt90) cc_final: 0.7325 (mmt90) REVERT: A 72 TYR cc_start: 0.6987 (m-80) cc_final: 0.6746 (m-80) REVERT: A 178 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8615 (m-70) REVERT: A 262 LYS cc_start: 0.7257 (mppt) cc_final: 0.6965 (mptt) REVERT: A 360 MET cc_start: 0.8761 (mmm) cc_final: 0.8255 (mmm) REVERT: A 376 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6372 (mm110) REVERT: E 72 TYR cc_start: 0.7030 (m-80) cc_final: 0.6788 (m-80) REVERT: E 203 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8531 (t70) REVERT: C 72 TYR cc_start: 0.6904 (m-80) cc_final: 0.6575 (m-80) REVERT: C 373 MET cc_start: 0.8035 (mtm) cc_final: 0.7798 (mtm) REVERT: C 376 GLN cc_start: 0.6762 (mm-40) cc_final: 0.6378 (mm110) outliers start: 32 outliers final: 14 residues processed: 208 average time/residue: 0.6880 time to fit residues: 157.1967 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 GLN 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 B residue 194 LYS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 235 VAL 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 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: 0.8980 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 118 optimal weight: 0.0070 chunk 149 optimal weight: 0.0370 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 GLN A 353 GLN A 369 ASN E 178 HIS E 369 ASN E 376 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 = 0.3559 r_free = 0.3559 target = 0.128367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103208 restraints weight = 18882.466| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.32 r_work: 0.3119 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16735 Z= 0.110 Angle : 0.486 7.880 22560 Z= 0.255 Chirality : 0.037 0.157 2385 Planarity : 0.004 0.031 2770 Dihedral : 12.953 108.019 2656 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.89 % Allowed : 12.27 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.19), residues: 1870 helix: 1.34 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.03 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.020 0.001 TYR D 68 PHE 0.018 0.001 PHE C 283 TRP 0.015 0.001 TRP A 309 HIS 0.003 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00215 (16735) covalent geometry : angle 0.48646 (22560) hydrogen bonds : bond 0.05314 ( 965) hydrogen bonds : angle 4.25490 ( 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 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.491 Fit side-chains REVERT: D 40 LEU cc_start: 0.8152 (tp) cc_final: 0.7666 (mt) REVERT: D 72 TYR cc_start: 0.6846 (m-10) cc_final: 0.6490 (m-80) REVERT: D 270 ASP cc_start: 0.7665 (t70) cc_final: 0.7403 (t0) REVERT: D 353 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: D 373 MET cc_start: 0.8012 (mtm) cc_final: 0.7802 (mtm) REVERT: B 40 LEU cc_start: 0.8199 (tp) cc_final: 0.7724 (mt) REVERT: B 262 LYS cc_start: 0.7121 (mppt) cc_final: 0.6841 (mptt) REVERT: A 51 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7345 (mmt90) REVERT: A 72 TYR cc_start: 0.6916 (m-80) cc_final: 0.6697 (m-80) REVERT: A 214 MET cc_start: 0.8348 (tpt) cc_final: 0.8129 (mmm) REVERT: A 262 LYS cc_start: 0.7128 (mppt) cc_final: 0.6807 (mptt) REVERT: A 360 MET cc_start: 0.8564 (mmm) cc_final: 0.8254 (mmm) REVERT: E 40 LEU cc_start: 0.8103 (tp) cc_final: 0.7586 (mt) REVERT: E 68 TYR cc_start: 0.7143 (t80) cc_final: 0.6575 (t80) REVERT: E 72 TYR cc_start: 0.7036 (m-80) cc_final: 0.6835 (m-80) REVERT: E 203 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8396 (t70) REVERT: C 72 TYR cc_start: 0.6912 (m-80) cc_final: 0.6672 (m-80) REVERT: C 373 MET cc_start: 0.8057 (mtm) cc_final: 0.7830 (mtm) REVERT: C 376 GLN cc_start: 0.6683 (mm-40) cc_final: 0.6247 (mm110) outliers start: 32 outliers final: 14 residues processed: 223 average time/residue: 0.6084 time to fit residues: 150.0588 Evaluate side-chains 201 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 45 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 235 VAL 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 235 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 101 optimal weight: 0.0980 chunk 125 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 GLN A 178 HIS A 369 ASN 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 = 0.3525 r_free = 0.3525 target = 0.125764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100275 restraints weight = 18821.839| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.32 r_work: 0.3075 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1831 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= 0.139 Angle : 0.520 8.006 22560 Z= 0.273 Chirality : 0.038 0.157 2385 Planarity : 0.004 0.034 2770 Dihedral : 12.557 104.481 2650 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.59 % Allowed : 12.63 % Favored : 85.78 % 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: 1.41 (0.19), residues: 1870 helix: 1.43 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.024 0.002 TYR D 97 PHE 0.025 0.002 PHE C 283 TRP 0.016 0.002 TRP E 309 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00299 (16735) covalent geometry : angle 0.52031 (22560) hydrogen bonds : bond 0.05909 ( 965) hydrogen bonds : angle 4.28213 ( 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 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.660 Fit side-chains REVERT: D 72 TYR cc_start: 0.6964 (m-10) cc_final: 0.6491 (m-80) REVERT: D 270 ASP cc_start: 0.7703 (t70) cc_final: 0.7446 (t0) REVERT: D 353 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: A 51 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7350 (mmt90) REVERT: A 72 TYR cc_start: 0.6929 (m-80) cc_final: 0.6679 (m-80) REVERT: A 262 LYS cc_start: 0.7016 (mppt) cc_final: 0.6811 (mptt) REVERT: A 360 MET cc_start: 0.8651 (mmm) cc_final: 0.8324 (mmm) REVERT: E 40 LEU cc_start: 0.8150 (tp) cc_final: 0.7624 (mt) REVERT: E 72 TYR cc_start: 0.6972 (m-80) cc_final: 0.6758 (m-80) REVERT: E 203 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8395 (t70) REVERT: C 72 TYR cc_start: 0.7001 (m-80) cc_final: 0.6767 (m-80) REVERT: C 270 ASP cc_start: 0.7564 (t0) cc_final: 0.7335 (t0) REVERT: C 376 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6264 (mm110) outliers start: 27 outliers final: 13 residues processed: 207 average time/residue: 0.5841 time to fit residues: 134.1672 Evaluate side-chains 191 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 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 45 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 235 VAL 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 129 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 142 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 GLN 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 = 0.3536 r_free = 0.3536 target = 0.126631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101207 restraints weight = 18807.533| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.32 r_work: 0.3088 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16735 Z= 0.129 Angle : 0.514 8.026 22560 Z= 0.269 Chirality : 0.038 0.159 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.219 101.147 2650 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.53 % Allowed : 13.22 % 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: 1.35 (0.19), residues: 1870 helix: 1.39 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.01 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 25 TYR 0.022 0.002 TYR D 68 PHE 0.028 0.001 PHE C 283 TRP 0.015 0.001 TRP E 309 HIS 0.004 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00272 (16735) covalent geometry : angle 0.51351 (22560) hydrogen bonds : bond 0.05708 ( 965) hydrogen bonds : angle 4.25154 ( 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 206 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.614 Fit side-chains REVERT: D 72 TYR cc_start: 0.6928 (m-10) cc_final: 0.6443 (m-80) REVERT: D 270 ASP cc_start: 0.7651 (t70) cc_final: 0.7424 (t0) REVERT: D 353 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: B 262 LYS cc_start: 0.7034 (mppt) cc_final: 0.6761 (mptt) REVERT: A 51 ARG cc_start: 0.7740 (mmt90) cc_final: 0.7359 (mmt90) REVERT: A 72 TYR cc_start: 0.6918 (m-80) cc_final: 0.6689 (m-80) REVERT: A 360 MET cc_start: 0.8603 (mmm) cc_final: 0.8280 (mmm) REVERT: E 40 LEU cc_start: 0.8139 (tp) cc_final: 0.7867 (tt) REVERT: E 72 TYR cc_start: 0.6969 (m-80) cc_final: 0.6758 (m-80) REVERT: E 203 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8432 (t70) REVERT: C 72 TYR cc_start: 0.6929 (m-80) cc_final: 0.6692 (m-80) REVERT: C 270 ASP cc_start: 0.7627 (t0) cc_final: 0.7397 (t0) REVERT: C 376 GLN cc_start: 0.6715 (mm-40) cc_final: 0.6257 (mm110) outliers start: 26 outliers final: 15 residues processed: 199 average time/residue: 0.6002 time to fit residues: 132.0026 Evaluate side-chains 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 235 VAL 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 A residue 75 LEU Chi-restraints excluded: chain A residue 235 VAL 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 235 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 145 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 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 = 0.3512 r_free = 0.3512 target = 0.124755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099168 restraints weight = 18864.188| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.32 r_work: 0.3057 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16735 Z= 0.161 Angle : 0.550 8.157 22560 Z= 0.289 Chirality : 0.040 0.157 2385 Planarity : 0.004 0.034 2770 Dihedral : 12.288 99.549 2650 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.65 % Allowed : 13.51 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 1870 helix: 1.37 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.09 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 25 TYR 0.025 0.002 TYR D 97 PHE 0.034 0.002 PHE C 283 TRP 0.016 0.002 TRP E 309 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00356 (16735) covalent geometry : angle 0.55020 (22560) hydrogen bonds : bond 0.06206 ( 965) hydrogen bonds : angle 4.34132 ( 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 207 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.626 Fit side-chains REVERT: D 72 TYR cc_start: 0.7004 (m-10) cc_final: 0.6502 (m-80) REVERT: D 270 ASP cc_start: 0.7699 (t70) cc_final: 0.7494 (t0) REVERT: D 353 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: A 51 ARG cc_start: 0.7712 (mmt90) cc_final: 0.7307 (mmt90) REVERT: A 72 TYR cc_start: 0.6906 (m-80) cc_final: 0.6684 (m-80) REVERT: A 214 MET cc_start: 0.8524 (tpt) cc_final: 0.8259 (mmm) REVERT: A 360 MET cc_start: 0.8693 (mmm) cc_final: 0.8385 (mmm) REVERT: E 72 TYR cc_start: 0.7001 (m-80) cc_final: 0.6758 (m-80) REVERT: E 203 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8449 (t70) REVERT: C 72 TYR cc_start: 0.6854 (m-80) cc_final: 0.6586 (m-80) REVERT: C 270 ASP cc_start: 0.7671 (t0) cc_final: 0.7453 (t0) outliers start: 28 outliers final: 16 residues processed: 200 average time/residue: 0.6584 time to fit residues: 145.6536 Evaluate side-chains 192 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 336 MET Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 235 VAL 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 307 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 78 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 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 = 0.3517 r_free = 0.3517 target = 0.125181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099693 restraints weight = 18769.716| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.31 r_work: 0.3065 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16735 Z= 0.153 Angle : 0.546 8.136 22560 Z= 0.287 Chirality : 0.039 0.158 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.235 97.920 2650 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.24 % Allowed : 13.86 % Favored : 84.90 % 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: 1.19 (0.18), residues: 1870 helix: 1.34 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.16 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 25 TYR 0.024 0.002 TYR E 97 PHE 0.034 0.002 PHE C 283 TRP 0.016 0.002 TRP E 309 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00336 (16735) covalent geometry : angle 0.54592 (22560) hydrogen bonds : bond 0.06082 ( 965) hydrogen bonds : angle 4.34142 ( 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 202 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.627 Fit side-chains REVERT: D 72 TYR cc_start: 0.6987 (m-10) cc_final: 0.6476 (m-80) REVERT: D 270 ASP cc_start: 0.7720 (t70) cc_final: 0.7514 (t0) REVERT: D 353 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: B 72 TYR cc_start: 0.6973 (m-80) cc_final: 0.6722 (m-10) REVERT: B 262 LYS cc_start: 0.7133 (mppt) cc_final: 0.6738 (mptt) REVERT: A 51 ARG cc_start: 0.7714 (mmt90) cc_final: 0.7351 (mmt90) REVERT: A 214 MET cc_start: 0.8521 (tpt) cc_final: 0.8259 (mmm) REVERT: A 270 ASP cc_start: 0.7553 (t70) cc_final: 0.7311 (t0) REVERT: A 360 MET cc_start: 0.8678 (mmm) cc_final: 0.8390 (mmm) REVERT: E 72 TYR cc_start: 0.6984 (m-80) cc_final: 0.6776 (m-80) REVERT: E 203 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8441 (t70) REVERT: C 72 TYR cc_start: 0.6880 (m-80) cc_final: 0.6614 (m-80) REVERT: C 270 ASP cc_start: 0.7694 (t0) cc_final: 0.7469 (t0) outliers start: 21 outliers final: 14 residues processed: 197 average time/residue: 0.6551 time to fit residues: 142.7470 Evaluate side-chains 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 336 MET Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 235 VAL 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 307 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 149 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 112 optimal weight: 0.0470 chunk 175 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 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 = 0.3555 r_free = 0.3555 target = 0.128160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102909 restraints weight = 18820.764| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.32 r_work: 0.3114 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16735 Z= 0.117 Angle : 0.503 7.819 22560 Z= 0.263 Chirality : 0.037 0.159 2385 Planarity : 0.004 0.032 2770 Dihedral : 11.882 97.190 2650 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.18 % Allowed : 13.98 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 1870 helix: 1.47 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.03 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.021 0.001 TYR A 68 PHE 0.030 0.001 PHE C 283 TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00238 (16735) covalent geometry : angle 0.50304 (22560) hydrogen bonds : bond 0.05409 ( 965) hydrogen bonds : angle 4.24160 ( 2775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5645.03 seconds wall clock time: 96 minutes 53.28 seconds (5813.28 seconds total)