Starting phenix.real_space_refine on Sat Jun 14 19:00:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1k_27133/06_2025/8d1k_27133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1k_27133/06_2025/8d1k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d1k_27133/06_2025/8d1k_27133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1k_27133/06_2025/8d1k_27133.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1k_27133/06_2025/8d1k_27133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1k_27133/06_2025/8d1k_27133.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 11.34, per 1000 atoms: 0.70 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: 4.39 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.45 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: 4.79 Time building geometry restraints manager: 5.19 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.390 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.054 0.011 TRP A 309 HIS 0.007 0.003 HIS C 267 PHE 0.028 0.006 PHE E 162 TYR 0.051 0.008 TYR D 97 ARG 0.035 0.003 ARG E 313 Details of bonding type rmsd hydrogen bonds : bond 0.14685 ( 965) hydrogen bonds : angle 5.48454 ( 2775) covalent geometry : bond 0.01297 (16735) covalent geometry : angle 1.27536 (22560) *********************** 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 : 1.980 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: 1.4412 time to fit residues: 373.0934 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 : 1.910 ------------------------------------------------------------------------------- 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 156 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.0170 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.126442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100978 restraints weight = 18778.340| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.32 r_work: 0.3082 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1273 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= 0.130 Angle : 0.539 8.222 22560 Z= 0.285 Chirality : 0.038 0.160 2385 Planarity : 0.004 0.025 2770 Dihedral : 14.954 117.204 2670 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.47 % Allowed : 10.74 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1870 helix: 1.15 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : 0.26 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 309 HIS 0.004 0.001 HIS C 178 PHE 0.021 0.002 PHE A 276 TYR 0.021 0.002 TYR C 97 ARG 0.005 0.001 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.06022 ( 965) hydrogen bonds : angle 4.42429 ( 2775) covalent geometry : bond 0.00268 (16735) covalent geometry : angle 0.53921 (22560) *********************** 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 : 2.050 Fit side-chains REVERT: D 262 LYS cc_start: 0.7034 (mmtm) cc_final: 0.6795 (mppt) REVERT: D 376 GLN cc_start: 0.6710 (mm-40) cc_final: 0.6352 (mm110) REVERT: B 68 TYR cc_start: 0.6722 (t80) cc_final: 0.6438 (t80) REVERT: B 376 GLN cc_start: 0.6905 (mm-40) cc_final: 0.6547 (mm110) REVERT: A 72 TYR cc_start: 0.6968 (m-80) cc_final: 0.6634 (m-10) REVERT: A 353 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: A 360 MET cc_start: 0.8741 (mmm) cc_final: 0.8494 (mmm) REVERT: A 376 GLN cc_start: 0.6681 (mm-40) cc_final: 0.6296 (mm110) REVERT: E 51 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7517 (mpt90) REVERT: E 56 GLU cc_start: 0.6718 (mp0) cc_final: 0.6012 (pt0) REVERT: E 68 TYR cc_start: 0.6976 (t80) cc_final: 0.6605 (t80) REVERT: E 72 TYR cc_start: 0.6817 (m-80) cc_final: 0.6589 (m-10) REVERT: E 259 ASN cc_start: 0.7097 (m-40) cc_final: 0.6791 (m110) REVERT: E 373 MET cc_start: 0.8041 (mtt) cc_final: 0.7749 (mtp) REVERT: C 72 TYR cc_start: 0.6865 (m-80) cc_final: 0.6613 (m-10) REVERT: C 376 GLN cc_start: 0.6738 (mm-40) cc_final: 0.6386 (mm110) outliers start: 25 outliers final: 13 residues processed: 206 average time/residue: 1.7174 time to fit residues: 389.3687 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 : 1.787 ------------------------------------------------------------------------------- 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 167 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.123887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098306 restraints weight = 18678.853| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.31 r_work: 0.3043 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16735 Z= 0.164 Angle : 0.557 8.279 22560 Z= 0.295 Chirality : 0.040 0.157 2385 Planarity : 0.004 0.036 2770 Dihedral : 14.377 113.984 2660 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.83 % Allowed : 10.74 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1870 helix: 1.16 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.11 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 309 HIS 0.005 0.002 HIS C 178 PHE 0.026 0.002 PHE B 248 TYR 0.027 0.002 TYR C 97 ARG 0.004 0.000 ARG C 25 Details of bonding type rmsd hydrogen bonds : bond 0.06487 ( 965) hydrogen bonds : angle 4.40815 ( 2775) covalent geometry : bond 0.00362 (16735) covalent geometry : angle 0.55675 (22560) *********************** 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 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 2.307 Fit side-chains REVERT: D 8 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: D 72 TYR cc_start: 0.7011 (m-10) cc_final: 0.6491 (m-80) REVERT: B 194 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8552 (ttmp) REVERT: B 376 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6537 (mm110) REVERT: A 51 ARG cc_start: 0.7476 (mmt180) cc_final: 0.7174 (mmt90) REVERT: A 72 TYR cc_start: 0.6822 (m-80) cc_final: 0.6519 (m-80) REVERT: A 353 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: A 360 MET cc_start: 0.8739 (mmm) cc_final: 0.8273 (mmm) REVERT: A 376 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6398 (mm110) REVERT: E 72 TYR cc_start: 0.6974 (m-80) cc_final: 0.6684 (m-80) REVERT: E 203 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8450 (t70) REVERT: C 51 ARG cc_start: 0.7762 (mmt90) cc_final: 0.7339 (mmt90) REVERT: C 72 TYR cc_start: 0.6974 (m-80) cc_final: 0.6751 (m-80) REVERT: C 376 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6321 (mm110) outliers start: 31 outliers final: 13 residues processed: 216 average time/residue: 1.6464 time to fit residues: 392.2088 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 : 2.053 ------------------------------------------------------------------------------- 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 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 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 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 64 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 168 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 118 optimal weight: 0.0270 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 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 = 0.3545 r_free = 0.3545 target = 0.127270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102005 restraints weight = 18833.766| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.32 r_work: 0.3100 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16735 Z= 0.118 Angle : 0.493 7.980 22560 Z= 0.260 Chirality : 0.037 0.158 2385 Planarity : 0.004 0.030 2770 Dihedral : 13.848 112.357 2658 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.59 % Allowed : 11.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 1870 helix: 1.32 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.10 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 309 HIS 0.005 0.001 HIS D 178 PHE 0.018 0.001 PHE B 248 TYR 0.020 0.001 TYR C 97 ARG 0.003 0.000 ARG D 47 Details of bonding type rmsd hydrogen bonds : bond 0.05560 ( 965) hydrogen bonds : angle 4.27882 ( 2775) covalent geometry : bond 0.00239 (16735) covalent geometry : angle 0.49325 (22560) *********************** 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 208 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.987 Fit side-chains REVERT: D 51 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7546 (mmt90) REVERT: D 72 TYR cc_start: 0.6758 (m-10) cc_final: 0.6438 (m-80) REVERT: D 373 MET cc_start: 0.7974 (mtm) cc_final: 0.7763 (mtm) REVERT: B 40 LEU cc_start: 0.8210 (tp) cc_final: 0.7737 (mt) REVERT: B 376 GLN cc_start: 0.6860 (mm-40) cc_final: 0.6479 (mm110) REVERT: A 51 ARG cc_start: 0.7518 (mmt180) cc_final: 0.7021 (mpt90) REVERT: A 72 TYR cc_start: 0.6962 (m-80) cc_final: 0.6759 (m-80) REVERT: A 360 MET cc_start: 0.8590 (mmm) cc_final: 0.8298 (mmm) REVERT: A 376 GLN cc_start: 0.6634 (mm-40) cc_final: 0.6298 (mm110) REVERT: E 40 LEU cc_start: 0.8139 (tp) cc_final: 0.7697 (mt) REVERT: E 51 ARG cc_start: 0.7903 (mmt90) cc_final: 0.7546 (mmt90) REVERT: E 72 TYR cc_start: 0.7110 (m-80) cc_final: 0.6799 (m-80) REVERT: E 203 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8420 (t70) REVERT: E 270 ASP cc_start: 0.7691 (t0) cc_final: 0.7471 (t0) REVERT: E 331 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7842 (ttp-110) REVERT: C 376 GLN cc_start: 0.6647 (mm-40) cc_final: 0.6319 (mm110) outliers start: 27 outliers final: 12 residues processed: 204 average time/residue: 1.3032 time to fit residues: 295.0305 Evaluate side-chains 183 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE 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 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 131 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 178 HIS 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 = 0.3501 r_free = 0.3501 target = 0.123754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098190 restraints weight = 19080.981| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.32 r_work: 0.3043 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16735 Z= 0.174 Angle : 0.553 8.204 22560 Z= 0.292 Chirality : 0.040 0.158 2385 Planarity : 0.004 0.033 2770 Dihedral : 13.627 111.294 2654 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.83 % Allowed : 12.15 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1870 helix: 1.21 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.06 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 309 HIS 0.006 0.001 HIS A 178 PHE 0.027 0.002 PHE B 248 TYR 0.027 0.002 TYR C 97 ARG 0.004 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.06452 ( 965) hydrogen bonds : angle 4.39221 ( 2775) covalent geometry : bond 0.00389 (16735) covalent geometry : angle 0.55289 (22560) *********************** 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 212 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.965 Fit side-chains REVERT: D 8 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: D 72 TYR cc_start: 0.6928 (m-10) cc_final: 0.6530 (m-80) REVERT: D 270 ASP cc_start: 0.7542 (t70) cc_final: 0.7265 (t0) REVERT: D 373 MET cc_start: 0.8035 (mtm) cc_final: 0.7835 (mtm) REVERT: B 194 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8546 (ttmp) REVERT: A 51 ARG cc_start: 0.7585 (mmt180) cc_final: 0.7102 (mpt90) REVERT: A 72 TYR cc_start: 0.6934 (m-80) cc_final: 0.6693 (m-80) REVERT: A 360 MET cc_start: 0.8729 (mmm) cc_final: 0.8461 (mmm) REVERT: A 376 GLN cc_start: 0.6775 (mm-40) cc_final: 0.6402 (mm110) REVERT: E 51 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7603 (mmt90) REVERT: E 72 TYR cc_start: 0.7068 (m-80) cc_final: 0.6768 (m-80) REVERT: E 203 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8482 (t70) REVERT: C 51 ARG cc_start: 0.7821 (mmt90) cc_final: 0.7428 (mmt90) REVERT: C 72 TYR cc_start: 0.6967 (m-80) cc_final: 0.6673 (m-80) REVERT: C 214 MET cc_start: 0.8579 (tpt) cc_final: 0.8279 (mmm) REVERT: C 373 MET cc_start: 0.8005 (mtm) cc_final: 0.7775 (mtm) REVERT: C 376 GLN cc_start: 0.6755 (mm-40) cc_final: 0.6326 (mm110) outliers start: 31 outliers final: 14 residues processed: 208 average time/residue: 1.7638 time to fit residues: 405.1823 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 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 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 109 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.125017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099615 restraints weight = 18867.586| |-----------------------------------------------------------------------------| r_work (start): 0.3160 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: 3.14 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1738 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= 0.147 Angle : 0.527 8.148 22560 Z= 0.278 Chirality : 0.039 0.157 2385 Planarity : 0.004 0.032 2770 Dihedral : 13.172 108.698 2654 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.77 % Allowed : 12.51 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 1870 helix: 1.18 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : -0.20 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 309 HIS 0.004 0.001 HIS C 178 PHE 0.023 0.002 PHE B 248 TYR 0.024 0.002 TYR C 97 ARG 0.003 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.06051 ( 965) hydrogen bonds : angle 4.33906 ( 2775) covalent geometry : bond 0.00319 (16735) covalent geometry : angle 0.52747 (22560) *********************** 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 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 1.861 Fit side-chains REVERT: D 8 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: D 51 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7648 (mpt90) REVERT: D 72 TYR cc_start: 0.6890 (m-10) cc_final: 0.6490 (m-80) REVERT: D 270 ASP cc_start: 0.7692 (t70) cc_final: 0.7403 (t0) REVERT: B 262 LYS cc_start: 0.7310 (mppt) cc_final: 0.6992 (mptt) REVERT: A 51 ARG cc_start: 0.7513 (mmt180) cc_final: 0.7020 (mpt90) REVERT: A 72 TYR cc_start: 0.6914 (m-80) cc_final: 0.6677 (m-80) REVERT: A 360 MET cc_start: 0.8687 (mmm) cc_final: 0.8411 (mmm) REVERT: E 72 TYR cc_start: 0.7080 (m-80) cc_final: 0.6794 (m-80) REVERT: E 203 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8428 (t70) REVERT: C 61 MET cc_start: 0.7354 (tpp) cc_final: 0.7147 (tpp) REVERT: C 72 TYR cc_start: 0.6966 (m-80) cc_final: 0.6667 (m-80) REVERT: C 203 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8407 (t70) REVERT: C 270 ASP cc_start: 0.7541 (t0) cc_final: 0.7303 (t0) REVERT: C 373 MET cc_start: 0.8066 (mtm) cc_final: 0.7845 (mtm) REVERT: C 376 GLN cc_start: 0.6692 (mm-40) cc_final: 0.6293 (mm110) outliers start: 30 outliers final: 16 residues processed: 210 average time/residue: 1.3129 time to fit residues: 305.4640 Evaluate side-chains 196 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 166 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.127069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101793 restraints weight = 18843.137| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.31 r_work: 0.3097 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16735 Z= 0.121 Angle : 0.495 7.913 22560 Z= 0.260 Chirality : 0.037 0.159 2385 Planarity : 0.004 0.032 2770 Dihedral : 12.539 104.746 2654 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.59 % Allowed : 12.80 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 1870 helix: 1.37 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.02 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 309 HIS 0.004 0.001 HIS E 178 PHE 0.025 0.001 PHE C 283 TYR 0.022 0.001 TYR A 68 ARG 0.002 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.05565 ( 965) hydrogen bonds : angle 4.25315 ( 2775) covalent geometry : bond 0.00248 (16735) covalent geometry : angle 0.49466 (22560) *********************** 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 211 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.927 Fit side-chains REVERT: D 8 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: D 51 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7707 (mpt90) REVERT: D 72 TYR cc_start: 0.6856 (m-10) cc_final: 0.6463 (m-80) REVERT: D 270 ASP cc_start: 0.7682 (t70) cc_final: 0.7413 (t0) REVERT: D 373 MET cc_start: 0.8018 (mtm) cc_final: 0.7785 (mtm) REVERT: B 51 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7656 (mpt90) REVERT: B 68 TYR cc_start: 0.7252 (t80) cc_final: 0.6993 (t80) REVERT: B 262 LYS cc_start: 0.7291 (mppt) cc_final: 0.7075 (mppt) REVERT: A 72 TYR cc_start: 0.6919 (m-80) cc_final: 0.6690 (m-80) REVERT: A 360 MET cc_start: 0.8598 (mmm) cc_final: 0.8282 (mmm) REVERT: E 72 TYR cc_start: 0.7146 (m-80) cc_final: 0.6841 (m-80) REVERT: E 203 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8442 (t70) REVERT: C 51 ARG cc_start: 0.7852 (mmt90) cc_final: 0.7520 (mmt90) REVERT: C 72 TYR cc_start: 0.6908 (m-80) cc_final: 0.6600 (m-80) REVERT: C 270 ASP cc_start: 0.7560 (t0) cc_final: 0.7340 (t0) REVERT: C 376 GLN cc_start: 0.6702 (mm-40) cc_final: 0.6292 (mm110) outliers start: 27 outliers final: 13 residues processed: 206 average time/residue: 1.4126 time to fit residues: 321.8696 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 172 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.0040 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 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 = 0.3559 r_free = 0.3559 target = 0.128501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103308 restraints weight = 18823.351| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.32 r_work: 0.3118 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16735 Z= 0.111 Angle : 0.487 8.285 22560 Z= 0.254 Chirality : 0.037 0.158 2385 Planarity : 0.004 0.032 2770 Dihedral : 12.011 100.477 2650 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.42 % Allowed : 13.16 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 1870 helix: 1.44 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.01 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS B 178 PHE 0.026 0.001 PHE C 283 TYR 0.023 0.001 TYR E 68 ARG 0.002 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.05325 ( 965) hydrogen bonds : angle 4.19473 ( 2775) covalent geometry : bond 0.00222 (16735) covalent geometry : angle 0.48659 (22560) *********************** 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 217 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.768 Fit side-chains REVERT: D 40 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7679 (mt) REVERT: D 51 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7677 (mpt90) REVERT: D 72 TYR cc_start: 0.6840 (m-10) cc_final: 0.6461 (m-80) REVERT: D 270 ASP cc_start: 0.7679 (t70) cc_final: 0.7451 (t0) REVERT: B 51 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7547 (mpt90) REVERT: B 68 TYR cc_start: 0.7234 (t80) cc_final: 0.6973 (t80) REVERT: B 262 LYS cc_start: 0.7064 (mppt) cc_final: 0.6753 (mptt) REVERT: A 51 ARG cc_start: 0.7642 (mmt90) cc_final: 0.7268 (mmt90) REVERT: A 72 TYR cc_start: 0.6953 (m-80) cc_final: 0.6737 (m-80) REVERT: A 214 MET cc_start: 0.8394 (tpt) cc_final: 0.8132 (mmm) REVERT: A 360 MET cc_start: 0.8564 (mmm) cc_final: 0.8220 (mmm) REVERT: E 75 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6036 (mp) REVERT: E 331 ARG cc_start: 0.8083 (ttp-110) cc_final: 0.7873 (ttp-110) REVERT: C 51 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7454 (mmt90) REVERT: C 72 TYR cc_start: 0.6897 (m-80) cc_final: 0.6621 (m-80) REVERT: C 270 ASP cc_start: 0.7670 (t0) cc_final: 0.7447 (t0) REVERT: C 376 GLN cc_start: 0.6665 (mm-40) cc_final: 0.6246 (mm110) outliers start: 24 outliers final: 13 residues processed: 211 average time/residue: 1.4107 time to fit residues: 333.6668 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU 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 B residue 75 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.124592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.099009 restraints weight = 18883.583| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.32 r_work: 0.3055 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16735 Z= 0.165 Angle : 0.551 8.772 22560 Z= 0.290 Chirality : 0.040 0.217 2385 Planarity : 0.004 0.034 2770 Dihedral : 12.180 99.153 2650 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.24 % Allowed : 13.33 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1870 helix: 1.37 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.08 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 309 HIS 0.004 0.001 HIS C 326 PHE 0.032 0.002 PHE C 283 TYR 0.022 0.002 TYR B 97 ARG 0.002 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.06223 ( 965) hydrogen bonds : angle 4.34523 ( 2775) covalent geometry : bond 0.00369 (16735) covalent geometry : angle 0.55083 (22560) *********************** 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 199 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.847 Fit side-chains REVERT: D 8 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: D 51 ARG cc_start: 0.7982 (mmt90) cc_final: 0.7713 (mpt90) REVERT: D 72 TYR cc_start: 0.6903 (m-10) cc_final: 0.6420 (m-80) REVERT: D 270 ASP cc_start: 0.7740 (t70) cc_final: 0.7521 (t0) REVERT: B 51 ARG cc_start: 0.7886 (mmt90) cc_final: 0.7552 (mpt90) REVERT: B 270 ASP cc_start: 0.7497 (t70) cc_final: 0.7221 (t0) REVERT: A 51 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7317 (mmt90) REVERT: A 72 TYR cc_start: 0.6950 (m-80) cc_final: 0.6709 (m-80) REVERT: A 360 MET cc_start: 0.8701 (mmm) cc_final: 0.8397 (mmm) REVERT: C 72 TYR cc_start: 0.6845 (m-80) cc_final: 0.6613 (m-80) REVERT: C 270 ASP cc_start: 0.7677 (t0) cc_final: 0.7424 (t0) outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 1.3654 time to fit residues: 295.5909 Evaluate side-chains 192 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.759 ------------------------------------------------------------------------------- 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 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 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 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 156 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.125666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100251 restraints weight = 18926.766| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.32 r_work: 0.3072 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16735 Z= 0.143 Angle : 0.533 8.477 22560 Z= 0.280 Chirality : 0.039 0.158 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.093 98.339 2650 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.06 % Allowed : 13.57 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1870 helix: 1.30 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.19 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 309 HIS 0.004 0.001 HIS B 178 PHE 0.036 0.002 PHE C 283 TYR 0.021 0.002 TYR E 68 ARG 0.002 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.05917 ( 965) hydrogen bonds : angle 4.32057 ( 2775) covalent geometry : bond 0.00309 (16735) covalent geometry : angle 0.53270 (22560) ********************** 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 196 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 1.963 Fit side-chains REVERT: D 8 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: D 51 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7716 (mpt90) REVERT: D 72 TYR cc_start: 0.6895 (m-10) cc_final: 0.6463 (m-80) REVERT: D 270 ASP cc_start: 0.7715 (t70) cc_final: 0.7491 (t0) REVERT: B 68 TYR cc_start: 0.7243 (t80) cc_final: 0.7010 (t80) REVERT: B 262 LYS cc_start: 0.7170 (mppt) cc_final: 0.6883 (mptt) REVERT: B 270 ASP cc_start: 0.7595 (t70) cc_final: 0.7317 (t0) REVERT: A 51 ARG cc_start: 0.7720 (mmt90) cc_final: 0.7329 (mmt90) REVERT: A 72 TYR cc_start: 0.6940 (m-80) cc_final: 0.6734 (m-80) REVERT: A 360 MET cc_start: 0.8654 (mmm) cc_final: 0.8361 (mmm) REVERT: C 72 TYR cc_start: 0.6752 (m-80) cc_final: 0.6522 (m-80) REVERT: C 270 ASP cc_start: 0.7687 (t0) cc_final: 0.7470 (t0) outliers start: 18 outliers final: 15 residues processed: 194 average time/residue: 1.3433 time to fit residues: 288.6293 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 : 2.034 ------------------------------------------------------------------------------- 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 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 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 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 116 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.126936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101584 restraints weight = 18936.710| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.32 r_work: 0.3092 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2023 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= 0.128 Angle : 0.517 8.344 22560 Z= 0.272 Chirality : 0.038 0.159 2385 Planarity : 0.004 0.033 2770 Dihedral : 11.910 97.441 2650 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.06 % Allowed : 13.63 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1870 helix: 1.45 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : 0.01 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 309 HIS 0.003 0.001 HIS C 178 PHE 0.034 0.002 PHE C 283 TYR 0.019 0.001 TYR A 68 ARG 0.002 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.05644 ( 965) hydrogen bonds : angle 4.27870 ( 2775) covalent geometry : bond 0.00269 (16735) covalent geometry : angle 0.51670 (22560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13032.71 seconds wall clock time: 228 minutes 26.00 seconds (13706.00 seconds total)