Starting phenix.real_space_refine on Tue Dec 31 19:10:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1k_27133/12_2024/8d1k_27133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1k_27133/12_2024/8d1k_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_27133/12_2024/8d1k_27133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1k_27133/12_2024/8d1k_27133.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1k_27133/12_2024/8d1k_27133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1k_27133/12_2024/8d1k_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.73, per 1000 atoms: 0.66 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: 4.53 Conformation dependent library (CDL) restraints added in 2.0 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: 1.40 Creating SS restraints... Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.559A pdb=" N ALA D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.882A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.646A pdb=" N LYS D 262 " --> pdb=" O ASN D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.696A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.559A pdb=" N ALA B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.883A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.646A pdb=" N LYS B 262 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.697A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.559A pdb=" N ALA A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.883A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.646A pdb=" N LYS A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.696A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.560A pdb=" N ALA E 10 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.882A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.646A pdb=" N LYS E 262 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.695A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.559A pdb=" N ALA C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.638A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 70 Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.747A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.882A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.645A pdb=" N LYS C 262 " --> pdb=" O ASN C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.696A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.519A pdb=" N TYR D 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.519A pdb=" N TYR E 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.519A pdb=" N TYR B 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.519A pdb=" N TYR C 347 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.519A pdb=" N TYR A 347 " --> pdb=" O GLN E 376 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 5.06 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 38.050 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.070 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:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.580 ------------------------------------------------------------------------------- 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= 0.837 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 *********************** 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 : 1.894 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: 1.5085 time to fit residues: 390.7958 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 : 2.007 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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= 0.173 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 *********************** 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 : 1.858 Fit side-chains REVERT: D 262 LYS cc_start: 0.7106 (mmtm) cc_final: 0.6693 (mppt) REVERT: D 376 GLN cc_start: 0.6898 (mm-40) cc_final: 0.6563 (mm110) REVERT: B 68 TYR cc_start: 0.6910 (t80) cc_final: 0.6594 (t80) REVERT: B 119 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8282 (tt0) REVERT: B 376 GLN cc_start: 0.7023 (mm-40) cc_final: 0.6697 (mm110) REVERT: A 56 GLU cc_start: 0.7540 (tp30) cc_final: 0.7307 (mp0) REVERT: A 72 TYR cc_start: 0.7108 (m-80) cc_final: 0.6733 (m-10) REVERT: A 119 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8265 (tt0) REVERT: A 360 MET cc_start: 0.8939 (mmm) cc_final: 0.8724 (mmm) REVERT: A 376 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6522 (mm110) REVERT: E 56 GLU cc_start: 0.7264 (mp0) cc_final: 0.6357 (pt0) REVERT: E 68 TYR cc_start: 0.7154 (t80) cc_final: 0.6754 (t80) REVERT: E 72 TYR cc_start: 0.6982 (m-80) cc_final: 0.6680 (m-10) REVERT: E 373 MET cc_start: 0.8242 (mtt) cc_final: 0.8022 (mtp) REVERT: C 72 TYR cc_start: 0.6995 (m-80) cc_final: 0.6713 (m-10) REVERT: C 376 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6599 (mm110) outliers start: 25 outliers final: 13 residues processed: 206 average time/residue: 1.5239 time to fit residues: 345.2923 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 : 1.970 ------------------------------------------------------------------------------- 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 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 93 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 0.0270 chunk 181 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 353 GLN A 369 ASN E 259 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1418 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= 0.218 Angle : 0.543 8.213 22560 Z= 0.288 Chirality : 0.039 0.157 2385 Planarity : 0.004 0.032 2770 Dihedral : 14.368 113.936 2660 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.83 % Allowed : 10.62 % Favored : 87.55 % 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: 1.13 (0.19), residues: 1870 helix: 1.15 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : 0.05 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 309 HIS 0.005 0.001 HIS C 178 PHE 0.025 0.002 PHE B 248 TYR 0.026 0.002 TYR C 97 ARG 0.004 0.000 ARG E 51 *********************** 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: 31 poor density : 183 time to evaluate : 1.953 Fit side-chains REVERT: D 8 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: D 72 TYR cc_start: 0.7177 (m-10) cc_final: 0.6579 (m-80) REVERT: D 262 LYS cc_start: 0.6955 (mmtm) cc_final: 0.6711 (mppt) REVERT: B 119 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8290 (tt0) REVERT: B 376 GLN cc_start: 0.7012 (mm-40) cc_final: 0.6677 (mm110) REVERT: A 56 GLU cc_start: 0.7520 (tp30) cc_final: 0.7286 (mp0) REVERT: A 72 TYR cc_start: 0.7016 (m-80) cc_final: 0.6660 (m-10) REVERT: A 119 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8243 (tt0) REVERT: A 360 MET cc_start: 0.8928 (mmm) cc_final: 0.8705 (mmm) REVERT: A 376 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6629 (mm110) REVERT: E 8 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8700 (mt0) REVERT: C 51 ARG cc_start: 0.7833 (mmt90) cc_final: 0.7450 (mmt90) REVERT: C 72 TYR cc_start: 0.7073 (m-80) cc_final: 0.6815 (m-80) REVERT: C 376 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6599 (mm110) outliers start: 31 outliers final: 13 residues processed: 211 average time/residue: 1.5639 time to fit residues: 365.0738 Evaluate side-chains 187 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 2.166 ------------------------------------------------------------------------------- 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 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 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 166 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1493 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= 0.272 Angle : 0.578 8.527 22560 Z= 0.305 Chirality : 0.041 0.158 2385 Planarity : 0.004 0.034 2770 Dihedral : 14.216 114.477 2658 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.71 % Allowed : 11.80 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.19), residues: 1870 helix: 1.09 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.01 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 309 HIS 0.007 0.002 HIS D 178 PHE 0.029 0.002 PHE B 248 TYR 0.028 0.002 TYR C 97 ARG 0.003 0.000 ARG C 125 *********************** 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 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.784 Fit side-chains REVERT: D 8 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: D 72 TYR cc_start: 0.6983 (m-10) cc_final: 0.6512 (m-80) REVERT: D 262 LYS cc_start: 0.7036 (mmtm) cc_final: 0.6748 (mppt) REVERT: B 119 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8292 (tt0) REVERT: B 262 LYS cc_start: 0.6981 (mppt) cc_final: 0.6780 (mppt) REVERT: B 376 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6606 (mm110) REVERT: A 51 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7501 (mmt90) REVERT: A 72 TYR cc_start: 0.7078 (m-80) cc_final: 0.6848 (m-80) REVERT: A 119 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8237 (tt0) REVERT: A 360 MET cc_start: 0.8948 (mmm) cc_final: 0.8287 (mmm) REVERT: A 376 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6695 (mm110) REVERT: E 72 TYR cc_start: 0.7092 (m-80) cc_final: 0.6835 (m-80) REVERT: C 72 TYR cc_start: 0.7077 (m-80) cc_final: 0.6795 (m-80) REVERT: C 203 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8676 (t70) REVERT: C 373 MET cc_start: 0.8242 (mtm) cc_final: 0.8035 (mtm) REVERT: C 376 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6591 (mm110) outliers start: 29 outliers final: 13 residues processed: 213 average time/residue: 1.4816 time to fit residues: 347.1716 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 : 1.972 ------------------------------------------------------------------------------- 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 A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 203 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 353 GLN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1570 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= 0.305 Angle : 0.595 8.606 22560 Z= 0.314 Chirality : 0.042 0.158 2385 Planarity : 0.004 0.033 2770 Dihedral : 14.107 114.655 2658 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.12 % Allowed : 12.15 % 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: 0.98 (0.19), residues: 1870 helix: 1.10 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -0.08 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 309 HIS 0.005 0.002 HIS C 326 PHE 0.031 0.002 PHE E 248 TYR 0.029 0.002 TYR C 97 ARG 0.003 0.000 ARG C 125 *********************** 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 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 2.012 Fit side-chains REVERT: D 8 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: D 72 TYR cc_start: 0.7041 (m-10) cc_final: 0.6579 (m-80) REVERT: B 262 LYS cc_start: 0.7009 (mppt) cc_final: 0.6764 (mppt) REVERT: A 51 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7557 (mmt90) REVERT: A 72 TYR cc_start: 0.7057 (m-80) cc_final: 0.6787 (m-80) REVERT: A 119 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8233 (tt0) REVERT: A 178 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8888 (m-70) REVERT: A 360 MET cc_start: 0.8946 (mmm) cc_final: 0.8634 (mmm) REVERT: E 72 TYR cc_start: 0.7114 (m-80) cc_final: 0.6876 (m-80) REVERT: C 203 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (t70) REVERT: C 270 ASP cc_start: 0.7712 (t0) cc_final: 0.7453 (t0) REVERT: C 376 GLN cc_start: 0.7000 (mm-40) cc_final: 0.6615 (mm110) outliers start: 36 outliers final: 14 residues processed: 214 average time/residue: 1.4036 time to fit residues: 332.3158 Evaluate side-chains 190 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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 A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1773 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= 0.175 Angle : 0.519 8.137 22560 Z= 0.272 Chirality : 0.038 0.157 2385 Planarity : 0.004 0.032 2770 Dihedral : 13.529 113.592 2658 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.59 % Allowed : 12.98 % 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: 0.97 (0.19), residues: 1870 helix: 1.14 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : -0.31 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 309 HIS 0.004 0.001 HIS C 178 PHE 0.021 0.001 PHE B 248 TYR 0.022 0.002 TYR C 97 ARG 0.002 0.000 ARG D 47 *********************** 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: 27 poor density : 187 time to evaluate : 2.117 Fit side-chains REVERT: D 8 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: D 72 TYR cc_start: 0.7088 (m-10) cc_final: 0.6589 (m-80) REVERT: B 51 ARG cc_start: 0.7961 (mmt90) cc_final: 0.7654 (mpt90) REVERT: B 119 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8278 (tt0) REVERT: A 51 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7508 (mmt90) REVERT: A 72 TYR cc_start: 0.7060 (m-80) cc_final: 0.6841 (m-80) REVERT: A 119 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8235 (tt0) REVERT: E 72 TYR cc_start: 0.7134 (m-80) cc_final: 0.6882 (m-80) REVERT: C 72 TYR cc_start: 0.7067 (m-80) cc_final: 0.6794 (m-80) REVERT: C 270 ASP cc_start: 0.7696 (t0) cc_final: 0.7452 (t0) REVERT: C 376 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6560 (mm110) outliers start: 27 outliers final: 14 residues processed: 207 average time/residue: 1.3632 time to fit residues: 312.9840 Evaluate side-chains 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 A residue 75 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 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 Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 0.0040 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 178 HIS E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1970 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= 0.153 Angle : 0.495 7.916 22560 Z= 0.258 Chirality : 0.037 0.158 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.797 112.360 2654 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.47 % Allowed : 13.81 % Favored : 84.72 % 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: 1.36 (0.18), residues: 1870 helix: 1.46 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.05 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 309 HIS 0.004 0.001 HIS A 178 PHE 0.024 0.001 PHE C 283 TYR 0.022 0.001 TYR E 68 ARG 0.004 0.000 ARG E 25 *********************** 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 204 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 2.010 Fit side-chains REVERT: D 72 TYR cc_start: 0.7100 (m-10) cc_final: 0.6650 (m-80) REVERT: D 270 ASP cc_start: 0.7477 (t70) cc_final: 0.7260 (t0) REVERT: B 51 ARG cc_start: 0.7966 (mmt90) cc_final: 0.7704 (mpt90) REVERT: B 178 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8768 (m-70) REVERT: A 51 ARG cc_start: 0.7865 (mmt90) cc_final: 0.7519 (mmt90) REVERT: A 72 TYR cc_start: 0.7120 (m-80) cc_final: 0.6874 (m-80) REVERT: E 72 TYR cc_start: 0.7191 (m-80) cc_final: 0.6933 (m-80) REVERT: C 72 TYR cc_start: 0.7097 (m-80) cc_final: 0.6833 (m-80) REVERT: C 270 ASP cc_start: 0.7790 (t0) cc_final: 0.7572 (t0) REVERT: C 376 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6566 (mm110) outliers start: 25 outliers final: 12 residues processed: 198 average time/residue: 1.4004 time to fit residues: 306.9716 Evaluate side-chains 185 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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 A residue 235 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2051 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= 0.152 Angle : 0.492 7.837 22560 Z= 0.258 Chirality : 0.037 0.158 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.191 111.092 2652 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.36 % Allowed : 14.16 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.19), residues: 1870 helix: 1.53 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.02 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 309 HIS 0.003 0.001 HIS B 178 PHE 0.027 0.001 PHE C 283 TYR 0.019 0.001 TYR E 97 ARG 0.004 0.000 ARG E 25 *********************** 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: 23 poor density : 183 time to evaluate : 1.978 Fit side-chains REVERT: D 72 TYR cc_start: 0.7114 (m-10) cc_final: 0.6654 (m-80) REVERT: B 51 ARG cc_start: 0.7990 (mmt90) cc_final: 0.7733 (mpt90) REVERT: B 119 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8276 (tt0) REVERT: A 51 ARG cc_start: 0.7829 (mmt90) cc_final: 0.7486 (mmt90) REVERT: A 72 TYR cc_start: 0.7149 (m-80) cc_final: 0.6920 (m-80) REVERT: C 72 TYR cc_start: 0.7123 (m-80) cc_final: 0.6861 (m-80) REVERT: C 270 ASP cc_start: 0.7784 (t0) cc_final: 0.7583 (t0) REVERT: C 376 GLN cc_start: 0.6889 (mm-40) cc_final: 0.6507 (mm110) outliers start: 23 outliers final: 14 residues processed: 204 average time/residue: 1.3992 time to fit residues: 317.3049 Evaluate side-chains 190 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 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 307 THR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 100 optimal weight: 0.0070 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS B 369 ASN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16735 Z= 0.170 Angle : 0.509 8.826 22560 Z= 0.266 Chirality : 0.038 0.172 2385 Planarity : 0.004 0.033 2770 Dihedral : 11.951 109.087 2650 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.00 % Allowed : 14.69 % Favored : 84.31 % 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: 1.43 (0.19), residues: 1870 helix: 1.50 (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 0.016 0.001 TRP A 309 HIS 0.003 0.001 HIS A 178 PHE 0.030 0.001 PHE C 283 TYR 0.022 0.002 TYR C 68 ARG 0.003 0.000 ARG E 25 *********************** 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 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.852 Fit side-chains REVERT: D 72 TYR cc_start: 0.7106 (m-10) cc_final: 0.6613 (m-80) REVERT: D 270 ASP cc_start: 0.7512 (t70) cc_final: 0.7261 (t0) REVERT: B 51 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7726 (mpt90) REVERT: B 119 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8280 (tt0) REVERT: A 51 ARG cc_start: 0.7817 (mmt90) cc_final: 0.7462 (mmt90) REVERT: A 72 TYR cc_start: 0.7135 (m-80) cc_final: 0.6887 (m-80) REVERT: E 75 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6083 (mp) REVERT: E 270 ASP cc_start: 0.7728 (t70) cc_final: 0.7377 (t0) REVERT: C 72 TYR cc_start: 0.7129 (m-80) cc_final: 0.6838 (m-80) outliers start: 17 outliers final: 13 residues processed: 193 average time/residue: 1.3584 time to fit residues: 291.3238 Evaluate side-chains 186 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 A residue 75 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 146 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 116 optimal weight: 0.0270 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16735 Z= 0.143 Angle : 0.491 8.589 22560 Z= 0.256 Chirality : 0.037 0.159 2385 Planarity : 0.004 0.032 2770 Dihedral : 11.563 104.560 2650 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.18 % Allowed : 14.75 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.19), residues: 1870 helix: 1.55 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.03 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS A 178 PHE 0.031 0.001 PHE C 283 TYR 0.020 0.001 TYR B 72 ARG 0.003 0.000 ARG E 25 ********************** 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 205 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 1.616 Fit side-chains REVERT: D 72 TYR cc_start: 0.7090 (m-10) cc_final: 0.6666 (m-80) REVERT: D 270 ASP cc_start: 0.7530 (t70) cc_final: 0.7237 (t0) REVERT: B 51 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7679 (mpt90) REVERT: B 119 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8278 (tt0) REVERT: A 51 ARG cc_start: 0.7809 (mmt90) cc_final: 0.7343 (mmt90) REVERT: A 75 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6001 (mp) REVERT: E 75 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6061 (mp) REVERT: E 270 ASP cc_start: 0.7704 (t70) cc_final: 0.7360 (t0) REVERT: C 51 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7597 (mpt90) REVERT: C 72 TYR cc_start: 0.7149 (m-80) cc_final: 0.6895 (m-80) outliers start: 20 outliers final: 15 residues processed: 203 average time/residue: 1.3439 time to fit residues: 302.7390 Evaluate side-chains 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 B residue 75 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 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 44 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 0.0770 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.127075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101613 restraints weight = 18763.027| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.31 r_work: 0.3096 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2087 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= 0.183 Angle : 0.518 8.894 22560 Z= 0.271 Chirality : 0.038 0.183 2385 Planarity : 0.004 0.034 2770 Dihedral : 11.504 99.907 2650 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.06 % Allowed : 14.87 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.19), residues: 1870 helix: 1.53 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : -0.04 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 309 HIS 0.003 0.001 HIS C 326 PHE 0.033 0.002 PHE C 283 TYR 0.021 0.002 TYR C 68 ARG 0.003 0.000 ARG E 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5738.47 seconds wall clock time: 104 minutes 43.47 seconds (6283.47 seconds total)