Starting phenix.real_space_refine on Wed Apr 30 23:23:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjw_39352/04_2025/8yjw_39352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjw_39352/04_2025/8yjw_39352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjw_39352/04_2025/8yjw_39352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjw_39352/04_2025/8yjw_39352.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjw_39352/04_2025/8yjw_39352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjw_39352/04_2025/8yjw_39352.cif" } resolution = 3.55 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 164 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 63 5.16 5 C 6067 2.51 5 N 1667 2.21 5 O 2086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9946 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "D" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2774 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "J" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 621 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "F" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 6.52, per 1000 atoms: 0.66 Number of scatterers: 9946 At special positions: 0 Unit cell: (102.09, 101.26, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 63 15.00 O 2086 8.00 N 1667 7.00 C 6067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 29.9% alpha, 24.9% beta 11 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.937A pdb=" N LYS B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'C' and resid 8 through 23 removed outlier: 4.088A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.740A pdb=" N ALA D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.520A pdb=" N ASN D 138 " --> pdb=" O THR D 134 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 231 removed outlier: 3.501A pdb=" N PHE D 223 " --> pdb=" O ASN D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 253 removed outlier: 3.569A pdb=" N ALA D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 removed outlier: 3.617A pdb=" N ILE D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 303 through 311 Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.826A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 23 removed outlier: 4.269A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 140 through 155 removed outlier: 4.369A pdb=" N HIS A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.558A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 4 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 112 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 71 removed outlier: 4.006A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 227 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 208 removed outlier: 5.207A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 67 through 71 removed outlier: 5.865A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 49 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 123 Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 208 removed outlier: 5.381A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 99 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 59 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.653A pdb=" N ALA D 175 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS D 30 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA D 176 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA D 32 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71 removed outlier: 3.521A pdb=" N MET A 68 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 34 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 226 433 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2601 1.33 - 1.46: 2082 1.46 - 1.58: 5315 1.58 - 1.70: 123 1.70 - 1.82: 102 Bond restraints: 10223 Sorted by residual: bond pdb=" CA MET D 191 " pdb=" CB MET D 191 " ideal model delta sigma weight residual 1.526 1.456 0.070 1.53e-02 4.27e+03 2.09e+01 bond pdb=" N ASP C 232 " pdb=" CA ASP C 232 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.01e+00 bond pdb=" C3' DA E 25 " pdb=" O3' DA E 25 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.92e+00 bond pdb=" C THR C 219 " pdb=" N PRO C 220 " ideal model delta sigma weight residual 1.335 1.354 -0.019 9.40e-03 1.13e+04 4.16e+00 bond pdb=" CB GLN D 281 " pdb=" CG GLN D 281 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 4.01e+00 ... (remaining 10218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 13550 2.46 - 4.93: 403 4.93 - 7.39: 78 7.39 - 9.86: 18 9.86 - 12.32: 10 Bond angle restraints: 14059 Sorted by residual: angle pdb=" N THR A 219 " pdb=" CA THR A 219 " pdb=" C THR A 219 " ideal model delta sigma weight residual 109.81 121.33 -11.52 2.21e+00 2.05e-01 2.72e+01 angle pdb=" C ALA C 231 " pdb=" N ASP C 232 " pdb=" CA ASP C 232 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C LYS D 314 " pdb=" N GLN D 315 " pdb=" CA GLN D 315 " ideal model delta sigma weight residual 122.82 129.56 -6.74 1.42e+00 4.96e-01 2.25e+01 angle pdb=" N MET C 244 " pdb=" CA MET C 244 " pdb=" C MET C 244 " ideal model delta sigma weight residual 114.56 108.73 5.83 1.27e+00 6.20e-01 2.11e+01 angle pdb=" CA GLN D 281 " pdb=" CB GLN D 281 " pdb=" CG GLN D 281 " ideal model delta sigma weight residual 114.10 123.25 -9.15 2.00e+00 2.50e-01 2.09e+01 ... (remaining 14054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 5783 35.34 - 70.67: 385 70.67 - 106.00: 10 106.00 - 141.34: 1 141.34 - 176.67: 1 Dihedral angle restraints: 6180 sinusoidal: 2931 harmonic: 3249 Sorted by residual: dihedral pdb=" CA GLU B 191 " pdb=" C GLU B 191 " pdb=" N GLU B 192 " pdb=" CA GLU B 192 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA HIS D 253 " pdb=" C HIS D 253 " pdb=" N LYS D 254 " pdb=" CA LYS D 254 " ideal model delta harmonic sigma weight residual -180.00 -153.76 -26.24 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA MET C 139 " pdb=" C MET C 139 " pdb=" N PRO C 140 " pdb=" CA PRO C 140 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1351 0.070 - 0.139: 223 0.139 - 0.209: 31 0.209 - 0.279: 10 0.279 - 0.349: 3 Chirality restraints: 1618 Sorted by residual: chirality pdb=" CG LEU D 144 " pdb=" CB LEU D 144 " pdb=" CD1 LEU D 144 " pdb=" CD2 LEU D 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB THR A 216 " pdb=" CA THR A 216 " pdb=" OG1 THR A 216 " pdb=" CG2 THR A 216 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB VAL D 52 " pdb=" CA VAL D 52 " pdb=" CG1 VAL D 52 " pdb=" CG2 VAL D 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1615 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO A 220 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 219 " 0.048 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO B 220 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 264 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO D 265 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.033 5.00e-02 4.00e+02 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2413 2.81 - 3.33: 8050 3.33 - 3.86: 17616 3.86 - 4.38: 19708 4.38 - 4.90: 33071 Nonbonded interactions: 80858 Sorted by model distance: nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR D 40 " pdb=" OP2 DT H 3 " model vdw 2.310 3.040 nonbonded pdb=" O SER B 31 " pdb=" OH TYR B 60 " model vdw 2.347 3.040 nonbonded pdb=" O ILE C 255 " pdb=" OG1 THR D 336 " model vdw 2.369 3.040 nonbonded pdb=" OG SER D 157 " pdb=" O GLU D 287 " model vdw 2.378 3.040 ... (remaining 80853 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' selection = chain 'B' selection = (chain 'C' and resid 1 through 254) } 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 group one per residue 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.710 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.006 0.070 10225 Z= 0.257 Angle : 1.052 12.323 14063 Z= 0.553 Chirality : 0.058 0.349 1618 Planarity : 0.008 0.084 1595 Dihedral : 20.201 176.673 4066 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.20 (0.21), residues: 1108 helix: -2.81 (0.20), residues: 323 sheet: -1.31 (0.27), residues: 340 loop : -2.02 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 28 HIS 0.008 0.001 HIS C 44 PHE 0.019 0.003 PHE D 42 TYR 0.024 0.003 TYR D 40 ARG 0.018 0.001 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.20503 ( 455) hydrogen bonds : angle 9.67495 ( 1271) SS BOND : bond 0.00202 ( 2) SS BOND : angle 1.55866 ( 4) covalent geometry : bond 0.00561 (10223) covalent geometry : angle 1.05224 (14059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.015 Fit side-chains REVERT: B 10 SER cc_start: 0.8346 (m) cc_final: 0.7806 (m) REVERT: B 84 ASN cc_start: 0.7420 (m-40) cc_final: 0.6660 (t0) REVERT: A 55 GLU cc_start: 0.6808 (mp0) cc_final: 0.6584 (tp30) REVERT: A 64 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.7113 (mtm110) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2175 time to fit residues: 51.1445 Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.0060 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 0.0970 overall best weight: 0.2732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 315 GLN A 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127230 restraints weight = 12598.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128276 restraints weight = 9778.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129679 restraints weight = 9215.901| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10225 Z= 0.134 Angle : 0.593 8.435 14063 Z= 0.324 Chirality : 0.043 0.146 1618 Planarity : 0.004 0.046 1595 Dihedral : 21.319 177.172 1923 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.83 % Allowed : 8.98 % Favored : 90.20 % 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: -2.13 (0.23), residues: 1108 helix: -0.91 (0.26), residues: 329 sheet: -1.32 (0.28), residues: 318 loop : -1.70 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 28 HIS 0.010 0.001 HIS C 246 PHE 0.010 0.001 PHE D 27 TYR 0.009 0.001 TYR D 40 ARG 0.004 0.000 ARG D 262 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 455) hydrogen bonds : angle 6.81297 ( 1271) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.43439 ( 4) covalent geometry : bond 0.00291 (10223) covalent geometry : angle 0.59268 (14059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.952 Fit side-chains REVERT: B 10 SER cc_start: 0.8346 (m) cc_final: 0.7936 (m) REVERT: B 84 ASN cc_start: 0.7666 (m-40) cc_final: 0.6969 (t0) REVERT: B 207 PHE cc_start: 0.8413 (m-10) cc_final: 0.8189 (m-10) REVERT: D 108 GLU cc_start: 0.7357 (tp30) cc_final: 0.7050 (tm-30) REVERT: D 263 LEU cc_start: 0.6372 (tt) cc_final: 0.6010 (tp) REVERT: A 141 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7684 (t) REVERT: A 170 SER cc_start: 0.8518 (m) cc_final: 0.8038 (t) outliers start: 8 outliers final: 1 residues processed: 162 average time/residue: 0.2100 time to fit residues: 48.3863 Evaluate side-chains 136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain A residue 141 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 30 optimal weight: 0.0370 chunk 105 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 98 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN C 125 GLN C 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124556 restraints weight = 12801.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126258 restraints weight = 9810.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127464 restraints weight = 9061.387| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10225 Z= 0.125 Angle : 0.552 8.384 14063 Z= 0.301 Chirality : 0.042 0.153 1618 Planarity : 0.004 0.046 1595 Dihedral : 21.217 176.187 1923 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.03 % Allowed : 12.18 % Favored : 86.79 % 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: -1.44 (0.24), residues: 1108 helix: 0.21 (0.28), residues: 323 sheet: -1.21 (0.27), residues: 336 loop : -1.47 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 274 HIS 0.007 0.001 HIS C 246 PHE 0.009 0.001 PHE D 126 TYR 0.010 0.001 TYR D 40 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 455) hydrogen bonds : angle 6.05058 ( 1271) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.33294 ( 4) covalent geometry : bond 0.00276 (10223) covalent geometry : angle 0.55167 (14059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.970 Fit side-chains REVERT: B 10 SER cc_start: 0.8462 (m) cc_final: 0.8089 (m) REVERT: B 84 ASN cc_start: 0.7718 (m-40) cc_final: 0.6988 (t0) REVERT: B 207 PHE cc_start: 0.8510 (m-80) cc_final: 0.8151 (m-10) REVERT: B 244 MET cc_start: 0.7276 (ppp) cc_final: 0.7025 (ppp) REVERT: C 207 PHE cc_start: 0.8728 (m-80) cc_final: 0.8413 (m-80) REVERT: D 67 MET cc_start: 0.6736 (ttm) cc_final: 0.6486 (ttp) REVERT: D 108 GLU cc_start: 0.7320 (tp30) cc_final: 0.7030 (tm-30) REVERT: D 263 LEU cc_start: 0.6584 (tt) cc_final: 0.6263 (tp) REVERT: A 16 LEU cc_start: 0.8463 (mm) cc_final: 0.8228 (mm) REVERT: A 25 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7335 (mt-10) REVERT: A 141 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7686 (t) REVERT: A 170 SER cc_start: 0.8471 (m) cc_final: 0.8030 (t) outliers start: 10 outliers final: 4 residues processed: 157 average time/residue: 0.2000 time to fit residues: 45.8893 Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain A residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.152802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119012 restraints weight = 12616.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119920 restraints weight = 10156.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121228 restraints weight = 10469.674| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10225 Z= 0.162 Angle : 0.568 8.897 14063 Z= 0.308 Chirality : 0.042 0.151 1618 Planarity : 0.003 0.041 1595 Dihedral : 21.108 178.000 1923 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.96 % Allowed : 13.83 % Favored : 84.21 % 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 (0.24), residues: 1108 helix: 0.66 (0.29), residues: 324 sheet: -1.20 (0.28), residues: 334 loop : -1.47 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 274 HIS 0.004 0.001 HIS C 44 PHE 0.012 0.002 PHE C 169 TYR 0.011 0.002 TYR C 211 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 455) hydrogen bonds : angle 5.89007 ( 1271) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.35866 ( 4) covalent geometry : bond 0.00364 (10223) covalent geometry : angle 0.56788 (14059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.025 Fit side-chains REVERT: B 10 SER cc_start: 0.8511 (m) cc_final: 0.8132 (m) REVERT: B 75 MET cc_start: 0.8336 (ttt) cc_final: 0.7768 (ttt) REVERT: B 84 ASN cc_start: 0.7705 (m-40) cc_final: 0.6975 (t0) REVERT: D 69 TYR cc_start: 0.7054 (m-10) cc_final: 0.6695 (m-80) REVERT: D 329 SER cc_start: 0.7394 (m) cc_final: 0.7067 (p) REVERT: A 16 LEU cc_start: 0.8651 (mm) cc_final: 0.8364 (mm) REVERT: A 141 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.7764 (t) REVERT: A 170 SER cc_start: 0.8549 (m) cc_final: 0.8100 (t) REVERT: A 235 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7980 (pt) outliers start: 19 outliers final: 12 residues processed: 160 average time/residue: 0.2004 time to fit residues: 46.2671 Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.152650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116934 restraints weight = 12614.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119516 restraints weight = 10375.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120887 restraints weight = 7045.666| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10225 Z= 0.179 Angle : 0.595 8.889 14063 Z= 0.319 Chirality : 0.043 0.178 1618 Planarity : 0.004 0.042 1595 Dihedral : 21.129 178.523 1923 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.58 % Allowed : 15.89 % Favored : 81.53 % 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: -1.09 (0.24), residues: 1108 helix: 0.77 (0.29), residues: 322 sheet: -1.07 (0.28), residues: 317 loop : -1.45 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 274 HIS 0.003 0.001 HIS C 246 PHE 0.012 0.002 PHE C 169 TYR 0.012 0.002 TYR C 211 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 455) hydrogen bonds : angle 5.94400 ( 1271) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.53245 ( 4) covalent geometry : bond 0.00407 (10223) covalent geometry : angle 0.59484 (14059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: B 10 SER cc_start: 0.8507 (m) cc_final: 0.8151 (m) REVERT: B 71 ASN cc_start: 0.8046 (t0) cc_final: 0.7703 (t0) REVERT: B 75 MET cc_start: 0.8383 (ttt) cc_final: 0.7881 (ttt) REVERT: B 84 ASN cc_start: 0.7818 (m-40) cc_final: 0.7046 (t0) REVERT: D 160 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: D 198 GLU cc_start: 0.5451 (mp0) cc_final: 0.5029 (tm-30) REVERT: D 288 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.7066 (p) REVERT: D 329 SER cc_start: 0.7452 (m) cc_final: 0.7110 (p) REVERT: A 16 LEU cc_start: 0.8636 (mm) cc_final: 0.8353 (mm) REVERT: A 141 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.7847 (t) REVERT: A 170 SER cc_start: 0.8589 (m) cc_final: 0.8092 (t) REVERT: A 235 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8107 (pt) outliers start: 25 outliers final: 15 residues processed: 160 average time/residue: 0.2424 time to fit residues: 56.2581 Evaluate side-chains 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116963 restraints weight = 12595.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120398 restraints weight = 9715.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121585 restraints weight = 6260.268| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10225 Z= 0.165 Angle : 0.582 8.735 14063 Z= 0.312 Chirality : 0.042 0.178 1618 Planarity : 0.003 0.042 1595 Dihedral : 21.082 178.942 1923 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.68 % Allowed : 16.82 % Favored : 80.50 % 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: -0.99 (0.25), residues: 1108 helix: 0.89 (0.29), residues: 323 sheet: -1.11 (0.28), residues: 315 loop : -1.34 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 274 HIS 0.003 0.001 HIS C 246 PHE 0.016 0.002 PHE B 207 TYR 0.014 0.002 TYR C 211 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 455) hydrogen bonds : angle 5.88485 ( 1271) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.50063 ( 4) covalent geometry : bond 0.00378 (10223) covalent geometry : angle 0.58163 (14059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.132 Fit side-chains REVERT: B 10 SER cc_start: 0.8506 (m) cc_final: 0.8161 (m) REVERT: B 71 ASN cc_start: 0.8116 (t0) cc_final: 0.7671 (t0) REVERT: B 75 MET cc_start: 0.8380 (ttt) cc_final: 0.7821 (ttt) REVERT: B 84 ASN cc_start: 0.7826 (m-40) cc_final: 0.7029 (t0) REVERT: D 148 MET cc_start: 0.7842 (tpp) cc_final: 0.6926 (ttm) REVERT: D 160 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: D 268 TYR cc_start: 0.6383 (m-10) cc_final: 0.6148 (m-10) REVERT: D 288 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7141 (p) REVERT: D 329 SER cc_start: 0.7506 (m) cc_final: 0.7195 (p) REVERT: A 16 LEU cc_start: 0.8597 (mm) cc_final: 0.8314 (mm) REVERT: A 141 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.7833 (t) REVERT: A 235 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8159 (pt) outliers start: 26 outliers final: 18 residues processed: 167 average time/residue: 0.2096 time to fit residues: 50.3465 Evaluate side-chains 161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 91 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN D 77 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117622 restraints weight = 12659.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121220 restraints weight = 9539.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122300 restraints weight = 6055.210| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10225 Z= 0.158 Angle : 0.579 8.477 14063 Z= 0.310 Chirality : 0.042 0.181 1618 Planarity : 0.003 0.043 1595 Dihedral : 21.015 179.697 1923 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.79 % Allowed : 17.13 % Favored : 80.08 % 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: -0.96 (0.25), residues: 1108 helix: 1.04 (0.29), residues: 323 sheet: -1.16 (0.29), residues: 297 loop : -1.39 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 274 HIS 0.003 0.001 HIS C 246 PHE 0.015 0.001 PHE B 207 TYR 0.013 0.001 TYR C 211 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 455) hydrogen bonds : angle 5.82569 ( 1271) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.46616 ( 4) covalent geometry : bond 0.00362 (10223) covalent geometry : angle 0.57909 (14059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.004 Fit side-chains REVERT: B 10 SER cc_start: 0.8504 (m) cc_final: 0.8155 (m) REVERT: B 71 ASN cc_start: 0.8070 (t0) cc_final: 0.7708 (t0) REVERT: B 84 ASN cc_start: 0.7845 (m-40) cc_final: 0.7049 (t0) REVERT: B 175 LEU cc_start: 0.8393 (mp) cc_final: 0.8125 (mp) REVERT: C 139 MET cc_start: 0.8211 (ptm) cc_final: 0.7773 (ptt) REVERT: D 148 MET cc_start: 0.7826 (tpp) cc_final: 0.7088 (ttm) REVERT: D 160 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: D 198 GLU cc_start: 0.5502 (mp0) cc_final: 0.5049 (tm-30) REVERT: D 268 TYR cc_start: 0.6432 (m-10) cc_final: 0.6217 (m-10) REVERT: D 288 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.7202 (p) REVERT: D 329 SER cc_start: 0.7551 (m) cc_final: 0.7234 (p) REVERT: A 16 LEU cc_start: 0.8593 (mm) cc_final: 0.8302 (mm) REVERT: A 141 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.7857 (t) REVERT: A 235 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8143 (pt) outliers start: 27 outliers final: 21 residues processed: 164 average time/residue: 0.2695 time to fit residues: 63.4141 Evaluate side-chains 167 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114880 restraints weight = 12664.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117744 restraints weight = 10102.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118906 restraints weight = 6784.097| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10225 Z= 0.192 Angle : 0.613 8.926 14063 Z= 0.325 Chirality : 0.043 0.190 1618 Planarity : 0.003 0.042 1595 Dihedral : 20.979 178.225 1923 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.41 % Allowed : 17.13 % Favored : 79.46 % 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: -1.08 (0.25), residues: 1108 helix: 0.94 (0.29), residues: 323 sheet: -1.41 (0.29), residues: 275 loop : -1.34 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 274 HIS 0.004 0.001 HIS C 44 PHE 0.015 0.002 PHE B 207 TYR 0.019 0.002 TYR D 40 ARG 0.002 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 455) hydrogen bonds : angle 5.92799 ( 1271) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.56542 ( 4) covalent geometry : bond 0.00442 (10223) covalent geometry : angle 0.61316 (14059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.157 Fit side-chains REVERT: B 10 SER cc_start: 0.8498 (m) cc_final: 0.8219 (m) REVERT: B 71 ASN cc_start: 0.8153 (t0) cc_final: 0.7752 (t0) REVERT: B 84 ASN cc_start: 0.7787 (m-40) cc_final: 0.7017 (t0) REVERT: B 175 LEU cc_start: 0.8412 (mp) cc_final: 0.8141 (mp) REVERT: C 207 PHE cc_start: 0.8973 (m-80) cc_final: 0.8697 (m-80) REVERT: D 148 MET cc_start: 0.7889 (tpp) cc_final: 0.7176 (ttm) REVERT: D 160 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: D 329 SER cc_start: 0.7702 (m) cc_final: 0.7078 (p) REVERT: A 16 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8370 (mm) REVERT: A 141 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.7906 (t) REVERT: A 235 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8243 (pt) REVERT: A 244 MET cc_start: 0.7574 (tpp) cc_final: 0.7062 (tpp) outliers start: 33 outliers final: 24 residues processed: 165 average time/residue: 0.2924 time to fit residues: 72.0099 Evaluate side-chains 160 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118058 restraints weight = 12482.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121245 restraints weight = 9577.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122331 restraints weight = 6294.776| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10225 Z= 0.144 Angle : 0.574 8.401 14063 Z= 0.307 Chirality : 0.042 0.185 1618 Planarity : 0.003 0.045 1595 Dihedral : 20.919 178.938 1923 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.48 % Allowed : 18.16 % Favored : 79.36 % 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: -1.01 (0.25), residues: 1108 helix: 1.02 (0.29), residues: 323 sheet: -1.47 (0.29), residues: 285 loop : -1.24 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 274 HIS 0.005 0.001 HIS C 44 PHE 0.012 0.001 PHE B 207 TYR 0.015 0.002 TYR A 133 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 455) hydrogen bonds : angle 5.78955 ( 1271) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.56893 ( 4) covalent geometry : bond 0.00332 (10223) covalent geometry : angle 0.57423 (14059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.931 Fit side-chains REVERT: B 10 SER cc_start: 0.8478 (m) cc_final: 0.8141 (m) REVERT: B 71 ASN cc_start: 0.8050 (t0) cc_final: 0.7673 (t0) REVERT: B 84 ASN cc_start: 0.7820 (m-40) cc_final: 0.7002 (t0) REVERT: B 175 LEU cc_start: 0.8372 (mp) cc_final: 0.8113 (mp) REVERT: C 139 MET cc_start: 0.8129 (ptm) cc_final: 0.7594 (ptt) REVERT: C 207 PHE cc_start: 0.8913 (m-80) cc_final: 0.8530 (m-80) REVERT: D 86 ASP cc_start: 0.7453 (m-30) cc_final: 0.7004 (m-30) REVERT: D 148 MET cc_start: 0.7840 (tpp) cc_final: 0.7166 (ttm) REVERT: D 160 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: D 198 GLU cc_start: 0.5412 (mp0) cc_final: 0.4906 (tm-30) REVERT: D 288 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7261 (p) REVERT: D 329 SER cc_start: 0.7669 (m) cc_final: 0.7037 (p) REVERT: A 16 LEU cc_start: 0.8583 (mm) cc_final: 0.8292 (mm) REVERT: A 141 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.7883 (t) REVERT: A 235 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8180 (pt) outliers start: 24 outliers final: 18 residues processed: 162 average time/residue: 0.1987 time to fit residues: 46.3387 Evaluate side-chains 161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.3980 chunk 58 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117930 restraints weight = 12530.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.121030 restraints weight = 9577.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122217 restraints weight = 6344.385| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10225 Z= 0.133 Angle : 0.571 9.315 14063 Z= 0.302 Chirality : 0.041 0.184 1618 Planarity : 0.003 0.044 1595 Dihedral : 20.828 177.618 1923 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.96 % Allowed : 18.58 % Favored : 79.46 % 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: -0.90 (0.25), residues: 1108 helix: 1.09 (0.29), residues: 323 sheet: -1.42 (0.28), residues: 293 loop : -1.13 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 274 HIS 0.005 0.001 HIS C 44 PHE 0.015 0.001 PHE B 207 TYR 0.012 0.001 TYR A 133 ARG 0.002 0.000 ARG D 73 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 455) hydrogen bonds : angle 5.66846 ( 1271) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.60927 ( 4) covalent geometry : bond 0.00304 (10223) covalent geometry : angle 0.57068 (14059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.081 Fit side-chains REVERT: B 10 SER cc_start: 0.8603 (m) cc_final: 0.8241 (m) REVERT: B 17 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7123 (mm-30) REVERT: B 71 ASN cc_start: 0.8044 (t0) cc_final: 0.7677 (t0) REVERT: B 84 ASN cc_start: 0.7772 (m-40) cc_final: 0.6954 (t0) REVERT: B 205 LEU cc_start: 0.7484 (mt) cc_final: 0.7028 (mp) REVERT: C 139 MET cc_start: 0.8193 (ptm) cc_final: 0.7698 (ptt) REVERT: C 207 PHE cc_start: 0.8844 (m-80) cc_final: 0.8443 (m-80) REVERT: D 86 ASP cc_start: 0.7368 (m-30) cc_final: 0.6918 (m-30) REVERT: D 141 CYS cc_start: 0.7224 (t) cc_final: 0.6698 (t) REVERT: D 148 MET cc_start: 0.7869 (tpp) cc_final: 0.7030 (ttm) REVERT: D 160 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: D 198 GLU cc_start: 0.5496 (mp0) cc_final: 0.5083 (tm-30) REVERT: D 288 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7150 (p) REVERT: D 329 SER cc_start: 0.7787 (m) cc_final: 0.7460 (p) REVERT: A 16 LEU cc_start: 0.8563 (mm) cc_final: 0.8302 (mm) REVERT: A 235 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8117 (pt) outliers start: 19 outliers final: 13 residues processed: 157 average time/residue: 0.2096 time to fit residues: 47.8505 Evaluate side-chains 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.151555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116625 restraints weight = 12504.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120023 restraints weight = 9567.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120975 restraints weight = 6186.714| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10225 Z= 0.186 Angle : 0.608 8.839 14063 Z= 0.319 Chirality : 0.043 0.197 1618 Planarity : 0.003 0.043 1595 Dihedral : 20.770 175.846 1923 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.17 % Allowed : 18.78 % Favored : 79.05 % 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: -1.00 (0.25), residues: 1108 helix: 0.97 (0.29), residues: 323 sheet: -1.50 (0.28), residues: 291 loop : -1.14 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 274 HIS 0.005 0.001 HIS C 44 PHE 0.017 0.002 PHE D 27 TYR 0.013 0.002 TYR C 211 ARG 0.003 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 455) hydrogen bonds : angle 5.80682 ( 1271) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.63369 ( 4) covalent geometry : bond 0.00434 (10223) covalent geometry : angle 0.60796 (14059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.91 seconds wall clock time: 60 minutes 13.71 seconds (3613.71 seconds total)