Starting phenix.real_space_refine on Sun Dec 29 06:33:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjw_39352/12_2024/8yjw_39352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjw_39352/12_2024/8yjw_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_39352/12_2024/8yjw_39352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjw_39352/12_2024/8yjw_39352.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjw_39352/12_2024/8yjw_39352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjw_39352/12_2024/8yjw_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-5532/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: 6.70, per 1000 atoms: 0.67 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: 2.40 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: 3.48 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: 3.54 Time building geometry restraints manager: 2.77 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.690 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.360 ------------------------------------------------------------------------------- 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 10223 Z= 0.356 Angle : 1.052 12.323 14059 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 *********************** 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 : 1.023 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: 0.2150 time to fit residues: 50.2089 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 : 1.034 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 10223 Z= 0.180 Angle : 0.593 8.435 14059 Z= 0.324 Chirality : 0.043 0.146 1618 Planarity : 0.004 0.046 1595 Dihedral : 21.319 177.173 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 *********************** 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 : 1.059 Fit side-chains REVERT: B 10 SER cc_start: 0.8282 (m) cc_final: 0.7867 (m) REVERT: B 84 ASN cc_start: 0.7590 (m-40) cc_final: 0.6969 (t0) REVERT: B 207 PHE cc_start: 0.8440 (m-10) cc_final: 0.8228 (m-10) REVERT: D 108 GLU cc_start: 0.7342 (tp30) cc_final: 0.7037 (tm-30) REVERT: D 263 LEU cc_start: 0.6369 (tt) cc_final: 0.6005 (tp) REVERT: A 68 MET cc_start: 0.7280 (pmm) cc_final: 0.7065 (ptp) REVERT: A 141 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7660 (t) REVERT: A 170 SER cc_start: 0.8561 (m) cc_final: 0.8105 (t) outliers start: 8 outliers final: 1 residues processed: 162 average time/residue: 0.2175 time to fit residues: 49.7098 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 : 1.115 ------------------------------------------------------------------------------- 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 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 D 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10223 Z= 0.185 Angle : 0.556 8.595 14059 Z= 0.303 Chirality : 0.042 0.147 1618 Planarity : 0.004 0.046 1595 Dihedral : 21.214 176.466 1923 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.14 % Allowed : 12.18 % Favored : 86.69 % 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: -1.52 (0.24), residues: 1108 helix: 0.12 (0.28), residues: 324 sheet: -1.24 (0.28), residues: 322 loop : -1.53 (0.26), residues: 462 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 0.009 0.001 TYR C 211 ARG 0.003 0.000 ARG C 91 *********************** 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: 11 poor density : 152 time to evaluate : 1.091 Fit side-chains REVERT: B 10 SER cc_start: 0.8397 (m) cc_final: 0.7927 (m) REVERT: B 84 ASN cc_start: 0.7660 (m-40) cc_final: 0.6946 (t0) REVERT: B 207 PHE cc_start: 0.8542 (m-80) cc_final: 0.8220 (m-10) REVERT: C 207 PHE cc_start: 0.8818 (m-80) cc_final: 0.8542 (m-80) REVERT: D 67 MET cc_start: 0.6783 (ttm) cc_final: 0.6528 (ttp) REVERT: D 108 GLU cc_start: 0.7280 (tp30) cc_final: 0.7005 (tm-30) REVERT: D 263 LEU cc_start: 0.6551 (tt) cc_final: 0.6220 (tp) REVERT: A 25 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7359 (mt-10) REVERT: A 141 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7690 (t) REVERT: A 170 SER cc_start: 0.8511 (m) cc_final: 0.8074 (t) outliers start: 11 outliers final: 5 residues processed: 156 average time/residue: 0.2078 time to fit residues: 46.8570 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 55 GLU 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 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10223 Z= 0.249 Angle : 0.582 9.280 14059 Z= 0.315 Chirality : 0.043 0.155 1618 Planarity : 0.004 0.042 1595 Dihedral : 21.136 177.967 1923 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.06 % Allowed : 13.83 % Favored : 84.11 % 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: -1.28 (0.24), residues: 1108 helix: 0.57 (0.29), residues: 324 sheet: -1.24 (0.27), residues: 334 loop : -1.48 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 274 HIS 0.005 0.001 HIS C 44 PHE 0.020 0.002 PHE D 283 TYR 0.011 0.002 TYR C 211 ARG 0.004 0.000 ARG C 91 *********************** 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 168 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.058 Fit side-chains REVERT: B 10 SER cc_start: 0.8491 (m) cc_final: 0.8120 (m) REVERT: B 75 MET cc_start: 0.8344 (ttt) cc_final: 0.7811 (ttt) REVERT: B 84 ASN cc_start: 0.7709 (m-40) cc_final: 0.6976 (t0) REVERT: C 119 MET cc_start: 0.6902 (ptt) cc_final: 0.6675 (ptt) REVERT: C 207 PHE cc_start: 0.8969 (m-80) cc_final: 0.8681 (m-80) REVERT: D 69 TYR cc_start: 0.7135 (m-10) cc_final: 0.6730 (m-80) REVERT: D 77 ASN cc_start: 0.7593 (m110) cc_final: 0.7383 (m110) REVERT: D 108 GLU cc_start: 0.7211 (tp30) cc_final: 0.7001 (tm-30) REVERT: D 281 GLN cc_start: 0.7401 (pp30) cc_final: 0.7170 (tm-30) REVERT: D 329 SER cc_start: 0.7406 (m) cc_final: 0.7078 (p) REVERT: A 16 LEU cc_start: 0.8673 (mm) cc_final: 0.8378 (mm) REVERT: A 141 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.7785 (t) REVERT: A 170 SER cc_start: 0.8624 (m) cc_final: 0.8151 (t) REVERT: A 235 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8021 (pt) outliers start: 20 outliers final: 13 residues processed: 161 average time/residue: 0.2115 time to fit residues: 48.6254 Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 55 GLU 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 233 VAL 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 93 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10223 Z= 0.274 Angle : 0.610 9.397 14059 Z= 0.326 Chirality : 0.043 0.182 1618 Planarity : 0.004 0.042 1595 Dihedral : 21.165 178.722 1923 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.79 % Allowed : 15.79 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1108 helix: 0.70 (0.29), residues: 322 sheet: -1.16 (0.27), residues: 325 loop : -1.44 (0.28), residues: 461 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 0.018 0.002 PHE B 207 TYR 0.013 0.002 TYR C 211 ARG 0.003 0.000 ARG C 91 *********************** 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 177 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.161 Fit side-chains REVERT: B 10 SER cc_start: 0.8477 (m) cc_final: 0.8187 (m) REVERT: B 75 MET cc_start: 0.8386 (ttt) cc_final: 0.7878 (ttt) REVERT: B 84 ASN cc_start: 0.7763 (m-40) cc_final: 0.7031 (t0) REVERT: D 160 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: D 198 GLU cc_start: 0.5383 (mp0) cc_final: 0.5043 (tm-30) REVERT: D 268 TYR cc_start: 0.6386 (m-10) cc_final: 0.6129 (m-10) REVERT: D 281 GLN cc_start: 0.7501 (pp30) cc_final: 0.7274 (tm-30) REVERT: D 288 VAL cc_start: 0.7432 (OUTLIER) cc_final: 0.7178 (p) REVERT: D 329 SER cc_start: 0.7541 (m) cc_final: 0.7223 (p) REVERT: A 16 LEU cc_start: 0.8690 (mm) cc_final: 0.8418 (mm) REVERT: A 141 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.7881 (t) REVERT: A 170 SER cc_start: 0.8610 (m) cc_final: 0.8134 (t) REVERT: A 235 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8208 (pt) outliers start: 27 outliers final: 18 residues processed: 165 average time/residue: 0.2115 time to fit residues: 50.0712 Evaluate side-chains 165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain C 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 73 ARG Chi-restraints excluded: chain D residue 134 THR 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 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 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.0270 chunk 27 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 108 optimal weight: 0.4980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10223 Z= 0.185 Angle : 0.555 8.569 14059 Z= 0.298 Chirality : 0.041 0.175 1618 Planarity : 0.003 0.044 1595 Dihedral : 21.061 178.208 1923 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.27 % Allowed : 17.03 % Favored : 80.70 % 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: 0.89 (0.29), residues: 325 sheet: -1.09 (0.29), residues: 307 loop : -1.41 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 274 HIS 0.003 0.001 HIS C 44 PHE 0.010 0.001 PHE B 207 TYR 0.013 0.001 TYR D 40 ARG 0.003 0.000 ARG C 91 *********************** 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 173 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.984 Fit side-chains REVERT: B 10 SER cc_start: 0.8454 (m) cc_final: 0.8112 (m) REVERT: B 17 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 84 ASN cc_start: 0.7740 (m-40) cc_final: 0.6989 (t0) REVERT: C 119 MET cc_start: 0.7089 (ptt) cc_final: 0.6852 (ptt) REVERT: C 207 PHE cc_start: 0.8869 (m-80) cc_final: 0.8483 (m-80) REVERT: D 86 ASP cc_start: 0.7506 (m-30) cc_final: 0.7151 (m-30) REVERT: D 268 TYR cc_start: 0.6336 (m-10) cc_final: 0.6107 (m-10) REVERT: D 281 GLN cc_start: 0.7498 (pp30) cc_final: 0.7280 (tm-30) REVERT: D 329 SER cc_start: 0.7431 (m) cc_final: 0.7153 (p) REVERT: A 141 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.7810 (t) REVERT: A 235 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8136 (pt) outliers start: 22 outliers final: 16 residues processed: 165 average time/residue: 0.2098 time to fit residues: 49.3890 Evaluate side-chains 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 109 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 224 THR 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 184 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 136 VAL 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 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10223 Z= 0.251 Angle : 0.593 8.997 14059 Z= 0.315 Chirality : 0.043 0.184 1618 Planarity : 0.003 0.043 1595 Dihedral : 21.006 179.220 1923 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.89 % Allowed : 17.34 % Favored : 79.77 % 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: -0.88 (0.25), residues: 1108 helix: 1.02 (0.29), residues: 321 sheet: -1.06 (0.28), residues: 325 loop : -1.29 (0.28), residues: 462 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 0.012 0.002 PHE C 169 TYR 0.014 0.002 TYR C 211 ARG 0.003 0.000 ARG C 91 *********************** 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 168 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.109 Fit side-chains REVERT: B 10 SER cc_start: 0.8464 (m) cc_final: 0.8169 (m) REVERT: B 84 ASN cc_start: 0.7780 (m-40) cc_final: 0.7027 (t0) REVERT: C 207 PHE cc_start: 0.8958 (m-80) cc_final: 0.8620 (m-80) REVERT: D 148 MET cc_start: 0.7812 (tpp) cc_final: 0.7102 (ttm) REVERT: D 198 GLU cc_start: 0.5512 (mp0) cc_final: 0.5019 (tm-30) REVERT: D 268 TYR cc_start: 0.6466 (m-10) cc_final: 0.6254 (m-10) REVERT: D 281 GLN cc_start: 0.7514 (pp30) cc_final: 0.7271 (tm-30) REVERT: D 288 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7204 (p) REVERT: D 329 SER cc_start: 0.7613 (m) cc_final: 0.7315 (p) REVERT: A 141 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.7909 (t) REVERT: A 235 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8225 (pt) outliers start: 28 outliers final: 22 residues processed: 157 average time/residue: 0.2180 time to fit residues: 49.1769 Evaluate side-chains 163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 167 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 116 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 224 THR 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 141 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 104 optimal weight: 0.0070 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10223 Z= 0.169 Angle : 0.558 7.794 14059 Z= 0.298 Chirality : 0.042 0.175 1618 Planarity : 0.003 0.044 1595 Dihedral : 20.914 179.638 1923 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.58 % Allowed : 18.06 % 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: -0.83 (0.25), residues: 1108 helix: 1.11 (0.29), residues: 325 sheet: -1.07 (0.29), residues: 299 loop : -1.30 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 274 HIS 0.003 0.001 HIS C 44 PHE 0.008 0.001 PHE D 207 TYR 0.012 0.001 TYR D 40 ARG 0.002 0.000 ARG C 91 *********************** 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 167 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.047 Fit side-chains REVERT: B 10 SER cc_start: 0.8443 (m) cc_final: 0.8113 (m) REVERT: B 17 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7055 (mm-30) REVERT: B 84 ASN cc_start: 0.7719 (m-40) cc_final: 0.6924 (t0) REVERT: C 207 PHE cc_start: 0.8871 (m-80) cc_final: 0.8516 (m-80) REVERT: D 86 ASP cc_start: 0.7476 (m-30) cc_final: 0.7084 (m-30) REVERT: D 148 MET cc_start: 0.7901 (tpp) cc_final: 0.6942 (ttm) REVERT: D 198 GLU cc_start: 0.5511 (mp0) cc_final: 0.5040 (tm-30) REVERT: D 281 GLN cc_start: 0.7474 (pp30) cc_final: 0.7258 (tm-30) REVERT: D 288 VAL cc_start: 0.7309 (OUTLIER) cc_final: 0.7043 (p) REVERT: D 329 SER cc_start: 0.7527 (m) cc_final: 0.7250 (p) REVERT: A 141 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.7840 (t) REVERT: A 235 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8157 (pt) outliers start: 25 outliers final: 18 residues processed: 159 average time/residue: 0.2155 time to fit residues: 50.0275 Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 109 GLU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C 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 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 177 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN D 266 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10223 Z= 0.302 Angle : 0.635 8.779 14059 Z= 0.332 Chirality : 0.044 0.358 1618 Planarity : 0.004 0.043 1595 Dihedral : 20.886 176.997 1923 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.10 % Allowed : 17.96 % Favored : 78.95 % 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: -0.92 (0.25), residues: 1108 helix: 0.96 (0.29), residues: 321 sheet: -1.17 (0.28), residues: 315 loop : -1.22 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 274 HIS 0.006 0.001 HIS C 44 PHE 0.011 0.002 PHE C 169 TYR 0.015 0.002 TYR C 211 ARG 0.003 0.000 ARG D 73 *********************** 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 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.028 Fit side-chains REVERT: B 10 SER cc_start: 0.8551 (m) cc_final: 0.8182 (m) REVERT: B 75 MET cc_start: 0.8385 (ttt) cc_final: 0.7859 (ttt) REVERT: B 84 ASN cc_start: 0.7759 (m-40) cc_final: 0.6979 (t0) REVERT: D 73 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7003 (ttm110) REVERT: D 148 MET cc_start: 0.7812 (tpp) cc_final: 0.7376 (ttm) REVERT: D 329 SER cc_start: 0.7633 (m) cc_final: 0.7333 (p) REVERT: A 141 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.7948 (t) REVERT: A 235 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8288 (pt) outliers start: 30 outliers final: 20 residues processed: 155 average time/residue: 0.2176 time to fit residues: 49.4848 Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 59 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 116 MET 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 84 VAL Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 177 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10223 Z= 0.235 Angle : 0.606 8.391 14059 Z= 0.319 Chirality : 0.043 0.282 1618 Planarity : 0.003 0.043 1595 Dihedral : 20.851 177.973 1923 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.37 % Allowed : 18.58 % 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: -0.99 (0.25), residues: 1108 helix: 0.97 (0.29), residues: 323 sheet: -1.40 (0.28), residues: 295 loop : -1.19 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 274 HIS 0.004 0.001 HIS C 44 PHE 0.008 0.001 PHE D 207 TYR 0.015 0.002 TYR D 40 ARG 0.003 0.000 ARG D 19 ********************** 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 157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.979 Fit side-chains REVERT: B 10 SER cc_start: 0.8536 (m) cc_final: 0.8176 (m) REVERT: B 17 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 84 ASN cc_start: 0.7784 (m-40) cc_final: 0.6981 (t0) REVERT: C 207 PHE cc_start: 0.8941 (m-80) cc_final: 0.8605 (m-80) REVERT: D 40 TYR cc_start: 0.7308 (m-10) cc_final: 0.7049 (m-10) REVERT: D 67 MET cc_start: 0.7015 (ttp) cc_final: 0.6778 (mtm) REVERT: D 148 MET cc_start: 0.7845 (tpp) cc_final: 0.7092 (ttm) REVERT: D 288 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7235 (p) REVERT: D 329 SER cc_start: 0.7663 (m) cc_final: 0.7373 (p) REVERT: A 235 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8242 (pt) outliers start: 23 outliers final: 16 residues processed: 150 average time/residue: 0.2024 time to fit residues: 44.3203 Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 109 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 121 LEU 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 141 CYS Chi-restraints excluded: chain D residue 177 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.0970 chunk 94 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.152845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117977 restraints weight = 12452.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121119 restraints weight = 9614.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122199 restraints weight = 6352.727| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10223 Z= 0.202 Angle : 0.593 10.164 14059 Z= 0.311 Chirality : 0.042 0.236 1618 Planarity : 0.003 0.044 1595 Dihedral : 20.766 177.040 1923 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.96 % Allowed : 19.30 % Favored : 78.74 % 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: 1.03 (0.29), residues: 325 sheet: -1.35 (0.28), residues: 295 loop : -1.14 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 274 HIS 0.007 0.001 HIS C 44 PHE 0.008 0.001 PHE D 207 TYR 0.015 0.002 TYR D 40 ARG 0.002 0.000 ARG D 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.82 seconds wall clock time: 41 minutes 23.37 seconds (2483.37 seconds total)