Starting phenix.real_space_refine on Thu Feb 13 02:24:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f8w_31494/02_2025/7f8w_31494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8w_31494/02_2025/7f8w_31494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f8w_31494/02_2025/7f8w_31494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8w_31494/02_2025/7f8w_31494.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8w_31494/02_2025/7f8w_31494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8w_31494/02_2025/7f8w_31494.cif" } resolution = 3.1 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5421 2.51 5 N 1449 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1850 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2347 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 300} Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 245 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "D" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 133 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PCA:plan-2': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2128 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 4.93, per 1000 atoms: 0.58 Number of scatterers: 8486 At special positions: 0 Unit cell: (128.535, 117.04, 90.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1556 8.00 N 1449 7.00 C 5421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 113 " distance=2.04 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " 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: 2.71 Conformation dependent library (CDL) restraints added in 992.5 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 14 sheets defined 32.9% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 4.260A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.529A pdb=" N PHE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A 57 " --> pdb=" O MET A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 4.224A pdb=" N TRP A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 273 through 280 removed outlier: 4.412A pdb=" N SER A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.662A pdb=" N GLU A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 79 through 82 removed outlier: 4.014A pdb=" N LYS D 82 " --> pdb=" O ASP D 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'R' and resid 56 through 81 removed outlier: 3.850A pdb=" N LEU R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 117 Proline residue: R 109 - end of helix Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 123 through 157 Processing helix chain 'R' and resid 158 through 166 Processing helix chain 'R' and resid 167 through 186 removed outlier: 3.604A pdb=" N MET R 186 " --> pdb=" O SER R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 226 Processing helix chain 'R' and resid 227 through 249 removed outlier: 3.524A pdb=" N LEU R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 359 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 362 through 367 Processing helix chain 'R' and resid 369 through 391 removed outlier: 3.787A pdb=" N SER R 379 " --> pdb=" O ILE R 375 " (cutoff:3.500A) Proline residue: R 387 - end of helix Processing helix chain 'R' and resid 394 through 405 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 4.641A pdb=" N LEU A 36 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE A 266 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 222 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.958A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.951A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.123A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.199A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.890A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.513A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 Processing sheet with id=AA9, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.766A pdb=" N THR D 86 " --> pdb=" O GLN D 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 28 through 29 removed outlier: 4.057A pdb=" N VAL D 29 " --> pdb=" O THR D 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 77 removed outlier: 3.878A pdb=" N PHE D 127 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AB4, first strand: chain 'D' and resid 163 through 165 removed outlier: 6.294A pdb=" N VAL D 164 " --> pdb=" O GLU D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 211 through 212 removed outlier: 5.337A pdb=" N LEU D 204 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU D 195 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 206 " --> pdb=" O TRP D 193 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR D 245 " --> pdb=" O PHE D 194 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.50 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: 1835 1.33 - 1.45: 2081 1.45 - 1.58: 4667 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 8674 Sorted by residual: bond pdb=" N MET D 247 " pdb=" CA MET D 247 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.26e-02 6.30e+03 8.86e+00 bond pdb=" N GLN D 248 " pdb=" CA GLN D 248 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.27e-02 6.20e+03 8.42e+00 bond pdb=" N CYS R 107 " pdb=" CA CYS R 107 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.06e+00 bond pdb=" N MET R 108 " pdb=" CA MET R 108 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.50e-03 1.11e+04 7.66e+00 bond pdb=" N MET R 134 " pdb=" CA MET R 134 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.64e+00 ... (remaining 8669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11233 2.24 - 4.48: 439 4.48 - 6.72: 68 6.72 - 8.97: 24 8.97 - 11.21: 7 Bond angle restraints: 11771 Sorted by residual: angle pdb=" C ARG D 208 " pdb=" N MET D 209 " pdb=" CA MET D 209 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N GLN D 248 " pdb=" CA GLN D 248 " pdb=" CB GLN D 248 " ideal model delta sigma weight residual 110.41 117.79 -7.38 1.63e+00 3.76e-01 2.05e+01 angle pdb=" CA ARG R 158 " pdb=" CB ARG R 158 " pdb=" CG ARG R 158 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" N PCA E 1 " pdb=" CA PCA E 1 " pdb=" CB PCA E 1 " ideal model delta sigma weight residual 110.50 103.43 7.07 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CA LYS A 17 " pdb=" CB LYS A 17 " pdb=" CG LYS A 17 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.64e+01 ... (remaining 11766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4644 17.98 - 35.95: 390 35.95 - 53.93: 76 53.93 - 71.91: 7 71.91 - 89.89: 7 Dihedral angle restraints: 5124 sinusoidal: 1980 harmonic: 3144 Sorted by residual: dihedral pdb=" CA VAL R 164 " pdb=" C VAL R 164 " pdb=" N TRP R 165 " pdb=" CA TRP R 165 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU A 33 " pdb=" C GLU A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 66 " pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1021 0.062 - 0.125: 251 0.125 - 0.187: 59 0.187 - 0.249: 5 0.249 - 0.311: 3 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CB THR A 254 " pdb=" CA THR A 254 " pdb=" OG1 THR A 254 " pdb=" CG2 THR A 254 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ARG R 158 " pdb=" N ARG R 158 " pdb=" C ARG R 158 " pdb=" CB ARG R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1336 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA E 1 " 0.066 2.00e-02 2.50e+03 4.39e-02 2.41e+01 pdb=" CA PCA E 1 " -0.055 2.00e-02 2.50e+03 pdb=" CG PCA E 1 " 0.021 2.00e-02 2.50e+03 pdb=" CD PCA E 1 " 0.009 2.00e-02 2.50e+03 pdb=" OE PCA E 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " 0.027 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP B 332 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 245 " 0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR D 245 " -0.062 2.00e-02 2.50e+03 pdb=" O TYR D 245 " 0.024 2.00e-02 2.50e+03 pdb=" N CYS D 246 " 0.021 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1991 2.80 - 3.32: 7783 3.32 - 3.85: 14432 3.85 - 4.37: 16155 4.37 - 4.90: 28184 Nonbonded interactions: 68545 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.273 3.040 nonbonded pdb=" O VAL A 13 " pdb=" OG SER A 16 " model vdw 2.294 3.040 nonbonded pdb=" OG SER D 47 " pdb=" OD1 ASP D 91 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.307 3.040 nonbonded pdb=" NZ LYS A 209 " pdb=" OD2 ASP B 228 " model vdw 2.313 3.120 ... (remaining 68540 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.260 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 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 : 0.005 0.062 8674 Z= 0.327 Angle : 1.039 11.208 11771 Z= 0.554 Chirality : 0.059 0.311 1339 Planarity : 0.008 0.087 1484 Dihedral : 14.087 89.886 3094 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -1.99 (0.23), residues: 1067 helix: -0.31 (0.26), residues: 308 sheet: -1.21 (0.33), residues: 242 loop : -2.00 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP B 332 HIS 0.013 0.002 HIS A 212 PHE 0.041 0.003 PHE B 234 TYR 0.022 0.002 TYR A 279 ARG 0.014 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.943 Fit side-chains REVERT: A 26 ASP cc_start: 0.6145 (m-30) cc_final: 0.5893 (m-30) REVERT: A 242 MET cc_start: 0.4577 (tpt) cc_final: 0.4270 (tpt) REVERT: A 306 MET cc_start: 0.5356 (tmm) cc_final: 0.5114 (ttt) REVERT: B 111 TYR cc_start: 0.6260 (m-80) cc_final: 0.5894 (m-80) REVERT: D 115 ARG cc_start: 0.6902 (ttp-170) cc_final: 0.6208 (ptt180) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2279 time to fit residues: 52.0446 Evaluate side-chains 120 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.211045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.177674 restraints weight = 10543.236| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 2.11 r_work: 0.4313 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.4175 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8674 Z= 0.441 Angle : 0.847 17.109 11771 Z= 0.435 Chirality : 0.050 0.165 1339 Planarity : 0.006 0.072 1484 Dihedral : 5.773 26.809 1189 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.95 % Allowed : 11.62 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.24), residues: 1067 helix: 0.39 (0.27), residues: 319 sheet: -1.48 (0.30), residues: 269 loop : -1.82 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 165 HIS 0.007 0.002 HIS D 184 PHE 0.029 0.003 PHE B 335 TYR 0.021 0.002 TYR B 85 ARG 0.006 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.903 Fit side-chains REVERT: A 26 ASP cc_start: 0.6555 (m-30) cc_final: 0.6231 (m-30) REVERT: A 33 GLU cc_start: 0.5486 (mp0) cc_final: 0.5184 (mp0) REVERT: A 242 MET cc_start: 0.4439 (tpt) cc_final: 0.4223 (tpt) REVERT: B 234 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.5926 (t80) REVERT: D 110 MET cc_start: 0.6892 (tpp) cc_final: 0.6486 (tpp) REVERT: R 186 MET cc_start: 0.2165 (tmm) cc_final: 0.1597 (ttt) outliers start: 18 outliers final: 13 residues processed: 147 average time/residue: 0.2028 time to fit residues: 41.1128 Evaluate side-chains 132 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.213499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.175111 restraints weight = 10679.628| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.52 r_work: 0.4337 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8674 Z= 0.236 Angle : 0.663 12.786 11771 Z= 0.344 Chirality : 0.044 0.162 1339 Planarity : 0.005 0.055 1484 Dihedral : 5.244 27.025 1189 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.71 % Allowed : 15.96 % Favored : 81.32 % 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: -1.30 (0.25), residues: 1067 helix: 0.94 (0.28), residues: 320 sheet: -1.53 (0.30), residues: 277 loop : -1.67 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 165 HIS 0.005 0.001 HIS R 207 PHE 0.018 0.002 PHE B 234 TYR 0.018 0.002 TYR A 319 ARG 0.004 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.962 Fit side-chains REVERT: A 26 ASP cc_start: 0.6393 (m-30) cc_final: 0.6085 (m-30) REVERT: B 217 MET cc_start: 0.6902 (ppp) cc_final: 0.6642 (ppp) REVERT: B 234 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.5758 (t80) REVERT: B 264 TYR cc_start: 0.5799 (m-10) cc_final: 0.5515 (m-10) REVERT: C 50 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.6064 (mm) REVERT: R 229 ILE cc_start: 0.6413 (OUTLIER) cc_final: 0.6109 (mt) REVERT: R 393 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.4893 (mmt) outliers start: 25 outliers final: 12 residues processed: 137 average time/residue: 0.1793 time to fit residues: 35.3520 Evaluate side-chains 130 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 HIS ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN D 130 GLN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.212866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.174727 restraints weight = 10550.683| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 2.50 r_work: 0.4336 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8674 Z= 0.225 Angle : 0.646 12.518 11771 Z= 0.332 Chirality : 0.043 0.199 1339 Planarity : 0.004 0.049 1484 Dihedral : 5.043 26.712 1189 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.37 % Allowed : 16.83 % Favored : 79.80 % 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: -1.11 (0.25), residues: 1067 helix: 1.26 (0.28), residues: 321 sheet: -1.56 (0.30), residues: 287 loop : -1.57 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 165 HIS 0.012 0.001 HIS A 212 PHE 0.017 0.002 PHE B 234 TYR 0.020 0.002 TYR R 380 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 1.084 Fit side-chains REVERT: A 26 ASP cc_start: 0.6199 (m-30) cc_final: 0.5913 (m-30) REVERT: A 317 ILE cc_start: 0.5544 (OUTLIER) cc_final: 0.5139 (mp) REVERT: B 42 ARG cc_start: 0.6166 (ttp80) cc_final: 0.5453 (tpt170) REVERT: B 234 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.5697 (t80) REVERT: B 264 TYR cc_start: 0.5805 (m-10) cc_final: 0.5520 (m-10) REVERT: C 50 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6191 (mm) REVERT: D 110 MET cc_start: 0.6741 (tpp) cc_final: 0.6386 (tpp) REVERT: R 73 MET cc_start: 0.6252 (tmm) cc_final: 0.5882 (tmm) REVERT: R 186 MET cc_start: 0.2644 (tmm) cc_final: 0.1575 (ttm) REVERT: R 229 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.6039 (mt) REVERT: R 393 MET cc_start: 0.5513 (OUTLIER) cc_final: 0.4877 (mmt) outliers start: 31 outliers final: 18 residues processed: 143 average time/residue: 0.2038 time to fit residues: 40.5790 Evaluate side-chains 136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.211045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.172658 restraints weight = 10596.898| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.49 r_work: 0.4313 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8674 Z= 0.251 Angle : 0.658 13.950 11771 Z= 0.335 Chirality : 0.044 0.172 1339 Planarity : 0.004 0.047 1484 Dihedral : 5.005 26.198 1189 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.02 % Allowed : 18.02 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.07 (0.25), residues: 1067 helix: 1.33 (0.28), residues: 321 sheet: -1.60 (0.30), residues: 287 loop : -1.53 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 165 HIS 0.004 0.001 HIS C 44 PHE 0.018 0.002 PHE B 234 TYR 0.016 0.002 TYR A 319 ARG 0.004 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.905 Fit side-chains REVERT: A 26 ASP cc_start: 0.6400 (m-30) cc_final: 0.6081 (m-30) REVERT: A 317 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5104 (mp) REVERT: B 42 ARG cc_start: 0.6156 (ttp80) cc_final: 0.5475 (tpt170) REVERT: B 217 MET cc_start: 0.7122 (ppp) cc_final: 0.6813 (ppp) REVERT: B 234 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.5861 (t80) REVERT: C 50 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6333 (mm) REVERT: D 183 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5448 (tt) REVERT: R 229 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.6107 (mt) REVERT: R 393 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.4970 (mmt) outliers start: 37 outliers final: 22 residues processed: 148 average time/residue: 0.1912 time to fit residues: 39.9218 Evaluate side-chains 136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.204719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.167461 restraints weight = 10531.116| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 2.30 r_work: 0.4260 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8674 Z= 0.357 Angle : 0.733 16.649 11771 Z= 0.374 Chirality : 0.046 0.267 1339 Planarity : 0.005 0.054 1484 Dihedral : 5.308 25.343 1189 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.23 % Allowed : 19.33 % Favored : 76.44 % 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: -1.27 (0.25), residues: 1067 helix: 1.02 (0.28), residues: 326 sheet: -1.67 (0.29), residues: 292 loop : -1.59 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 165 HIS 0.006 0.002 HIS A 212 PHE 0.025 0.003 PHE B 234 TYR 0.020 0.002 TYR A 319 ARG 0.004 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.905 Fit side-chains REVERT: A 24 ARG cc_start: 0.5394 (tpp80) cc_final: 0.4894 (ttt180) REVERT: A 26 ASP cc_start: 0.6535 (m-30) cc_final: 0.6226 (m-30) REVERT: A 33 GLU cc_start: 0.5488 (OUTLIER) cc_final: 0.4462 (mp0) REVERT: B 42 ARG cc_start: 0.6037 (ttp80) cc_final: 0.5651 (tpt170) REVERT: B 217 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7053 (ppp) REVERT: B 234 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6294 (t80) REVERT: C 50 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6494 (mm) REVERT: D 110 MET cc_start: 0.6740 (tpp) cc_final: 0.6393 (tpp) REVERT: R 186 MET cc_start: 0.3070 (tmm) cc_final: 0.2202 (mtp) REVERT: R 229 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6522 (mt) outliers start: 39 outliers final: 26 residues processed: 145 average time/residue: 0.2070 time to fit residues: 41.2605 Evaluate side-chains 144 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.206493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.167522 restraints weight = 10748.263| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.52 r_work: 0.4263 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8674 Z= 0.296 Angle : 0.700 14.811 11771 Z= 0.356 Chirality : 0.045 0.212 1339 Planarity : 0.005 0.050 1484 Dihedral : 5.218 26.284 1189 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.45 % Allowed : 19.44 % Favored : 76.11 % 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: -1.24 (0.25), residues: 1067 helix: 1.06 (0.28), residues: 326 sheet: -1.63 (0.30), residues: 292 loop : -1.60 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 99 HIS 0.004 0.001 HIS B 62 PHE 0.021 0.002 PHE B 234 TYR 0.020 0.002 TYR A 319 ARG 0.003 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.927 Fit side-chains REVERT: A 22 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.6170 (t0) REVERT: A 24 ARG cc_start: 0.5290 (tpp80) cc_final: 0.4831 (ttt180) REVERT: A 26 ASP cc_start: 0.6439 (m-30) cc_final: 0.5913 (m-30) REVERT: A 33 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4315 (mp0) REVERT: A 317 ILE cc_start: 0.5578 (OUTLIER) cc_final: 0.5206 (mp) REVERT: B 42 ARG cc_start: 0.6122 (ttp80) cc_final: 0.5597 (mmt180) REVERT: B 217 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6960 (ppp) REVERT: B 234 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6140 (t80) REVERT: C 38 MET cc_start: 0.4605 (mmt) cc_final: 0.4240 (mpp) REVERT: D 110 MET cc_start: 0.6852 (tpp) cc_final: 0.6435 (tpp) REVERT: R 134 MET cc_start: 0.5705 (mmp) cc_final: 0.4864 (mmp) REVERT: R 229 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6336 (mp) outliers start: 41 outliers final: 28 residues processed: 151 average time/residue: 0.1997 time to fit residues: 42.1692 Evaluate side-chains 153 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 382 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 65 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.210780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.175024 restraints weight = 10657.517| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 2.24 r_work: 0.4324 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4186 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8674 Z= 0.234 Angle : 0.663 12.958 11771 Z= 0.337 Chirality : 0.044 0.183 1339 Planarity : 0.004 0.046 1484 Dihedral : 5.038 26.652 1189 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.34 % Allowed : 20.74 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1067 helix: 1.22 (0.28), residues: 327 sheet: -1.57 (0.30), residues: 286 loop : -1.63 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 346 HIS 0.005 0.001 HIS A 212 PHE 0.017 0.002 PHE B 234 TYR 0.018 0.002 TYR A 319 ARG 0.004 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.976 Fit side-chains REVERT: A 22 ASN cc_start: 0.6436 (OUTLIER) cc_final: 0.6231 (t0) REVERT: A 24 ARG cc_start: 0.5219 (tpp80) cc_final: 0.4739 (ttt180) REVERT: A 26 ASP cc_start: 0.6500 (m-30) cc_final: 0.5978 (m-30) REVERT: A 33 GLU cc_start: 0.5385 (OUTLIER) cc_final: 0.4458 (mp0) REVERT: A 317 ILE cc_start: 0.5474 (OUTLIER) cc_final: 0.5134 (mp) REVERT: B 42 ARG cc_start: 0.6169 (ttp80) cc_final: 0.5614 (mmt180) REVERT: B 217 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6980 (ppp) REVERT: B 234 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6144 (t80) REVERT: C 38 MET cc_start: 0.4650 (mmt) cc_final: 0.4260 (mpp) REVERT: D 110 MET cc_start: 0.6699 (tpp) cc_final: 0.6306 (tpp) REVERT: R 134 MET cc_start: 0.5651 (mmp) cc_final: 0.4844 (mmp) REVERT: R 229 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6487 (mt) outliers start: 40 outliers final: 26 residues processed: 151 average time/residue: 0.1960 time to fit residues: 41.4524 Evaluate side-chains 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 382 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 HIS ** 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 = 0.4796 r_free = 0.4796 target = 0.210272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.175143 restraints weight = 10561.117| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 2.17 r_work: 0.4331 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4194 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8674 Z= 0.234 Angle : 0.664 13.584 11771 Z= 0.335 Chirality : 0.044 0.179 1339 Planarity : 0.004 0.046 1484 Dihedral : 4.966 26.448 1189 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.91 % Allowed : 21.82 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.26), residues: 1067 helix: 1.33 (0.28), residues: 323 sheet: -1.59 (0.31), residues: 272 loop : -1.68 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 165 HIS 0.005 0.001 HIS A 212 PHE 0.018 0.002 PHE B 234 TYR 0.017 0.001 TYR A 319 ARG 0.006 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.892 Fit side-chains REVERT: A 24 ARG cc_start: 0.5186 (tpp80) cc_final: 0.4695 (ttt180) REVERT: A 26 ASP cc_start: 0.6531 (m-30) cc_final: 0.6010 (m-30) REVERT: A 33 GLU cc_start: 0.5213 (OUTLIER) cc_final: 0.4309 (mp0) REVERT: A 317 ILE cc_start: 0.5283 (OUTLIER) cc_final: 0.4928 (mp) REVERT: B 42 ARG cc_start: 0.6149 (ttp80) cc_final: 0.5628 (mmt180) REVERT: B 217 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6994 (ppp) REVERT: B 234 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.5929 (t80) REVERT: C 38 MET cc_start: 0.4554 (mmt) cc_final: 0.4212 (mpp) REVERT: D 110 MET cc_start: 0.6804 (tpp) cc_final: 0.6429 (tpp) REVERT: D 183 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5800 (tt) REVERT: R 134 MET cc_start: 0.5667 (mmp) cc_final: 0.4845 (mmp) REVERT: R 229 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6532 (mt) outliers start: 36 outliers final: 28 residues processed: 148 average time/residue: 0.1974 time to fit residues: 40.9073 Evaluate side-chains 150 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 382 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.6980 chunk 94 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 204 GLN ** R 207 HIS ** 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 = 0.4790 r_free = 0.4790 target = 0.209588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.174360 restraints weight = 10592.019| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 2.17 r_work: 0.4321 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4184 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8674 Z= 0.255 Angle : 0.679 13.827 11771 Z= 0.343 Chirality : 0.044 0.237 1339 Planarity : 0.004 0.045 1484 Dihedral : 4.978 26.026 1189 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.02 % Allowed : 21.50 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.26), residues: 1067 helix: 1.27 (0.28), residues: 327 sheet: -1.58 (0.31), residues: 272 loop : -1.67 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 99 HIS 0.005 0.001 HIS A 212 PHE 0.020 0.002 PHE B 234 TYR 0.020 0.002 TYR A 319 ARG 0.005 0.000 ARG A 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.894 Fit side-chains REVERT: A 24 ARG cc_start: 0.5183 (tpp80) cc_final: 0.4668 (ttt180) REVERT: A 26 ASP cc_start: 0.6416 (m-30) cc_final: 0.5972 (m-30) REVERT: A 33 GLU cc_start: 0.5139 (OUTLIER) cc_final: 0.4222 (mp0) REVERT: A 317 ILE cc_start: 0.5286 (OUTLIER) cc_final: 0.4916 (mp) REVERT: B 42 ARG cc_start: 0.6155 (ttp80) cc_final: 0.5702 (mmt180) REVERT: B 217 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7020 (ppp) REVERT: B 234 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6310 (t80) REVERT: B 297 TRP cc_start: 0.7749 (m100) cc_final: 0.7494 (m100) REVERT: C 38 MET cc_start: 0.4837 (mmt) cc_final: 0.4406 (mpp) REVERT: D 100 MET cc_start: 0.6048 (mmt) cc_final: 0.5836 (mmm) REVERT: D 110 MET cc_start: 0.6811 (tpp) cc_final: 0.6431 (tpp) REVERT: R 229 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6508 (mt) outliers start: 37 outliers final: 31 residues processed: 142 average time/residue: 0.2052 time to fit residues: 40.5224 Evaluate side-chains 151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 382 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.0970 chunk 85 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.0370 chunk 65 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.211284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.173998 restraints weight = 10659.241| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.41 r_work: 0.4337 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8674 Z= 0.205 Angle : 0.659 10.746 11771 Z= 0.332 Chirality : 0.043 0.194 1339 Planarity : 0.004 0.041 1484 Dihedral : 4.825 25.426 1189 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.58 % Allowed : 22.04 % Favored : 74.38 % 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: -1.07 (0.26), residues: 1067 helix: 1.44 (0.28), residues: 323 sheet: -1.54 (0.31), residues: 272 loop : -1.69 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 346 HIS 0.005 0.001 HIS A 212 PHE 0.015 0.001 PHE B 292 TYR 0.016 0.001 TYR D 119 ARG 0.005 0.000 ARG A 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6094.58 seconds wall clock time: 108 minutes 31.20 seconds (6511.20 seconds total)