Starting phenix.real_space_refine on Thu Mar 13 04:04:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f8w_31494/03_2025/7f8w_31494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8w_31494/03_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_31494/03_2025/7f8w_31494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8w_31494/03_2025/7f8w_31494.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8w_31494/03_2025/7f8w_31494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8w_31494/03_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.75, per 1000 atoms: 0.68 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: 2.95 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.99 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: 2.44 Time building geometry restraints manager: 2.70 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: 6.700 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 23.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- 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 : 0.847 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: 0.2119 time to fit residues: 48.3232 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 : 0.857 ------------------------------------------------------------------------------- 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 = 0.177685 restraints weight = 10543.227| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 2.11 r_work: 0.4315 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.4176 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4176 ------------------------------------------------------------------------------- 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 : 0.869 Fit side-chains REVERT: A 26 ASP cc_start: 0.6552 (m-30) cc_final: 0.6227 (m-30) REVERT: A 33 GLU cc_start: 0.5489 (mp0) cc_final: 0.5186 (mp0) REVERT: A 242 MET cc_start: 0.4434 (tpt) cc_final: 0.4215 (tpt) REVERT: B 234 PHE cc_start: 0.7005 (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: 0.2162 (tmm) cc_final: 0.1595 (ttt) outliers start: 18 outliers final: 13 residues processed: 147 average time/residue: 0.2141 time to fit residues: 43.2695 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 : 0.947 ------------------------------------------------------------------------------- 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: 8.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 95 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.214669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.176546 restraints weight = 10658.733| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 2.51 r_work: 0.4354 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8674 Z= 0.217 Angle : 0.651 11.844 11771 Z= 0.338 Chirality : 0.043 0.164 1339 Planarity : 0.005 0.054 1484 Dihedral : 5.181 26.885 1189 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.71 % Allowed : 15.64 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.25), residues: 1067 helix: 0.97 (0.27), residues: 320 sheet: -1.59 (0.30), residues: 269 loop : -1.68 (0.27), residues: 478 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 0.016 0.002 PHE B 234 TYR 0.018 0.001 TYR A 319 ARG 0.005 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 : 0.921 Fit side-chains REVERT: A 26 ASP cc_start: 0.6321 (m-30) cc_final: 0.5982 (m-30) REVERT: A 306 MET cc_start: 0.6069 (tmm) cc_final: 0.5243 (ttt) REVERT: B 217 MET cc_start: 0.6881 (ppp) cc_final: 0.6621 (ppp) REVERT: B 234 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.5702 (t80) REVERT: B 264 TYR cc_start: 0.5786 (m-10) cc_final: 0.5501 (m-10) REVERT: C 50 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6144 (mm) REVERT: R 229 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.6080 (mt) REVERT: R 393 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.4880 (mmt) outliers start: 25 outliers final: 12 residues processed: 137 average time/residue: 0.1780 time to fit residues: 35.3577 Evaluate side-chains 128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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: 0.0870 chunk 61 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 ** 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 = 0.4827 r_free = 0.4827 target = 0.213952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.176022 restraints weight = 10527.917| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 2.50 r_work: 0.4349 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8674 Z= 0.216 Angle : 0.636 12.007 11771 Z= 0.327 Chirality : 0.043 0.192 1339 Planarity : 0.004 0.048 1484 Dihedral : 4.992 26.973 1189 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.93 % Allowed : 16.61 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1067 helix: 1.27 (0.28), residues: 320 sheet: -1.60 (0.30), residues: 269 loop : -1.60 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 165 HIS 0.004 0.001 HIS C 44 PHE 0.016 0.002 PHE B 234 TYR 0.020 0.001 TYR R 380 ARG 0.003 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 145 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.839 Fit side-chains REVERT: A 26 ASP cc_start: 0.6204 (m-30) cc_final: 0.5946 (m-30) REVERT: A 317 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5084 (mp) REVERT: B 42 ARG cc_start: 0.6170 (ttp80) cc_final: 0.5468 (tpt170) REVERT: B 264 TYR cc_start: 0.5745 (m-10) cc_final: 0.5464 (m-10) REVERT: C 50 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6189 (mm) REVERT: D 110 MET cc_start: 0.6694 (tpp) cc_final: 0.6351 (tpp) REVERT: R 73 MET cc_start: 0.6249 (tmm) cc_final: 0.5878 (tmm) REVERT: R 74 LEU cc_start: 0.5591 (OUTLIER) cc_final: 0.5370 (mp) REVERT: R 186 MET cc_start: 0.2620 (tmm) cc_final: 0.1528 (ttm) REVERT: R 229 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.6040 (mt) REVERT: R 393 MET cc_start: 0.5485 (OUTLIER) cc_final: 0.4876 (mmt) outliers start: 27 outliers final: 15 residues processed: 138 average time/residue: 0.1951 time to fit residues: 37.8066 Evaluate side-chains 130 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 74 LEU Chi-restraints excluded: chain R residue 105 VAL 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: 0.9980 chunk 44 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** 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 = 0.4797 r_free = 0.4797 target = 0.210977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.172562 restraints weight = 10571.163| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.49 r_work: 0.4311 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8674 Z= 0.250 Angle : 0.652 14.001 11771 Z= 0.335 Chirality : 0.044 0.178 1339 Planarity : 0.004 0.047 1484 Dihedral : 4.976 26.400 1189 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.13 % Allowed : 18.13 % Favored : 77.74 % 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: -1.02 (0.25), residues: 1067 helix: 1.42 (0.28), residues: 321 sheet: -1.62 (0.29), residues: 289 loop : -1.51 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 165 HIS 0.009 0.001 HIS A 212 PHE 0.015 0.002 PHE B 234 TYR 0.018 0.002 TYR A 319 ARG 0.005 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 158 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.920 Fit side-chains REVERT: A 26 ASP cc_start: 0.6406 (m-30) cc_final: 0.6092 (m-30) REVERT: A 317 ILE cc_start: 0.5474 (OUTLIER) cc_final: 0.5100 (mp) REVERT: B 42 ARG cc_start: 0.6176 (ttp80) cc_final: 0.5529 (tpt170) REVERT: B 217 MET cc_start: 0.7103 (ppp) cc_final: 0.6801 (ppp) REVERT: B 234 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6221 (t80) REVERT: C 50 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6333 (mm) REVERT: D 183 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5430 (tt) REVERT: R 229 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.6097 (mt) outliers start: 38 outliers final: 22 residues processed: 149 average time/residue: 0.1921 time to fit residues: 40.5138 Evaluate side-chains 138 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 194 ILE 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 231 GLN ** 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 = 0.4804 r_free = 0.4804 target = 0.211434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.173320 restraints weight = 10518.393| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.48 r_work: 0.4319 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8674 Z= 0.234 Angle : 0.659 13.059 11771 Z= 0.336 Chirality : 0.044 0.218 1339 Planarity : 0.004 0.045 1484 Dihedral : 4.939 25.296 1189 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.91 % Allowed : 19.44 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.25), residues: 1067 helix: 1.38 (0.28), residues: 323 sheet: -1.69 (0.30), residues: 281 loop : -1.56 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 346 HIS 0.004 0.001 HIS C 44 PHE 0.018 0.002 PHE A 286 TYR 0.015 0.002 TYR A 319 ARG 0.003 0.000 ARG A 15 *********************** 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 153 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.974 Fit side-chains REVERT: A 26 ASP cc_start: 0.6418 (m-30) cc_final: 0.6116 (m-30) REVERT: B 42 ARG cc_start: 0.6099 (ttp80) cc_final: 0.5672 (tpt170) REVERT: B 217 MET cc_start: 0.7129 (ppp) cc_final: 0.6831 (ppp) REVERT: B 234 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6175 (t80) REVERT: B 264 TYR cc_start: 0.5866 (m-10) cc_final: 0.5590 (m-10) REVERT: C 50 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6466 (mt) REVERT: D 110 MET cc_start: 0.6609 (tpp) cc_final: 0.5981 (tpp) REVERT: D 183 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5274 (tt) REVERT: R 229 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.6077 (mt) REVERT: R 393 MET cc_start: 0.5868 (ttm) cc_final: 0.5279 (mmt) outliers start: 36 outliers final: 25 residues processed: 145 average time/residue: 0.1976 time to fit residues: 40.0091 Evaluate side-chains 140 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 194 ILE 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 178 THR 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 166 VAL 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 382 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN R 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.210671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.174659 restraints weight = 10700.489| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.24 r_work: 0.4317 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.4180 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8674 Z= 0.271 Angle : 0.684 14.339 11771 Z= 0.347 Chirality : 0.044 0.196 1339 Planarity : 0.004 0.047 1484 Dihedral : 4.979 24.782 1189 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.02 % Allowed : 20.41 % Favored : 75.57 % 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: 1.32 (0.28), residues: 323 sheet: -1.63 (0.31), residues: 279 loop : -1.59 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 165 HIS 0.007 0.001 HIS R 207 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 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 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.901 Fit side-chains REVERT: A 23 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5736 (mp) REVERT: A 26 ASP cc_start: 0.6586 (m-30) cc_final: 0.6273 (m-30) REVERT: B 42 ARG cc_start: 0.6249 (ttp80) cc_final: 0.5735 (tpt170) REVERT: B 217 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7063 (ppp) REVERT: B 234 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6363 (t80) REVERT: C 38 MET cc_start: 0.4572 (mmt) cc_final: 0.4137 (mpp) REVERT: C 50 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6544 (mt) REVERT: R 229 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6431 (mt) REVERT: R 393 MET cc_start: 0.5899 (ttm) cc_final: 0.5294 (mmt) outliers start: 37 outliers final: 24 residues processed: 142 average time/residue: 0.1953 time to fit residues: 38.9529 Evaluate side-chains 139 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 23 LEU 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.0370 chunk 15 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.210244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.172582 restraints weight = 10520.698| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 2.40 r_work: 0.4317 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8674 Z= 0.221 Angle : 0.671 12.175 11771 Z= 0.337 Chirality : 0.044 0.175 1339 Planarity : 0.004 0.045 1484 Dihedral : 4.883 24.273 1189 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.69 % Allowed : 21.06 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.26), residues: 1067 helix: 1.33 (0.28), residues: 323 sheet: -1.67 (0.31), residues: 271 loop : -1.50 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 165 HIS 0.003 0.001 HIS C 44 PHE 0.015 0.002 PHE B 292 TYR 0.016 0.001 TYR A 319 ARG 0.005 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 153 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.933 Fit side-chains REVERT: A 24 ARG cc_start: 0.4695 (tpt-90) cc_final: 0.4368 (ttt180) REVERT: A 26 ASP cc_start: 0.6433 (m-30) cc_final: 0.6181 (m-30) REVERT: B 42 ARG cc_start: 0.6080 (ttp80) cc_final: 0.5606 (mmt180) REVERT: B 217 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6889 (ppp) REVERT: B 234 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6261 (t80) REVERT: C 38 MET cc_start: 0.4691 (mmt) cc_final: 0.4276 (mpp) REVERT: R 134 MET cc_start: 0.5550 (mmp) cc_final: 0.5283 (mmp) REVERT: R 229 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6246 (mt) REVERT: R 393 MET cc_start: 0.5716 (ttm) cc_final: 0.5138 (mmt) outliers start: 34 outliers final: 24 residues processed: 144 average time/residue: 0.1960 time to fit residues: 39.5787 Evaluate side-chains 140 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 178 THR Chi-restraints excluded: chain B residue 217 MET 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.211844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.176785 restraints weight = 10572.970| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 2.18 r_work: 0.4290 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8674 Z= 0.226 Angle : 0.672 12.585 11771 Z= 0.337 Chirality : 0.043 0.178 1339 Planarity : 0.004 0.043 1484 Dihedral : 4.861 23.862 1189 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.26 % Allowed : 21.61 % Favored : 75.14 % 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 (0.26), residues: 1067 helix: 1.36 (0.28), residues: 323 sheet: -1.66 (0.31), residues: 271 loop : -1.44 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 99 HIS 0.005 0.001 HIS R 207 PHE 0.015 0.002 PHE A 195 TYR 0.017 0.001 TYR A 319 ARG 0.005 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 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.976 Fit side-chains REVERT: A 24 ARG cc_start: 0.4828 (tpt-90) cc_final: 0.4478 (ttt180) REVERT: A 26 ASP cc_start: 0.6516 (m-30) cc_final: 0.6192 (m-30) REVERT: B 42 ARG cc_start: 0.6163 (ttp80) cc_final: 0.5613 (mmt180) REVERT: B 217 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6981 (ppp) REVERT: B 234 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6396 (t80) REVERT: C 38 MET cc_start: 0.4728 (mmt) cc_final: 0.4299 (mpp) REVERT: D 183 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5290 (tt) REVERT: R 229 ILE cc_start: 0.6389 (OUTLIER) cc_final: 0.6088 (mt) REVERT: R 393 MET cc_start: 0.5869 (ttm) cc_final: 0.5204 (mmt) outliers start: 30 outliers final: 24 residues processed: 143 average time/residue: 0.2132 time to fit residues: 41.7840 Evaluate side-chains 146 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 178 THR Chi-restraints excluded: chain B residue 217 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.0980 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 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 268 ASN R 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.209815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.173044 restraints weight = 10577.674| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.36 r_work: 0.4278 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8674 Z= 0.224 Angle : 0.675 12.267 11771 Z= 0.339 Chirality : 0.044 0.215 1339 Planarity : 0.004 0.043 1484 Dihedral : 4.869 25.447 1189 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.82 % Allowed : 22.48 % Favored : 74.70 % 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: -0.98 (0.26), residues: 1067 helix: 1.39 (0.28), residues: 323 sheet: -1.64 (0.31), residues: 271 loop : -1.43 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 99 HIS 0.005 0.001 HIS R 207 PHE 0.016 0.002 PHE A 195 TYR 0.016 0.001 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 147 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.965 Fit side-chains REVERT: A 24 ARG cc_start: 0.4598 (tpt-90) cc_final: 0.4292 (ttt180) REVERT: A 26 ASP cc_start: 0.6384 (m-30) cc_final: 0.6081 (m-30) REVERT: B 42 ARG cc_start: 0.6005 (ttp80) cc_final: 0.5652 (mmt180) REVERT: B 217 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6777 (ppp) REVERT: B 234 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6359 (t80) REVERT: C 38 MET cc_start: 0.4615 (mmt) cc_final: 0.4296 (mpp) REVERT: R 186 MET cc_start: 0.3650 (tmm) cc_final: 0.2845 (tpp) REVERT: R 229 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6231 (mt) REVERT: R 393 MET cc_start: 0.5725 (ttm) cc_final: 0.5155 (mmt) outliers start: 26 outliers final: 23 residues processed: 137 average time/residue: 0.2098 time to fit residues: 39.9363 Evaluate side-chains 139 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 178 THR Chi-restraints excluded: chain B residue 217 MET 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 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 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 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: 0.5980 chunk 49 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 268 ASN R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.211919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.173461 restraints weight = 10763.500| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.53 r_work: 0.4308 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8674 Z= 0.188 Angle : 0.666 9.943 11771 Z= 0.333 Chirality : 0.043 0.173 1339 Planarity : 0.004 0.042 1484 Dihedral : 4.764 26.566 1189 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.61 % Allowed : 22.91 % 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: -0.96 (0.26), residues: 1067 helix: 1.41 (0.28), residues: 323 sheet: -1.60 (0.31), residues: 271 loop : -1.45 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 99 HIS 0.003 0.001 HIS C 44 PHE 0.015 0.002 PHE B 292 TYR 0.027 0.001 TYR R 380 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: 6236.86 seconds wall clock time: 107 minutes 17.92 seconds (6437.92 seconds total)