Starting phenix.real_space_refine on Sat Jul 26 16:35:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbb_39900/07_2025/8zbb_39900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbb_39900/07_2025/8zbb_39900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zbb_39900/07_2025/8zbb_39900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbb_39900/07_2025/8zbb_39900.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbb_39900/07_2025/8zbb_39900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbb_39900/07_2025/8zbb_39900.cif" } resolution = 3.11 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= 0.011 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 40 5.16 5 C 5617 2.51 5 N 1440 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8719 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4492 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 18, 'TRANS': 563} Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1682 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 7.25, per 1000 atoms: 0.83 Number of scatterers: 8719 At special positions: 0 Unit cell: (89.64, 106.24, 140.104, 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 40 16.00 O 1622 8.00 N 1440 7.00 C 5617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " 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: 2.03 Conformation dependent library (CDL) restraints added in 947.7 milliseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 46.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 32 through 42 removed outlier: 3.720A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 removed outlier: 4.311A pdb=" N TYR A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.901A pdb=" N ASP A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 101 removed outlier: 3.852A pdb=" N TRP A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 136 Processing helix chain 'A' and resid 140 through 161 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 172 through 194 removed outlier: 4.369A pdb=" N TYR A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TRP A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Proline residue: A 186 - end of helix Processing helix chain 'A' and resid 200 through 217 removed outlier: 3.596A pdb=" N LYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 removed outlier: 3.852A pdb=" N ASP A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 279 removed outlier: 3.527A pdb=" N GLU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.680A pdb=" N ALA A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.800A pdb=" N ALA A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Proline residue: A 317 - end of helix removed outlier: 3.739A pdb=" N ARG A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.512A pdb=" N LEU A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 removed outlier: 4.238A pdb=" N LEU A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N THR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 389 removed outlier: 3.742A pdb=" N VAL A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 406 removed outlier: 3.909A pdb=" N ASN A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 removed outlier: 4.123A pdb=" N TRP A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 448 removed outlier: 3.744A pdb=" N MET A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 removed outlier: 3.659A pdb=" N GLY A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 495 through 505 removed outlier: 3.799A pdb=" N ILE A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 516 removed outlier: 3.627A pdb=" N LEU A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 553 Processing helix chain 'A' and resid 561 through 593 Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.729A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.770A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 4.147A pdb=" N GLN K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'L' and resid 123 through 129 Processing helix chain 'L' and resid 151 through 155 removed outlier: 3.694A pdb=" N ASN L 154 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 190 removed outlier: 3.573A pdb=" N GLU L 189 " --> pdb=" O ALA L 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.271A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 136 through 137 removed outlier: 3.742A pdb=" N VAL H 195 " --> pdb=" O HIS H 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AA5, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.930A pdb=" N LEU K 18 " --> pdb=" O MET K 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.963A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 20 through 25 Processing sheet with id=AA8, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.512A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.512A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 Processing sheet with id=AB2, first strand: chain 'L' and resid 146 through 149 502 hydrogen bonds defined for protein. 1398 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: 2.62 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2738 1.34 - 1.46: 2158 1.46 - 1.58: 3965 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 8925 Sorted by residual: bond pdb=" CA PRO A 74 " pdb=" C PRO A 74 " ideal model delta sigma weight residual 1.514 1.504 0.010 5.50e-03 3.31e+04 3.19e+00 bond pdb=" C VAL A 306 " pdb=" N PRO A 307 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.26e+00 bond pdb=" CB ASN A 326 " pdb=" CG ASN A 326 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.20e+00 bond pdb=" CB MET A 345 " pdb=" CG MET A 345 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.96e+00 bond pdb=" CA THR A 242 " pdb=" CB THR A 242 " ideal model delta sigma weight residual 1.534 1.551 -0.018 1.30e-02 5.92e+03 1.91e+00 ... (remaining 8920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11784 1.84 - 3.68: 293 3.68 - 5.52: 52 5.52 - 7.36: 12 7.36 - 9.21: 3 Bond angle restraints: 12144 Sorted by residual: angle pdb=" N VAL A 471 " pdb=" CA VAL A 471 " pdb=" C VAL A 471 " ideal model delta sigma weight residual 113.71 109.63 4.08 9.50e-01 1.11e+00 1.84e+01 angle pdb=" CA MET A 345 " pdb=" CB MET A 345 " pdb=" CG MET A 345 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.32e+01 angle pdb=" N LEU A 201 " pdb=" CA LEU A 201 " pdb=" C LEU A 201 " ideal model delta sigma weight residual 110.97 114.42 -3.45 1.09e+00 8.42e-01 1.00e+01 angle pdb=" C PRO A 244 " pdb=" N LYS A 245 " pdb=" CA LYS A 245 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.43e+00 angle pdb=" C CYS H 154 " pdb=" N LEU H 155 " pdb=" CA LEU H 155 " ideal model delta sigma weight residual 122.81 118.44 4.37 1.57e+00 4.06e-01 7.74e+00 ... (remaining 12139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 4492 16.30 - 32.59: 531 32.59 - 48.89: 175 48.89 - 65.19: 28 65.19 - 81.49: 12 Dihedral angle restraints: 5238 sinusoidal: 1961 harmonic: 3277 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 145.60 -52.60 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual -86.00 -134.68 48.68 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CA ASP A 200 " pdb=" C ASP A 200 " pdb=" N LEU A 201 " pdb=" CA LEU A 201 " ideal model delta harmonic sigma weight residual -180.00 -152.10 -27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 5235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 847 0.032 - 0.065: 378 0.065 - 0.097: 112 0.097 - 0.130: 45 0.130 - 0.162: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CB VAL H 67 " pdb=" CA VAL H 67 " pdb=" CG1 VAL H 67 " pdb=" CG2 VAL H 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA ILE K 98 " pdb=" N ILE K 98 " pdb=" C ILE K 98 " pdb=" CB ILE K 98 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1383 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE L 120 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO L 121 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 121 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO L 121 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO H 109 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 136 " -0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO H 137 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO H 137 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 137 " -0.030 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2080 2.79 - 3.32: 8029 3.32 - 3.85: 13689 3.85 - 4.37: 15111 4.37 - 4.90: 26995 Nonbonded interactions: 65904 Sorted by model distance: nonbonded pdb=" CE MET K 83 " pdb=" CD2 LEU K 86 " model vdw 2.266 3.880 nonbonded pdb=" O LEU A 463 " pdb=" CG1 VAL A 466 " model vdw 2.367 3.460 nonbonded pdb=" O CYS H 25 " pdb=" OG1 THR H 81 " model vdw 2.424 3.040 nonbonded pdb=" O ASP A 252 " pdb=" OD1 ASP A 252 " model vdw 2.440 3.040 nonbonded pdb=" O LEU A 336 " pdb=" CD1 LEU A 336 " model vdw 2.511 3.460 ... (remaining 65899 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: 9.690 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 0.004 0.049 8930 Z= 0.195 Angle : 0.746 9.205 12154 Z= 0.418 Chirality : 0.042 0.162 1386 Planarity : 0.005 0.061 1523 Dihedral : 16.194 81.487 3127 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.86 % Allowed : 26.35 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.43 (0.26), residues: 1131 helix: 2.13 (0.24), residues: 454 sheet: -0.05 (0.35), residues: 233 loop : -1.54 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 117 HIS 0.006 0.001 HIS H 214 PHE 0.032 0.002 PHE A 530 TYR 0.035 0.002 TYR H 53 ARG 0.004 0.001 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.11295 ( 493) hydrogen bonds : angle 5.71143 ( 1398) SS BOND : bond 0.00650 ( 5) SS BOND : angle 0.83232 ( 10) covalent geometry : bond 0.00405 ( 8925) covalent geometry : angle 0.74605 (12144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8386 (tp) cc_final: 0.8151 (mt) REVERT: A 411 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6372 (tp) REVERT: A 420 MET cc_start: 0.6006 (mmp) cc_final: 0.4879 (ptp) REVERT: L 5 MET cc_start: 0.0024 (ttm) cc_final: -0.0486 (ttt) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 0.1709 time to fit residues: 23.1269 Evaluate side-chains 79 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain L residue 175 TYR Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 88 optimal weight: 0.0030 chunk 34 optimal weight: 0.0770 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.243860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.218103 restraints weight = 12273.023| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 1.59 r_work: 0.4330 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8930 Z= 0.122 Angle : 0.568 8.403 12154 Z= 0.294 Chirality : 0.040 0.142 1386 Planarity : 0.004 0.057 1523 Dihedral : 5.568 54.990 1235 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.10 % Allowed : 25.38 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1131 helix: 2.52 (0.24), residues: 449 sheet: 0.59 (0.37), residues: 214 loop : -1.37 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 545 HIS 0.004 0.001 HIS H 214 PHE 0.014 0.001 PHE A 259 TYR 0.013 0.001 TYR L 92 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 493) hydrogen bonds : angle 4.73226 ( 1398) SS BOND : bond 0.00485 ( 5) SS BOND : angle 0.73779 ( 10) covalent geometry : bond 0.00261 ( 8925) covalent geometry : angle 0.56787 (12144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.4755 (t80) REVERT: A 193 LEU cc_start: 0.8343 (tp) cc_final: 0.8130 (mt) REVERT: A 420 MET cc_start: 0.5952 (mmp) cc_final: 0.4799 (ptp) REVERT: A 545 TRP cc_start: 0.7683 (t60) cc_final: 0.7377 (t60) REVERT: H 108 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6176 (tp30) REVERT: H 135 VAL cc_start: 0.5542 (OUTLIER) cc_final: 0.5298 (t) REVERT: K 83 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.4850 (ttm) REVERT: L 5 MET cc_start: -0.0100 (ttm) cc_final: -0.0709 (ttt) outliers start: 38 outliers final: 22 residues processed: 106 average time/residue: 0.1995 time to fit residues: 31.0780 Evaluate side-chains 100 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 159 TYR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 81 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.241421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.217774 restraints weight = 12457.144| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 1.57 r_work: 0.4307 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8930 Z= 0.132 Angle : 0.566 7.032 12154 Z= 0.294 Chirality : 0.039 0.136 1386 Planarity : 0.004 0.055 1523 Dihedral : 5.092 49.731 1229 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.32 % Allowed : 25.70 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.94 (0.26), residues: 1131 helix: 2.57 (0.24), residues: 450 sheet: 0.57 (0.37), residues: 212 loop : -1.38 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 117 HIS 0.004 0.001 HIS H 214 PHE 0.018 0.001 PHE A 259 TYR 0.013 0.001 TYR L 94 ARG 0.004 0.000 ARG K 38 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 493) hydrogen bonds : angle 4.65680 ( 1398) SS BOND : bond 0.00517 ( 5) SS BOND : angle 0.72036 ( 10) covalent geometry : bond 0.00292 ( 8925) covalent geometry : angle 0.56575 (12144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 80 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.4838 (t80) REVERT: A 303 TYR cc_start: 0.3708 (OUTLIER) cc_final: 0.1924 (m-80) REVERT: A 336 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7896 (pp) REVERT: A 545 TRP cc_start: 0.7683 (t60) cc_final: 0.7340 (t60) REVERT: H 135 VAL cc_start: 0.5555 (OUTLIER) cc_final: 0.5311 (t) REVERT: K 83 MET cc_start: 0.5355 (OUTLIER) cc_final: 0.5007 (ttm) REVERT: L 5 MET cc_start: -0.0001 (ttm) cc_final: -0.0640 (ttt) outliers start: 40 outliers final: 24 residues processed: 108 average time/residue: 0.1656 time to fit residues: 26.6058 Evaluate side-chains 107 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 159 TYR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 185 GLN K 82 GLN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.239767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.213956 restraints weight = 12315.755| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 1.72 r_work: 0.4277 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8930 Z= 0.141 Angle : 0.584 8.243 12154 Z= 0.301 Chirality : 0.040 0.141 1386 Planarity : 0.004 0.051 1523 Dihedral : 5.169 52.927 1229 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.08 % Allowed : 25.38 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.86 (0.26), residues: 1131 helix: 2.52 (0.24), residues: 450 sheet: 0.47 (0.36), residues: 212 loop : -1.42 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 50 HIS 0.005 0.001 HIS H 214 PHE 0.018 0.001 PHE A 259 TYR 0.011 0.001 TYR L 92 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 493) hydrogen bonds : angle 4.67467 ( 1398) SS BOND : bond 0.00509 ( 5) SS BOND : angle 0.72609 ( 10) covalent geometry : bond 0.00314 ( 8925) covalent geometry : angle 0.58388 (12144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 79 time to evaluate : 0.839 Fit side-chains REVERT: A 52 PHE cc_start: 0.6156 (OUTLIER) cc_final: 0.4934 (t80) REVERT: A 193 LEU cc_start: 0.8701 (tp) cc_final: 0.8324 (mt) REVERT: A 303 TYR cc_start: 0.3855 (OUTLIER) cc_final: 0.2169 (m-80) REVERT: A 336 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7943 (pp) REVERT: A 420 MET cc_start: 0.5953 (mmp) cc_final: 0.4829 (ptp) REVERT: A 516 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6138 (tm-30) REVERT: A 545 TRP cc_start: 0.7650 (t60) cc_final: 0.7221 (t60) REVERT: H 24 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7422 (t) REVERT: H 135 VAL cc_start: 0.5651 (OUTLIER) cc_final: 0.5368 (t) REVERT: K 83 MET cc_start: 0.5426 (OUTLIER) cc_final: 0.4985 (ttm) REVERT: L 5 MET cc_start: -0.0082 (ttm) cc_final: -0.0551 (ttt) outliers start: 47 outliers final: 29 residues processed: 115 average time/residue: 0.1685 time to fit residues: 28.5587 Evaluate side-chains 112 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 159 TYR Chi-restraints excluded: chain H residue 168 TRP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.240726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.218106 restraints weight = 12263.384| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 1.62 r_work: 0.4306 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8930 Z= 0.116 Angle : 0.538 6.641 12154 Z= 0.279 Chirality : 0.039 0.133 1386 Planarity : 0.004 0.052 1523 Dihedral : 5.039 56.874 1229 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.54 % Allowed : 26.46 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1131 helix: 2.63 (0.24), residues: 449 sheet: 0.51 (0.37), residues: 213 loop : -1.38 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS H 214 PHE 0.015 0.001 PHE A 259 TYR 0.010 0.001 TYR L 92 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 493) hydrogen bonds : angle 4.53805 ( 1398) SS BOND : bond 0.00449 ( 5) SS BOND : angle 0.69383 ( 10) covalent geometry : bond 0.00254 ( 8925) covalent geometry : angle 0.53793 (12144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.4880 (t80) REVERT: A 193 LEU cc_start: 0.8614 (tp) cc_final: 0.8298 (mt) REVERT: A 303 TYR cc_start: 0.3838 (OUTLIER) cc_final: 0.2154 (m-80) REVERT: A 336 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7920 (pp) REVERT: A 420 MET cc_start: 0.5894 (mmp) cc_final: 0.4786 (ptp) REVERT: A 516 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6152 (tm-30) REVERT: A 545 TRP cc_start: 0.7719 (t60) cc_final: 0.7325 (t60) REVERT: H 135 VAL cc_start: 0.5667 (OUTLIER) cc_final: 0.5432 (t) REVERT: L 5 MET cc_start: 0.0229 (ttm) cc_final: -0.0474 (ttt) outliers start: 42 outliers final: 29 residues processed: 113 average time/residue: 0.1645 time to fit residues: 27.6700 Evaluate side-chains 113 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 168 TRP Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 97 optimal weight: 0.0170 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.239556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.216455 restraints weight = 12226.444| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 1.63 r_work: 0.4289 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8930 Z= 0.125 Angle : 0.556 6.564 12154 Z= 0.288 Chirality : 0.039 0.194 1386 Planarity : 0.004 0.051 1523 Dihedral : 4.691 48.146 1226 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.40 % Allowed : 25.92 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1131 helix: 2.49 (0.24), residues: 455 sheet: 0.47 (0.37), residues: 207 loop : -1.37 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS H 214 PHE 0.017 0.001 PHE A 259 TYR 0.012 0.001 TYR K 94 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 493) hydrogen bonds : angle 4.57697 ( 1398) SS BOND : bond 0.00394 ( 5) SS BOND : angle 0.57018 ( 10) covalent geometry : bond 0.00279 ( 8925) covalent geometry : angle 0.55638 (12144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 82 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.4901 (t80) REVERT: A 193 LEU cc_start: 0.8643 (tp) cc_final: 0.8322 (mt) REVERT: A 303 TYR cc_start: 0.3872 (OUTLIER) cc_final: 0.2176 (m-80) REVERT: A 336 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7937 (pp) REVERT: A 420 MET cc_start: 0.5930 (mmp) cc_final: 0.4755 (ptp) REVERT: A 545 TRP cc_start: 0.7706 (t60) cc_final: 0.7292 (t60) REVERT: H 135 VAL cc_start: 0.5649 (OUTLIER) cc_final: 0.5385 (t) REVERT: L 5 MET cc_start: 0.0289 (ttm) cc_final: -0.0429 (ttt) REVERT: L 90 GLN cc_start: 0.8429 (tt0) cc_final: 0.8184 (tt0) outliers start: 50 outliers final: 39 residues processed: 121 average time/residue: 0.1672 time to fit residues: 30.0444 Evaluate side-chains 120 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 159 TYR Chi-restraints excluded: chain H residue 168 TRP Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.237812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.212571 restraints weight = 12356.451| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 1.64 r_work: 0.4269 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8930 Z= 0.139 Angle : 0.574 6.550 12154 Z= 0.299 Chirality : 0.040 0.141 1386 Planarity : 0.004 0.051 1523 Dihedral : 4.803 48.635 1226 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.18 % Allowed : 26.03 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.82 (0.26), residues: 1131 helix: 2.39 (0.25), residues: 457 sheet: 0.45 (0.36), residues: 209 loop : -1.37 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 50 HIS 0.004 0.001 HIS H 214 PHE 0.030 0.002 PHE A 530 TYR 0.014 0.001 TYR A 152 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 493) hydrogen bonds : angle 4.65931 ( 1398) SS BOND : bond 0.00470 ( 5) SS BOND : angle 0.58150 ( 10) covalent geometry : bond 0.00312 ( 8925) covalent geometry : angle 0.57376 (12144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 76 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.4961 (t80) REVERT: A 193 LEU cc_start: 0.8707 (tp) cc_final: 0.8340 (mt) REVERT: A 303 TYR cc_start: 0.3946 (OUTLIER) cc_final: 0.2273 (m-80) REVERT: A 336 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7911 (pp) REVERT: A 420 MET cc_start: 0.6060 (mmp) cc_final: 0.4863 (ptp) REVERT: A 545 TRP cc_start: 0.7675 (t60) cc_final: 0.7232 (t60) REVERT: H 135 VAL cc_start: 0.5624 (OUTLIER) cc_final: 0.5373 (t) REVERT: L 5 MET cc_start: 0.0235 (ttm) cc_final: -0.0604 (ttt) REVERT: L 90 GLN cc_start: 0.8471 (tt0) cc_final: 0.8233 (tt0) outliers start: 48 outliers final: 41 residues processed: 113 average time/residue: 0.1677 time to fit residues: 28.2381 Evaluate side-chains 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 74 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 159 TYR Chi-restraints excluded: chain H residue 168 TRP Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 50 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.238698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.215830 restraints weight = 12457.275| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 1.59 r_work: 0.4293 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8930 Z= 0.120 Angle : 0.546 6.488 12154 Z= 0.284 Chirality : 0.039 0.136 1386 Planarity : 0.004 0.051 1523 Dihedral : 4.680 48.809 1226 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.86 % Allowed : 26.57 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1131 helix: 2.49 (0.24), residues: 456 sheet: 0.56 (0.37), residues: 206 loop : -1.39 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS H 214 PHE 0.030 0.001 PHE A 530 TYR 0.009 0.001 TYR L 92 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 493) hydrogen bonds : angle 4.55768 ( 1398) SS BOND : bond 0.00420 ( 5) SS BOND : angle 0.58894 ( 10) covalent geometry : bond 0.00267 ( 8925) covalent geometry : angle 0.54576 (12144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5001 (t80) REVERT: A 193 LEU cc_start: 0.8660 (tp) cc_final: 0.8330 (mt) REVERT: A 303 TYR cc_start: 0.3887 (OUTLIER) cc_final: 0.2321 (m-80) REVERT: A 336 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7937 (pp) REVERT: A 420 MET cc_start: 0.5929 (mmp) cc_final: 0.4780 (ptp) REVERT: A 545 TRP cc_start: 0.7720 (t60) cc_final: 0.7316 (t60) REVERT: L 5 MET cc_start: 0.0346 (ttm) cc_final: -0.0502 (ttt) REVERT: L 74 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7344 (tp) REVERT: L 90 GLN cc_start: 0.8466 (tt0) cc_final: 0.8230 (tt0) outliers start: 45 outliers final: 37 residues processed: 115 average time/residue: 0.1615 time to fit residues: 27.9913 Evaluate side-chains 116 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 168 TRP Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 9.9990 chunk 6 optimal weight: 0.0170 chunk 104 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.239277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.214316 restraints weight = 12332.049| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 1.68 r_work: 0.4285 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8930 Z= 0.116 Angle : 0.545 6.325 12154 Z= 0.282 Chirality : 0.039 0.138 1386 Planarity : 0.004 0.051 1523 Dihedral : 4.599 48.763 1226 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.64 % Allowed : 26.35 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1131 helix: 2.43 (0.24), residues: 461 sheet: 0.38 (0.36), residues: 214 loop : -1.26 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS H 214 PHE 0.036 0.001 PHE A 530 TYR 0.014 0.001 TYR A 152 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 493) hydrogen bonds : angle 4.51262 ( 1398) SS BOND : bond 0.00402 ( 5) SS BOND : angle 0.63710 ( 10) covalent geometry : bond 0.00256 ( 8925) covalent geometry : angle 0.54460 (12144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 84 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.4931 (t80) REVERT: A 193 LEU cc_start: 0.8697 (tp) cc_final: 0.8346 (mt) REVERT: A 303 TYR cc_start: 0.3832 (OUTLIER) cc_final: 0.2241 (m-80) REVERT: A 336 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7880 (pp) REVERT: A 420 MET cc_start: 0.5972 (mmp) cc_final: 0.4780 (ptp) REVERT: A 545 TRP cc_start: 0.7688 (t60) cc_final: 0.7275 (t60) REVERT: K 18 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5658 (tp) REVERT: L 5 MET cc_start: 0.0270 (ttm) cc_final: -0.0571 (ttt) REVERT: L 74 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7364 (tp) REVERT: L 90 GLN cc_start: 0.8458 (tt0) cc_final: 0.8220 (tt0) outliers start: 43 outliers final: 37 residues processed: 117 average time/residue: 0.1843 time to fit residues: 32.7569 Evaluate side-chains 122 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 358 PHE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 168 TRP Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.0020 chunk 76 optimal weight: 0.0670 chunk 35 optimal weight: 6.9990 chunk 87 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 overall best weight: 0.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.240523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.216680 restraints weight = 12388.550| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 1.71 r_work: 0.4314 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8930 Z= 0.102 Angle : 0.523 6.730 12154 Z= 0.270 Chirality : 0.038 0.141 1386 Planarity : 0.004 0.052 1523 Dihedral : 4.436 48.684 1226 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.46 % Allowed : 27.65 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1131 helix: 2.46 (0.24), residues: 466 sheet: 0.76 (0.36), residues: 206 loop : -1.36 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 328 HIS 0.002 0.000 HIS H 214 PHE 0.042 0.001 PHE A 530 TYR 0.009 0.001 TYR H 159 ARG 0.005 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 493) hydrogen bonds : angle 4.34320 ( 1398) SS BOND : bond 0.00382 ( 5) SS BOND : angle 0.60684 ( 10) covalent geometry : bond 0.00220 ( 8925) covalent geometry : angle 0.52271 (12144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.914 Fit side-chains REVERT: A 52 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.4909 (t80) REVERT: A 193 LEU cc_start: 0.8633 (tp) cc_final: 0.8313 (mt) REVERT: A 303 TYR cc_start: 0.3780 (OUTLIER) cc_final: 0.2157 (m-80) REVERT: A 336 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7864 (pp) REVERT: A 420 MET cc_start: 0.5819 (mmp) cc_final: 0.4666 (ptp) REVERT: A 545 TRP cc_start: 0.7684 (t60) cc_final: 0.7291 (t60) REVERT: L 5 MET cc_start: 0.0314 (ttm) cc_final: -0.0421 (ttt) REVERT: L 74 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7385 (tp) REVERT: L 90 GLN cc_start: 0.8417 (tt0) cc_final: 0.8046 (tt0) outliers start: 32 outliers final: 24 residues processed: 109 average time/residue: 0.1655 time to fit residues: 27.2379 Evaluate side-chains 109 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 205 TRP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 168 TRP Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 223 GLN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.239915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.215490 restraints weight = 12438.599| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 1.67 r_work: 0.4292 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8930 Z= 0.115 Angle : 0.550 8.412 12154 Z= 0.281 Chirality : 0.039 0.140 1386 Planarity : 0.004 0.052 1523 Dihedral : 4.483 48.719 1226 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.56 % Allowed : 27.65 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1131 helix: 2.43 (0.24), residues: 467 sheet: 0.51 (0.36), residues: 214 loop : -1.24 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS H 214 PHE 0.039 0.001 PHE A 530 TYR 0.009 0.001 TYR L 92 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 493) hydrogen bonds : angle 4.41000 ( 1398) SS BOND : bond 0.00392 ( 5) SS BOND : angle 0.55388 ( 10) covalent geometry : bond 0.00254 ( 8925) covalent geometry : angle 0.54963 (12144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4931.59 seconds wall clock time: 85 minutes 31.38 seconds (5131.38 seconds total)