Starting phenix.real_space_refine on Wed Sep 17 12:42:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbb_39900/09_2025/8zbb_39900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbb_39900/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zbb_39900/09_2025/8zbb_39900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbb_39900/09_2025/8zbb_39900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zbb_39900/09_2025/8zbb_39900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbb_39900/09_2025/8zbb_39900.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.11, per 1000 atoms: 0.24 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: 0.71 Conformation dependent library (CDL) restraints added in 446.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.27 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: 1.21 Time building geometry restraints manager: 0.96 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: 8.150 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG A 232 TYR 0.035 0.002 TYR H 53 PHE 0.032 0.002 PHE A 530 TRP 0.028 0.002 TRP H 117 HIS 0.006 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8925) covalent geometry : angle 0.74605 (12144) SS BOND : bond 0.00650 ( 5) SS BOND : angle 0.83232 ( 10) hydrogen bonds : bond 0.11295 ( 493) hydrogen bonds : angle 5.71143 ( 1398) *********************** 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 : 0.326 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: 0.0748 time to fit residues: 10.1216 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 : 0.312 ------------------------------------------------------------------------------- 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 108 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4745 r_free = 0.4745 target = 0.243437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.220030 restraints weight = 12479.885| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 1.59 r_work: 0.4326 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.0726 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= 0.126 Angle : 0.573 8.281 12154 Z= 0.297 Chirality : 0.040 0.142 1386 Planarity : 0.004 0.057 1523 Dihedral : 5.598 55.440 1235 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.10 % Allowed : 25.81 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1131 helix: 2.50 (0.24), residues: 449 sheet: 0.60 (0.37), residues: 212 loop : -1.39 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.014 0.001 TYR L 94 PHE 0.015 0.001 PHE A 259 TRP 0.021 0.001 TRP A 545 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8925) covalent geometry : angle 0.57329 (12144) SS BOND : bond 0.00486 ( 5) SS BOND : angle 0.73362 ( 10) hydrogen bonds : bond 0.04252 ( 493) hydrogen bonds : angle 4.74851 ( 1398) *********************** 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 115 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.4825 (t80) REVERT: A 420 MET cc_start: 0.5953 (mmp) cc_final: 0.4815 (ptp) REVERT: A 545 TRP cc_start: 0.7740 (t60) cc_final: 0.7535 (t60) REVERT: H 108 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6199 (tp30) REVERT: H 135 VAL cc_start: 0.5571 (OUTLIER) cc_final: 0.5326 (t) REVERT: K 83 MET cc_start: 0.5286 (OUTLIER) cc_final: 0.4936 (ttm) REVERT: L 5 MET cc_start: 0.0097 (ttm) cc_final: -0.0478 (ttt) outliers start: 38 outliers final: 21 residues processed: 105 average time/residue: 0.0788 time to fit residues: 12.0969 Evaluate side-chains 96 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 103 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.243075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.219741 restraints weight = 12345.641| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 1.60 r_work: 0.4319 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.1026 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= 0.119 Angle : 0.543 6.715 12154 Z= 0.283 Chirality : 0.039 0.136 1386 Planarity : 0.004 0.055 1523 Dihedral : 5.002 49.706 1229 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.00 % Allowed : 25.92 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.26), residues: 1131 helix: 2.62 (0.24), residues: 450 sheet: 0.63 (0.37), residues: 212 loop : -1.36 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 38 TYR 0.011 0.001 TYR L 92 PHE 0.016 0.001 PHE A 259 TRP 0.014 0.001 TRP H 117 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8925) covalent geometry : angle 0.54323 (12144) SS BOND : bond 0.00475 ( 5) SS BOND : angle 0.71966 ( 10) hydrogen bonds : bond 0.03939 ( 493) hydrogen bonds : angle 4.58953 ( 1398) *********************** 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 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.4826 (t80) REVERT: A 303 TYR cc_start: 0.3754 (OUTLIER) cc_final: 0.1888 (m-80) REVERT: A 336 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7885 (pp) REVERT: A 545 TRP cc_start: 0.7675 (t60) cc_final: 0.7327 (t60) REVERT: H 135 VAL cc_start: 0.5632 (OUTLIER) cc_final: 0.5415 (t) REVERT: K 83 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.4925 (ttm) REVERT: L 5 MET cc_start: 0.0053 (ttm) cc_final: -0.0584 (ttt) outliers start: 37 outliers final: 22 residues processed: 111 average time/residue: 0.0793 time to fit residues: 12.9917 Evaluate side-chains 106 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 159 TYR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 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 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 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82 GLN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.237472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.211649 restraints weight = 12488.265| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 1.59 r_work: 0.4261 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8930 Z= 0.172 Angle : 0.642 8.830 12154 Z= 0.330 Chirality : 0.042 0.148 1386 Planarity : 0.005 0.051 1523 Dihedral : 5.269 53.587 1228 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.94 % Allowed : 25.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.26), residues: 1131 helix: 2.26 (0.24), residues: 455 sheet: 0.33 (0.36), residues: 207 loop : -1.46 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 38 TYR 0.014 0.002 TYR L 94 PHE 0.021 0.002 PHE L 120 TRP 0.021 0.002 TRP H 117 HIS 0.006 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8925) covalent geometry : angle 0.64190 (12144) SS BOND : bond 0.00536 ( 5) SS BOND : angle 0.63753 ( 10) hydrogen bonds : bond 0.04877 ( 493) hydrogen bonds : angle 4.84322 ( 1398) *********************** 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 133 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 78 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.4929 (t80) REVERT: A 193 LEU cc_start: 0.8744 (tp) cc_final: 0.8351 (mt) REVERT: A 303 TYR cc_start: 0.3971 (OUTLIER) cc_final: 0.2286 (m-80) REVERT: A 336 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7995 (pp) REVERT: A 420 MET cc_start: 0.6038 (mmp) cc_final: 0.4866 (ptp) REVERT: A 545 TRP cc_start: 0.7653 (t60) cc_final: 0.7212 (t60) REVERT: H 24 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7475 (t) REVERT: H 135 VAL cc_start: 0.5621 (OUTLIER) cc_final: 0.5305 (t) REVERT: K 38 ARG cc_start: 0.2391 (OUTLIER) cc_final: 0.1532 (ptp-170) REVERT: K 83 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.5130 (ttm) REVERT: L 5 MET cc_start: -0.0160 (ttm) cc_final: -0.0680 (ttt) REVERT: L 90 GLN cc_start: 0.8500 (tt0) cc_final: 0.8269 (tt0) REVERT: L 107 GLU cc_start: 0.5393 (mm-30) cc_final: 0.5162 (mp0) outliers start: 55 outliers final: 37 residues processed: 121 average time/residue: 0.0759 time to fit residues: 13.6274 Evaluate side-chains 118 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 74 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 207 THR Chi-restraints excluded: chain A residue 248 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 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 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 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 38 ARG 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 61 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 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 36 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 105 optimal weight: 0.3980 chunk 106 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4718 r_free = 0.4718 target = 0.239391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.214219 restraints weight = 12372.376| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 1.64 r_work: 0.4281 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.1543 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= 0.128 Angle : 0.561 6.526 12154 Z= 0.292 Chirality : 0.039 0.138 1386 Planarity : 0.004 0.051 1523 Dihedral : 5.109 56.768 1228 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.40 % Allowed : 26.13 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.26), residues: 1131 helix: 2.41 (0.24), residues: 455 sheet: 0.36 (0.36), residues: 207 loop : -1.45 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 38 TYR 0.013 0.001 TYR A 152 PHE 0.016 0.001 PHE A 259 TRP 0.016 0.001 TRP H 50 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8925) covalent geometry : angle 0.56115 (12144) SS BOND : bond 0.00449 ( 5) SS BOND : angle 0.67444 ( 10) hydrogen bonds : bond 0.04083 ( 493) hydrogen bonds : angle 4.66400 ( 1398) *********************** 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 129 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 79 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.4957 (t80) REVERT: A 193 LEU cc_start: 0.8720 (tp) cc_final: 0.8356 (mt) REVERT: A 303 TYR cc_start: 0.3977 (OUTLIER) cc_final: 0.2285 (m-80) REVERT: A 336 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7897 (pp) REVERT: A 420 MET cc_start: 0.6030 (mmp) cc_final: 0.4873 (ptp) REVERT: A 545 TRP cc_start: 0.7696 (t60) cc_final: 0.7250 (t60) REVERT: H 135 VAL cc_start: 0.5662 (OUTLIER) cc_final: 0.5410 (t) REVERT: K 38 ARG cc_start: 0.2414 (OUTLIER) cc_final: 0.1677 (ptp-170) REVERT: K 83 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.4975 (ttm) REVERT: L 5 MET cc_start: -0.0026 (ttm) cc_final: -0.0877 (ttt) REVERT: L 90 GLN cc_start: 0.8503 (tt0) cc_final: 0.8229 (tt0) REVERT: L 107 GLU cc_start: 0.5412 (mm-30) cc_final: 0.5183 (mp0) outliers start: 50 outliers final: 37 residues processed: 117 average time/residue: 0.0788 time to fit residues: 13.2967 Evaluate side-chains 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 76 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 306 VAL Chi-restraints excluded: chain A residue 336 LEU 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 10 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 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 38 ARG 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 61 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 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4705 r_free = 0.4705 target = 0.237938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.214201 restraints weight = 12301.690| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 1.51 r_work: 0.4287 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4181 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.1701 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= 0.136 Angle : 0.575 6.687 12154 Z= 0.299 Chirality : 0.040 0.208 1386 Planarity : 0.004 0.050 1523 Dihedral : 4.855 48.458 1226 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.94 % Allowed : 25.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.26), residues: 1131 helix: 2.38 (0.24), residues: 456 sheet: 0.33 (0.36), residues: 207 loop : -1.42 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 38 TYR 0.011 0.001 TYR L 92 PHE 0.018 0.001 PHE A 259 TRP 0.017 0.001 TRP H 50 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8925) covalent geometry : angle 0.57536 (12144) SS BOND : bond 0.00470 ( 5) SS BOND : angle 0.62606 ( 10) hydrogen bonds : bond 0.04204 ( 493) hydrogen bonds : angle 4.70752 ( 1398) *********************** 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: 55 poor density : 77 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6271 (OUTLIER) cc_final: 0.4935 (t80) REVERT: A 193 LEU cc_start: 0.8829 (tp) cc_final: 0.8382 (mt) REVERT: A 303 TYR cc_start: 0.4098 (OUTLIER) cc_final: 0.2341 (m-80) REVERT: A 336 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7997 (pp) REVERT: A 420 MET cc_start: 0.6216 (mmp) cc_final: 0.4891 (ptp) REVERT: A 545 TRP cc_start: 0.7685 (t60) cc_final: 0.7248 (t60) REVERT: H 135 VAL cc_start: 0.5758 (OUTLIER) cc_final: 0.5438 (t) REVERT: K 38 ARG cc_start: 0.2780 (OUTLIER) cc_final: 0.1894 (ptp-170) REVERT: L 5 MET cc_start: 0.0019 (ttm) cc_final: -0.0809 (ttt) REVERT: L 74 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7485 (tp) REVERT: L 90 GLN cc_start: 0.8514 (tt0) cc_final: 0.8229 (tt0) REVERT: L 107 GLU cc_start: 0.5672 (mm-30) cc_final: 0.5361 (mp0) outliers start: 55 outliers final: 41 residues processed: 120 average time/residue: 0.0764 time to fit residues: 13.4292 Evaluate side-chains 122 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 38 ARG 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 61 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 Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 81 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4718 r_free = 0.4718 target = 0.239426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.213557 restraints weight = 12469.229| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 1.67 r_work: 0.4286 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.1884 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= 0.120 Angle : 0.547 6.095 12154 Z= 0.285 Chirality : 0.039 0.156 1386 Planarity : 0.004 0.051 1523 Dihedral : 4.713 48.674 1226 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.97 % Allowed : 25.92 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1131 helix: 2.48 (0.24), residues: 456 sheet: 0.55 (0.37), residues: 204 loop : -1.46 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.012 0.001 TYR K 94 PHE 0.030 0.001 PHE A 530 TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8925) covalent geometry : angle 0.54725 (12144) SS BOND : bond 0.00460 ( 5) SS BOND : angle 0.68015 ( 10) hydrogen bonds : bond 0.03805 ( 493) hydrogen bonds : angle 4.57647 ( 1398) *********************** 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 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6228 (OUTLIER) cc_final: 0.5021 (t80) REVERT: A 193 LEU cc_start: 0.8727 (tp) cc_final: 0.8359 (mt) REVERT: A 303 TYR cc_start: 0.3983 (OUTLIER) cc_final: 0.2333 (m-80) REVERT: A 336 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7916 (pp) REVERT: A 420 MET cc_start: 0.5910 (mmp) cc_final: 0.4784 (ptp) REVERT: A 545 TRP cc_start: 0.7686 (t60) cc_final: 0.7275 (t60) REVERT: L 5 MET cc_start: 0.0125 (ttm) cc_final: -0.0635 (ttt) REVERT: L 25 ARG cc_start: 0.6873 (ttm-80) cc_final: 0.6574 (ttp80) REVERT: L 74 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7381 (tp) REVERT: L 90 GLN cc_start: 0.8486 (tt0) cc_final: 0.8179 (tt0) REVERT: L 107 GLU cc_start: 0.5434 (mm-30) cc_final: 0.5223 (mp0) outliers start: 46 outliers final: 37 residues processed: 114 average time/residue: 0.0740 time to fit residues: 12.6595 Evaluate side-chains 118 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4695 r_free = 0.4695 target = 0.236778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.211089 restraints weight = 12343.227| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 1.65 r_work: 0.4261 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2002 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= 0.140 Angle : 0.580 6.794 12154 Z= 0.301 Chirality : 0.040 0.141 1386 Planarity : 0.004 0.050 1523 Dihedral : 4.808 48.832 1226 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.08 % Allowed : 25.81 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.26), residues: 1131 helix: 2.35 (0.24), residues: 457 sheet: 0.20 (0.35), residues: 219 loop : -1.38 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.013 0.001 TYR A 152 PHE 0.029 0.001 PHE A 530 TRP 0.017 0.001 TRP H 50 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8925) covalent geometry : angle 0.58035 (12144) SS BOND : bond 0.00450 ( 5) SS BOND : angle 0.66965 ( 10) hydrogen bonds : bond 0.04246 ( 493) hydrogen bonds : angle 4.69679 ( 1398) *********************** 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 124 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 77 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.4978 (t80) REVERT: A 303 TYR cc_start: 0.4050 (OUTLIER) cc_final: 0.2392 (m-80) REVERT: A 336 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7956 (pp) REVERT: A 420 MET cc_start: 0.5998 (mmp) cc_final: 0.4853 (ptp) REVERT: A 545 TRP cc_start: 0.7720 (t60) cc_final: 0.7274 (t60) REVERT: L 5 MET cc_start: -0.0104 (ttm) cc_final: -0.0641 (ttt) REVERT: L 25 ARG cc_start: 0.6905 (ttm-80) cc_final: 0.6461 (ttp-110) REVERT: L 74 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7389 (tp) REVERT: L 90 GLN cc_start: 0.8526 (tt0) cc_final: 0.8249 (tt0) REVERT: L 107 GLU cc_start: 0.5647 (mm-30) cc_final: 0.5428 (mp0) outliers start: 47 outliers final: 40 residues processed: 113 average time/residue: 0.0732 time to fit residues: 12.4690 Evaluate side-chains 118 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 74 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 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 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 23 THR Chi-restraints excluded: chain L residue 55 LEU 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 Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 0.0070 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.237932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.212431 restraints weight = 12236.769| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 1.61 r_work: 0.4276 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8930 Z= 0.124 Angle : 0.566 11.916 12154 Z= 0.291 Chirality : 0.039 0.136 1386 Planarity : 0.004 0.051 1523 Dihedral : 4.732 49.109 1226 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.43 % Allowed : 26.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.26), residues: 1131 helix: 2.42 (0.24), residues: 456 sheet: 0.62 (0.37), residues: 201 loop : -1.46 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.010 0.001 TYR A 152 PHE 0.035 0.001 PHE A 530 TRP 0.015 0.001 TRP H 50 HIS 0.003 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8925) covalent geometry : angle 0.56578 (12144) SS BOND : bond 0.00418 ( 5) SS BOND : angle 0.65338 ( 10) hydrogen bonds : bond 0.03902 ( 493) hydrogen bonds : angle 4.61215 ( 1398) *********************** 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 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.6241 (OUTLIER) cc_final: 0.5026 (t80) REVERT: A 193 LEU cc_start: 0.8756 (tp) cc_final: 0.8385 (mt) REVERT: A 303 TYR cc_start: 0.4028 (OUTLIER) cc_final: 0.2360 (m-80) REVERT: A 336 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7886 (pp) REVERT: A 420 MET cc_start: 0.5935 (mmp) cc_final: 0.4802 (ptp) REVERT: A 545 TRP cc_start: 0.7723 (t60) cc_final: 0.7301 (t60) REVERT: L 5 MET cc_start: -0.0109 (ttm) cc_final: -0.0493 (ttt) REVERT: L 25 ARG cc_start: 0.6847 (ttm-80) cc_final: 0.6433 (ttp-110) REVERT: L 74 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7383 (tp) REVERT: L 90 GLN cc_start: 0.8503 (tt0) cc_final: 0.8197 (tt0) REVERT: L 107 GLU cc_start: 0.5746 (mm-30) cc_final: 0.5514 (mp0) outliers start: 41 outliers final: 37 residues processed: 110 average time/residue: 0.0739 time to fit residues: 12.3001 Evaluate side-chains 117 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 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 74 LEU Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 109 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4691 r_free = 0.4691 target = 0.236260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.213418 restraints weight = 12338.500| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 1.55 r_work: 0.4272 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8930 Z= 0.130 Angle : 0.579 9.995 12154 Z= 0.298 Chirality : 0.040 0.138 1386 Planarity : 0.004 0.051 1523 Dihedral : 4.766 49.262 1226 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.18 % Allowed : 25.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.26), residues: 1131 helix: 2.36 (0.24), residues: 457 sheet: 0.39 (0.36), residues: 211 loop : -1.44 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.010 0.001 TYR L 92 PHE 0.032 0.001 PHE A 530 TRP 0.016 0.001 TRP H 50 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8925) covalent geometry : angle 0.57857 (12144) SS BOND : bond 0.00427 ( 5) SS BOND : angle 0.66499 ( 10) hydrogen bonds : bond 0.04090 ( 493) hydrogen bonds : angle 4.65147 ( 1398) ********************** 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 130 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.283 Fit side-chains REVERT: A 52 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.4938 (t80) REVERT: A 193 LEU cc_start: 0.8736 (tp) cc_final: 0.8359 (mt) REVERT: A 303 TYR cc_start: 0.3990 (OUTLIER) cc_final: 0.2329 (m-80) REVERT: A 336 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7899 (pp) REVERT: A 420 MET cc_start: 0.5886 (mmp) cc_final: 0.4760 (ptp) REVERT: A 545 TRP cc_start: 0.7756 (t60) cc_final: 0.7333 (t60) REVERT: H 178 HIS cc_start: 0.3324 (OUTLIER) cc_final: 0.2642 (m90) REVERT: L 5 MET cc_start: 0.0006 (ttm) cc_final: -0.0502 (ttt) REVERT: L 25 ARG cc_start: 0.6847 (ttm-80) cc_final: 0.6453 (ttp-110) REVERT: L 74 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7379 (tp) REVERT: L 90 GLN cc_start: 0.8516 (tt0) cc_final: 0.8229 (tt0) outliers start: 48 outliers final: 39 residues processed: 120 average time/residue: 0.0710 time to fit residues: 12.6599 Evaluate side-chains 121 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 178 HIS 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 23 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 24 optimal weight: 0.0870 chunk 101 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 = 0.4714 r_free = 0.4714 target = 0.238978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.215701 restraints weight = 12392.373| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 1.54 r_work: 0.4305 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4206 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8930 Z= 0.111 Angle : 0.557 10.281 12154 Z= 0.285 Chirality : 0.039 0.140 1386 Planarity : 0.004 0.051 1523 Dihedral : 4.609 49.321 1226 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.46 % Allowed : 27.32 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1131 helix: 2.48 (0.24), residues: 460 sheet: 0.65 (0.37), residues: 201 loop : -1.37 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.014 0.001 TYR A 152 PHE 0.038 0.001 PHE A 530 TRP 0.015 0.001 TRP A 328 HIS 0.002 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8925) covalent geometry : angle 0.55651 (12144) SS BOND : bond 0.00395 ( 5) SS BOND : angle 0.67675 ( 10) hydrogen bonds : bond 0.03490 ( 493) hydrogen bonds : angle 4.47849 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.15 seconds wall clock time: 41 minutes 4.30 seconds (2464.30 seconds total)