Starting phenix.real_space_refine on Wed Sep 17 03:50:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jds_61398/09_2025/9jds_61398.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jds_61398/09_2025/9jds_61398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jds_61398/09_2025/9jds_61398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jds_61398/09_2025/9jds_61398.map" model { file = "/net/cci-nas-00/data/ceres_data/9jds_61398/09_2025/9jds_61398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jds_61398/09_2025/9jds_61398.cif" } resolution = 3.4 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= 0.001 sd= 0.057 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 20 5.16 5 C 2320 2.51 5 N 546 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 3456 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3441 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 1.00, per 1000 atoms: 0.29 Number of scatterers: 3456 At special positions: 0 Unit cell: (78.1, 61.6, 85.8, 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 20 16.00 O 570 8.00 N 546 7.00 C 2320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 467 " 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: 0.22 Conformation dependent library (CDL) restraints added in 92.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 66.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.627A pdb=" N ALA A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.840A pdb=" N GLN A 73 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.924A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 87 " --> pdb=" O GLN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 107 removed outlier: 3.563A pdb=" N THR A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.576A pdb=" N ASP A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 4.160A pdb=" N PHE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.854A pdb=" N ILE A 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.773A pdb=" N TYR A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.561A pdb=" N VAL A 185 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.546A pdb=" N PHE A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 199' Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.530A pdb=" N ILE A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.726A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 removed outlier: 3.657A pdb=" N PHE A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 292 removed outlier: 4.056A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 3.913A pdb=" N ALA A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 removed outlier: 3.680A pdb=" N LEU A 296 " --> pdb=" O ASP A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.974A pdb=" N LEU A 304 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.924A pdb=" N HIS A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.879A pdb=" N ARG A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 366 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.520A pdb=" N ALA A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 420 through 436 removed outlier: 4.170A pdb=" N MET A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 removed outlier: 4.384A pdb=" N VAL A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 312 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: 0.41 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 495 1.30 - 1.43: 1147 1.43 - 1.56: 1901 1.56 - 1.70: 0 1.70 - 1.83: 31 Bond restraints: 3574 Sorted by residual: bond pdb=" N SER A 348 " pdb=" CA SER A 348 " ideal model delta sigma weight residual 1.459 1.536 -0.077 1.15e-02 7.56e+03 4.45e+01 bond pdb=" CA VAL A 151 " pdb=" CB VAL A 151 " ideal model delta sigma weight residual 1.540 1.451 0.088 1.37e-02 5.33e+03 4.15e+01 bond pdb=" C LYS A 347 " pdb=" N SER A 348 " ideal model delta sigma weight residual 1.331 1.420 -0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" C VAL A 151 " pdb=" O VAL A 151 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.23e-02 6.61e+03 3.66e+01 bond pdb=" CA SER A 348 " pdb=" C SER A 348 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.49e-02 4.50e+03 2.95e+01 ... (remaining 3569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.04: 4821 6.04 - 12.07: 49 12.07 - 18.11: 7 18.11 - 24.15: 0 24.15 - 30.19: 1 Bond angle restraints: 4878 Sorted by residual: angle pdb=" N ILE A 155 " pdb=" CA ILE A 155 " pdb=" C ILE A 155 " ideal model delta sigma weight residual 113.47 96.34 17.13 1.01e+00 9.80e-01 2.88e+02 angle pdb=" N ILE A 349 " pdb=" CA ILE A 349 " pdb=" C ILE A 349 " ideal model delta sigma weight residual 109.34 139.53 -30.19 2.08e+00 2.31e-01 2.11e+02 angle pdb=" N THR A 183 " pdb=" CA THR A 183 " pdb=" C THR A 183 " ideal model delta sigma weight residual 111.71 125.05 -13.34 1.15e+00 7.56e-01 1.35e+02 angle pdb=" N SER A 348 " pdb=" CA SER A 348 " pdb=" C SER A 348 " ideal model delta sigma weight residual 113.38 125.70 -12.32 1.17e+00 7.31e-01 1.11e+02 angle pdb=" N MET A 424 " pdb=" CA MET A 424 " pdb=" C MET A 424 " ideal model delta sigma weight residual 111.07 122.12 -11.05 1.07e+00 8.73e-01 1.07e+02 ... (remaining 4873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.58: 1730 11.58 - 23.16: 206 23.16 - 34.74: 32 34.74 - 46.32: 15 46.32 - 57.90: 5 Dihedral angle restraints: 1988 sinusoidal: 734 harmonic: 1254 Sorted by residual: dihedral pdb=" C ILE A 349 " pdb=" N ILE A 349 " pdb=" CA ILE A 349 " pdb=" CB ILE A 349 " ideal model delta harmonic sigma weight residual -122.00 -165.61 43.61 0 2.50e+00 1.60e-01 3.04e+02 dihedral pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CA ILE A 349 " pdb=" CB ILE A 349 " ideal model delta harmonic sigma weight residual 123.40 165.44 -42.04 0 2.50e+00 1.60e-01 2.83e+02 dihedral pdb=" N SER A 348 " pdb=" C SER A 348 " pdb=" CA SER A 348 " pdb=" CB SER A 348 " ideal model delta harmonic sigma weight residual 122.80 155.05 -32.25 0 2.50e+00 1.60e-01 1.66e+02 ... (remaining 1985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 518 0.381 - 0.762: 12 0.762 - 1.143: 5 1.143 - 1.524: 1 1.524 - 1.905: 1 Chirality restraints: 537 Sorted by residual: chirality pdb=" CA ILE A 349 " pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CB ILE A 349 " both_signs ideal model delta sigma weight residual False 2.43 0.53 1.91 2.00e-01 2.50e+01 9.07e+01 chirality pdb=" CA SER A 348 " pdb=" N SER A 348 " pdb=" C SER A 348 " pdb=" CB SER A 348 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CA HIS A 44 " pdb=" N HIS A 44 " pdb=" C HIS A 44 " pdb=" CB HIS A 44 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 534 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 348 " -0.032 2.00e-02 2.50e+03 6.29e-02 3.95e+01 pdb=" C SER A 348 " 0.109 2.00e-02 2.50e+03 pdb=" O SER A 348 " -0.040 2.00e-02 2.50e+03 pdb=" N ILE A 349 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 375 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 357 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO A 358 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " -0.043 5.00e-02 4.00e+02 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 643 2.76 - 3.30: 2997 3.30 - 3.83: 5262 3.83 - 4.37: 6390 4.37 - 4.90: 10832 Nonbonded interactions: 26124 Sorted by model distance: nonbonded pdb=" O ALA A 182 " pdb=" CG1 VAL A 185 " model vdw 2.228 3.460 nonbonded pdb=" O TYR A 95 " pdb=" OG SER A 98 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 101 " pdb=" ND1 HIS A 257 " model vdw 2.328 3.120 nonbonded pdb=" N ILE A 155 " pdb=" N ALA A 156 " model vdw 2.359 2.560 nonbonded pdb=" OG SER A 78 " pdb=" OH TYR A 235 " model vdw 2.389 3.040 ... (remaining 26119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.650 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 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 : 0.009 0.089 3575 Z= 0.540 Angle : 1.475 30.187 4880 Z= 0.918 Chirality : 0.170 1.905 537 Planarity : 0.010 0.081 588 Dihedral : 10.587 57.896 1183 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.12 % Allowed : 2.81 % Favored : 96.07 % Cbeta Deviations : 3.74 % Peptide Plane: Cis-proline : 0.00 % 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: -6.75 (0.24), residues: 427 helix: -4.65 (0.12), residues: 297 sheet: None (None), residues: 0 loop : -3.37 (0.46), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 453 TYR 0.029 0.002 TYR A 163 PHE 0.035 0.003 PHE A 370 TRP 0.020 0.003 TRP A 122 HIS 0.008 0.002 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00916 ( 3574) covalent geometry : angle 1.47495 ( 4878) SS BOND : bond 0.00210 ( 1) SS BOND : angle 2.44213 ( 2) hydrogen bonds : bond 0.33067 ( 109) hydrogen bonds : angle 10.97795 ( 312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.113 Fit side-chains REVERT: A 190 PHE cc_start: 0.3659 (m-80) cc_final: 0.2830 (m-80) REVERT: A 203 MET cc_start: 0.7989 (mtm) cc_final: 0.7754 (mtt) REVERT: A 271 MET cc_start: 0.7457 (tpp) cc_final: 0.7072 (mtt) REVERT: A 413 LYS cc_start: 0.8445 (mmpt) cc_final: 0.8013 (mppt) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.0534 time to fit residues: 4.4749 Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 409 ASN A 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130049 restraints weight = 4862.764| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.24 r_work: 0.3356 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3575 Z= 0.147 Angle : 0.633 5.964 4880 Z= 0.337 Chirality : 0.044 0.220 537 Planarity : 0.006 0.068 588 Dihedral : 7.212 47.963 469 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.12 % Allowed : 9.83 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.04 (0.33), residues: 427 helix: -3.49 (0.21), residues: 288 sheet: None (None), residues: 0 loop : -2.49 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 311 TYR 0.013 0.001 TYR A 269 PHE 0.017 0.001 PHE A 370 TRP 0.014 0.001 TRP A 260 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3574) covalent geometry : angle 0.63125 ( 4878) SS BOND : bond 0.00725 ( 1) SS BOND : angle 2.50643 ( 2) hydrogen bonds : bond 0.05014 ( 109) hydrogen bonds : angle 5.99319 ( 312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.097 Fit side-chains REVERT: A 76 MET cc_start: 0.7644 (ttm) cc_final: 0.7327 (tpp) REVERT: A 271 MET cc_start: 0.7743 (tpp) cc_final: 0.7297 (mtt) REVERT: A 315 VAL cc_start: 0.8239 (p) cc_final: 0.8009 (p) REVERT: A 373 PHE cc_start: 0.8534 (t80) cc_final: 0.8244 (t80) outliers start: 4 outliers final: 1 residues processed: 58 average time/residue: 0.0510 time to fit residues: 3.9353 Evaluate side-chains 50 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131219 restraints weight = 4794.328| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.34 r_work: 0.3373 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3575 Z= 0.102 Angle : 0.542 5.995 4880 Z= 0.285 Chirality : 0.040 0.206 537 Planarity : 0.005 0.057 588 Dihedral : 5.544 32.527 464 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.69 % Allowed : 10.39 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.04 (0.36), residues: 427 helix: -2.59 (0.25), residues: 287 sheet: None (None), residues: 0 loop : -2.47 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.010 0.001 TYR A 269 PHE 0.016 0.001 PHE A 370 TRP 0.010 0.001 TRP A 260 HIS 0.001 0.000 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3574) covalent geometry : angle 0.54170 ( 4878) SS BOND : bond 0.00249 ( 1) SS BOND : angle 1.25272 ( 2) hydrogen bonds : bond 0.03680 ( 109) hydrogen bonds : angle 4.86614 ( 312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.165 Fit side-chains REVERT: A 263 GLN cc_start: 0.8343 (mp10) cc_final: 0.8080 (mp10) REVERT: A 271 MET cc_start: 0.7757 (tpp) cc_final: 0.7287 (mtt) REVERT: A 373 PHE cc_start: 0.8539 (t80) cc_final: 0.8293 (t80) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.0636 time to fit residues: 4.3285 Evaluate side-chains 48 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 464 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 32 optimal weight: 0.0030 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131496 restraints weight = 4660.232| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.23 r_work: 0.3380 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3575 Z= 0.102 Angle : 0.515 5.745 4880 Z= 0.268 Chirality : 0.039 0.172 537 Planarity : 0.004 0.053 588 Dihedral : 5.119 23.023 464 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.09 % Allowed : 9.83 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.59 (0.38), residues: 427 helix: -2.14 (0.27), residues: 290 sheet: None (None), residues: 0 loop : -2.55 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 105 TYR 0.009 0.001 TYR A 269 PHE 0.015 0.001 PHE A 370 TRP 0.008 0.001 TRP A 209 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3574) covalent geometry : angle 0.51499 ( 4878) SS BOND : bond 0.00232 ( 1) SS BOND : angle 1.11335 ( 2) hydrogen bonds : bond 0.03165 ( 109) hydrogen bonds : angle 4.53012 ( 312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.144 Fit side-chains REVERT: A 107 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7221 (mtm180) REVERT: A 256 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7874 (ptm) REVERT: A 263 GLN cc_start: 0.8336 (mp10) cc_final: 0.8109 (mp10) REVERT: A 271 MET cc_start: 0.7561 (tpp) cc_final: 0.7059 (mtt) REVERT: A 357 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6918 (mm) REVERT: A 373 PHE cc_start: 0.8484 (t80) cc_final: 0.8203 (t80) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.0573 time to fit residues: 3.9302 Evaluate side-chains 53 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 464 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129395 restraints weight = 4756.561| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.25 r_work: 0.3357 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3575 Z= 0.106 Angle : 0.514 5.713 4880 Z= 0.267 Chirality : 0.041 0.267 537 Planarity : 0.004 0.051 588 Dihedral : 4.990 20.478 464 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.53 % Allowed : 10.67 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.15 (0.39), residues: 427 helix: -1.82 (0.29), residues: 285 sheet: None (None), residues: 0 loop : -2.32 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.009 0.001 TYR A 269 PHE 0.014 0.001 PHE A 370 TRP 0.007 0.001 TRP A 209 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3574) covalent geometry : angle 0.51384 ( 4878) SS BOND : bond 0.00223 ( 1) SS BOND : angle 1.04935 ( 2) hydrogen bonds : bond 0.03111 ( 109) hydrogen bonds : angle 4.40476 ( 312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.098 Fit side-chains REVERT: A 107 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7297 (mtm180) REVERT: A 185 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7640 (p) REVERT: A 263 GLN cc_start: 0.8352 (mp10) cc_final: 0.8082 (mp10) REVERT: A 271 MET cc_start: 0.7566 (tpp) cc_final: 0.7030 (mtt) REVERT: A 357 LEU cc_start: 0.7241 (mt) cc_final: 0.7023 (mm) REVERT: A 373 PHE cc_start: 0.8504 (t80) cc_final: 0.8163 (t80) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.0562 time to fit residues: 3.6716 Evaluate side-chains 54 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 464 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.0010 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.0030 chunk 14 optimal weight: 0.0010 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 overall best weight: 0.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132214 restraints weight = 4710.984| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.26 r_work: 0.3397 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3575 Z= 0.082 Angle : 0.478 5.810 4880 Z= 0.247 Chirality : 0.039 0.227 537 Planarity : 0.004 0.048 588 Dihedral : 4.632 19.784 464 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.53 % Allowed : 11.52 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.73 (0.40), residues: 427 helix: -1.48 (0.30), residues: 285 sheet: None (None), residues: 0 loop : -2.21 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.008 0.001 TYR A 269 PHE 0.014 0.001 PHE A 370 TRP 0.007 0.001 TRP A 209 HIS 0.003 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 3574) covalent geometry : angle 0.47833 ( 4878) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.68642 ( 2) hydrogen bonds : bond 0.02530 ( 109) hydrogen bonds : angle 4.11549 ( 312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.126 Fit side-chains REVERT: A 107 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7379 (mtm180) REVERT: A 185 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7745 (p) REVERT: A 256 MET cc_start: 0.8334 (ptm) cc_final: 0.8134 (ptm) REVERT: A 263 GLN cc_start: 0.8323 (mp10) cc_final: 0.8078 (mp10) REVERT: A 271 MET cc_start: 0.7677 (tpp) cc_final: 0.7189 (mtt) REVERT: A 357 LEU cc_start: 0.7566 (mt) cc_final: 0.7320 (mm) REVERT: A 413 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7248 (mppt) REVERT: A 452 VAL cc_start: 0.7999 (t) cc_final: 0.7797 (t) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.0564 time to fit residues: 3.7874 Evaluate side-chains 51 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 464 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124937 restraints weight = 4943.979| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.26 r_work: 0.3298 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3575 Z= 0.160 Angle : 0.563 5.574 4880 Z= 0.293 Chirality : 0.043 0.209 537 Planarity : 0.005 0.054 588 Dihedral : 5.121 22.251 464 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.81 % Allowed : 11.80 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.02 (0.40), residues: 427 helix: -1.66 (0.29), residues: 292 sheet: None (None), residues: 0 loop : -2.46 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 352 TYR 0.014 0.001 TYR A 163 PHE 0.017 0.002 PHE A 451 TRP 0.009 0.001 TRP A 364 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3574) covalent geometry : angle 0.56290 ( 4878) SS BOND : bond 0.00346 ( 1) SS BOND : angle 1.30675 ( 2) hydrogen bonds : bond 0.03776 ( 109) hydrogen bonds : angle 4.53923 ( 312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.126 Fit side-chains REVERT: A 107 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7499 (mtm180) REVERT: A 263 GLN cc_start: 0.8371 (mp10) cc_final: 0.8162 (mp10) REVERT: A 271 MET cc_start: 0.7571 (tpp) cc_final: 0.6997 (mtt) REVERT: A 357 LEU cc_start: 0.7339 (mt) cc_final: 0.7138 (mm) REVERT: A 413 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7438 (mppt) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.0569 time to fit residues: 4.1609 Evaluate side-chains 57 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 464 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126780 restraints weight = 4825.995| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.23 r_work: 0.3324 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3575 Z= 0.119 Angle : 0.522 5.859 4880 Z= 0.269 Chirality : 0.041 0.194 537 Planarity : 0.004 0.049 588 Dihedral : 4.990 22.808 464 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.09 % Allowed : 12.08 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.86 (0.40), residues: 427 helix: -1.51 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -2.46 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.010 0.001 TYR A 163 PHE 0.023 0.001 PHE A 451 TRP 0.009 0.001 TRP A 337 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3574) covalent geometry : angle 0.52141 ( 4878) SS BOND : bond 0.00241 ( 1) SS BOND : angle 1.00897 ( 2) hydrogen bonds : bond 0.03161 ( 109) hydrogen bonds : angle 4.40023 ( 312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.121 Fit side-chains REVERT: A 107 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7417 (mtm180) REVERT: A 263 GLN cc_start: 0.8339 (mp10) cc_final: 0.8119 (mp10) REVERT: A 271 MET cc_start: 0.7546 (tpp) cc_final: 0.6962 (mtt) REVERT: A 357 LEU cc_start: 0.7339 (mt) cc_final: 0.7105 (mm) REVERT: A 413 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7486 (mppt) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.0610 time to fit residues: 4.6424 Evaluate side-chains 60 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 464 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125155 restraints weight = 4796.895| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.26 r_work: 0.3299 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3575 Z= 0.143 Angle : 0.547 5.746 4880 Z= 0.282 Chirality : 0.042 0.184 537 Planarity : 0.004 0.052 588 Dihedral : 5.102 23.801 464 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.37 % Allowed : 11.80 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.88 (0.40), residues: 427 helix: -1.50 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -2.55 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 453 TYR 0.011 0.001 TYR A 163 PHE 0.025 0.001 PHE A 451 TRP 0.011 0.001 TRP A 364 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3574) covalent geometry : angle 0.54675 ( 4878) SS BOND : bond 0.00293 ( 1) SS BOND : angle 1.11400 ( 2) hydrogen bonds : bond 0.03409 ( 109) hydrogen bonds : angle 4.49377 ( 312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.101 Fit side-chains REVERT: A 107 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7599 (mtm180) REVERT: A 110 LYS cc_start: 0.7256 (mmtt) cc_final: 0.6826 (mttt) REVERT: A 185 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7716 (p) REVERT: A 263 GLN cc_start: 0.8346 (mp10) cc_final: 0.8044 (mp10) REVERT: A 271 MET cc_start: 0.7697 (tpp) cc_final: 0.7090 (mtt) REVERT: A 357 LEU cc_start: 0.7532 (mt) cc_final: 0.7304 (mm) REVERT: A 413 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7523 (mppt) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.0589 time to fit residues: 4.4764 Evaluate side-chains 62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 464 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127099 restraints weight = 4862.344| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.27 r_work: 0.3324 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3575 Z= 0.110 Angle : 0.515 5.847 4880 Z= 0.265 Chirality : 0.041 0.182 537 Planarity : 0.004 0.047 588 Dihedral : 4.940 23.797 464 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.37 % Allowed : 11.52 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.72 (0.40), residues: 427 helix: -1.37 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -2.50 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.009 0.001 TYR A 269 PHE 0.028 0.001 PHE A 451 TRP 0.010 0.001 TRP A 337 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3574) covalent geometry : angle 0.51480 ( 4878) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.91460 ( 2) hydrogen bonds : bond 0.02993 ( 109) hydrogen bonds : angle 4.31891 ( 312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.115 Fit side-chains REVERT: A 107 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7419 (mtm180) REVERT: A 185 VAL cc_start: 0.7762 (OUTLIER) cc_final: 0.7556 (p) REVERT: A 263 GLN cc_start: 0.8296 (mp10) cc_final: 0.7992 (mp10) REVERT: A 271 MET cc_start: 0.7604 (tpp) cc_final: 0.6994 (mtt) REVERT: A 357 LEU cc_start: 0.7433 (mt) cc_final: 0.7176 (mm) REVERT: A 413 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7409 (mppt) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.0577 time to fit residues: 4.0006 Evaluate side-chains 56 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 464 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126702 restraints weight = 4829.942| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.28 r_work: 0.3316 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3575 Z= 0.118 Angle : 0.521 5.746 4880 Z= 0.268 Chirality : 0.041 0.179 537 Planarity : 0.004 0.050 588 Dihedral : 4.889 23.456 464 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.65 % Allowed : 11.52 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.40), residues: 427 helix: -1.29 (0.31), residues: 289 sheet: None (None), residues: 0 loop : -2.44 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.010 0.001 TYR A 163 PHE 0.028 0.001 PHE A 451 TRP 0.010 0.001 TRP A 364 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3574) covalent geometry : angle 0.52116 ( 4878) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.96476 ( 2) hydrogen bonds : bond 0.03057 ( 109) hydrogen bonds : angle 4.31299 ( 312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 848.14 seconds wall clock time: 15 minutes 13.03 seconds (913.03 seconds total)