Starting phenix.real_space_refine on Tue Aug 4 19:13:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t9p_55723/08_2026/9t9p_55723.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t9p_55723/08_2026/9t9p_55723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t9p_55723/08_2026/9t9p_55723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t9p_55723/08_2026/9t9p_55723.map" model { file = "/net/cci-nas-00/data/ceres_data/9t9p_55723/08_2026/9t9p_55723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t9p_55723/08_2026/9t9p_55723.cif" } resolution = 3.0 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= -0.002 sd= 1.270 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 23 5.16 5 C 3917 2.51 5 N 1036 2.21 5 O 1139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6115 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1920 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "B" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4170 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 20, 'TRANS': 511} Chain breaks: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'ZMA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.04, per 1000 atoms: 0.17 Number of scatterers: 6115 At special positions: 0 Unit cell: (76.82, 68.47, 151.135, 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 23 16.00 O 1139 8.00 N 1036 7.00 C 3917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 514 " 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: 0.31 Conformation dependent library (CDL) restraints added in 318.2 milliseconds 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 50.4% alpha, 16.2% 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 59 through 63 Processing helix chain 'A' and resid 98 through 103 removed outlier: 4.043A pdb=" N SER A 103 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.887A pdb=" N SER A 181 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 4.091A pdb=" N SER A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.594A pdb=" N LEU A 258 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 259 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.824A pdb=" N GLN A 293 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 34 removed outlier: 3.508A pdb=" N CYS B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 58 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.982A pdb=" N THR B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 108 removed outlier: 5.191A pdb=" N VAL B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 86 " --> pdb=" O CYS B 82 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.546A pdb=" N GLY B 142 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.503A pdb=" N VAL B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 186 through 227 removed outlier: 4.296A pdb=" N ARG B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.210A pdb=" N ALA B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.927A pdb=" N ASN B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.846A pdb=" N ASN B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 379 removed outlier: 3.540A pdb=" N ALA B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 396 removed outlier: 3.648A pdb=" N ARG B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 511 removed outlier: 4.417A pdb=" N ILE B 460 " --> pdb=" O ASP B 456 " (cutoff:3.500A) Proline residue: B 500 - end of helix removed outlier: 3.552A pdb=" N CYS B 511 " --> pdb=" O PHE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 544 removed outlier: 3.868A pdb=" N MET B 522 " --> pdb=" O PRO B 518 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 524 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER B 533 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 534 " --> pdb=" O HIS B 530 " (cutoff:3.500A) Proline residue: B 537 - end of helix Processing helix chain 'B' and resid 544 through 555 removed outlier: 3.947A pdb=" N ARG B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 71 removed outlier: 4.086A pdb=" N ALA A 68 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 71 removed outlier: 4.086A pdb=" N ALA A 68 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 76 " --> pdb=" O TRP A 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.849A pdb=" N ALA A 107 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.521A pdb=" N ALA A 146 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 183 through 188 removed outlier: 3.950A pdb=" N ALA A 185 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.742A pdb=" N LEU A 235 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 225 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 233 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY A 227 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 263 through 266 removed outlier: 3.657A pdb=" N ALA A 263 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 244 removed outlier: 3.780A pdb=" N THR B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 251 through 252 355 hydrogen bonds defined for protein. 981 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: 0.88 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1990 1.34 - 1.46: 1279 1.46 - 1.58: 2941 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 6243 Sorted by residual: bond pdb=" C11 ZMA B 901 " pdb=" N10 ZMA B 901 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C24 ZMA B 901 " pdb=" O25 ZMA B 901 " ideal model delta sigma weight residual 1.345 1.373 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C23 ZMA B 901 " pdb=" C24 ZMA B 901 " ideal model delta sigma weight residual 1.355 1.331 0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C18 ZMA B 901 " pdb=" N12 ZMA B 901 " ideal model delta sigma weight residual 1.322 1.346 -0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C THR B 138 " pdb=" N PRO B 139 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 ... (remaining 6238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 8302 1.23 - 2.45: 157 2.45 - 3.68: 28 3.68 - 4.90: 12 4.90 - 6.13: 3 Bond angle restraints: 8502 Sorted by residual: angle pdb=" N TYR B 523 " pdb=" CA TYR B 523 " pdb=" C TYR B 523 " ideal model delta sigma weight residual 111.24 108.00 3.24 1.29e+00 6.01e-01 6.29e+00 angle pdb=" C ASN B 145 " pdb=" N CYS B 146 " pdb=" CA CYS B 146 " ideal model delta sigma weight residual 121.70 125.96 -4.26 1.80e+00 3.09e-01 5.60e+00 angle pdb=" N LEU B 499 " pdb=" CA LEU B 499 " pdb=" C LEU B 499 " ideal model delta sigma weight residual 109.81 114.82 -5.01 2.21e+00 2.05e-01 5.14e+00 angle pdb=" C LEU B 519 " pdb=" N TRP B 520 " pdb=" CA TRP B 520 " ideal model delta sigma weight residual 120.38 122.98 -2.60 1.37e+00 5.33e-01 3.59e+00 angle pdb=" C TYR B 245 " pdb=" N ARG B 246 " pdb=" CA ARG B 246 " ideal model delta sigma weight residual 121.80 126.09 -4.29 2.44e+00 1.68e-01 3.09e+00 ... (remaining 8497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 3268 16.02 - 32.04: 277 32.04 - 48.05: 82 48.05 - 64.07: 33 64.07 - 80.08: 6 Dihedral angle restraints: 3666 sinusoidal: 1370 harmonic: 2296 Sorted by residual: dihedral pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " pdb=" SG CYS B 514 " pdb=" CB CYS B 514 " ideal model delta sinusoidal sigma weight residual -86.00 -156.77 70.77 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CA ASP B 314 " pdb=" CB ASP B 314 " pdb=" CG ASP B 314 " pdb=" OD1 ASP B 314 " ideal model delta sinusoidal sigma weight residual -30.00 -84.97 54.97 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" N ARG B 552 " pdb=" CA ARG B 552 " pdb=" CB ARG B 552 " pdb=" CG ARG B 552 " ideal model delta sinusoidal sigma weight residual -180.00 -121.26 -58.74 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 569 0.026 - 0.051: 235 0.051 - 0.077: 107 0.077 - 0.102: 38 0.102 - 0.128: 35 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA PRO B 500 " pdb=" N PRO B 500 " pdb=" C PRO B 500 " pdb=" CB PRO B 500 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL A 44 " pdb=" N VAL A 44 " pdb=" C VAL A 44 " pdb=" CB VAL A 44 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 981 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 523 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C TYR B 523 " -0.064 2.00e-02 2.50e+03 pdb=" O TYR B 523 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU B 524 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 522 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C MET B 522 " 0.058 2.00e-02 2.50e+03 pdb=" O MET B 522 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR B 523 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 141 " 0.193 9.50e-02 1.11e+02 8.70e-02 5.97e+00 pdb=" NE ARG A 141 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 141 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 141 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 141 " 0.000 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 3452 3.02 - 3.49: 6038 3.49 - 3.96: 9707 3.96 - 4.43: 10896 4.43 - 4.90: 18205 Nonbonded interactions: 48298 Sorted by model distance: nonbonded pdb=" N ASP A 67 " pdb=" OD1 ASP A 67 " model vdw 2.551 3.120 nonbonded pdb=" C11 ZMA B 901 " pdb=" N16 ZMA B 901 " model vdw 2.611 2.672 nonbonded pdb=" N ASP B 449 " pdb=" OD1 ASP B 449 " model vdw 2.623 3.120 nonbonded pdb=" N SER B 364 " pdb=" O SER B 364 " model vdw 2.638 2.496 nonbonded pdb=" C SER B 90 " pdb=" OG SER B 90 " model vdw 2.639 2.616 ... (remaining 48293 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: 0.010 Normalize map: mean=0, sd=1: 4.300 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.990 Find NCS groups from input model: 0.020 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 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 : 0.002 0.034 6246 Z= 0.106 Angle : 0.459 6.127 8508 Z= 0.243 Chirality : 0.040 0.128 984 Planarity : 0.007 0.087 1080 Dihedral : 14.486 80.084 2185 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % 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 are not related in a simple way. whole: 0.48 (0.31), residues: 797 helix: 1.02 (0.30), residues: 335 sheet: 0.76 (0.50), residues: 102 loop : -0.41 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 141 TYR 0.009 0.001 TYR B 9 PHE 0.011 0.001 PHE B 44 TRP 0.014 0.001 TRP B 433 HIS 0.001 0.000 HIS B 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.11 ( 6243) covalent geometry : angle 0.45851 / 0.24 ( 8502) SS BOND : bond 0.00037 / 0.01 ( 3) SS BOND : angle 0.55949 / 0.35 ( 6) hydrogen bonds : bond 0.10697 / 7.19 ( 352) hydrogen bonds : angle 5.72350 / 3.79 ( 981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.145 Fit side-chains REVERT: A 223 ASP cc_start: 0.7006 (m-30) cc_final: 0.6687 (m-30) REVERT: B 217 ASP cc_start: 0.6128 (m-30) cc_final: 0.5783 (m-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.3506 time to fit residues: 50.1607 Evaluate side-chains 83 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN B 42 ASN B 163 GLN B 289 ASN B 295 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.217467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.198026 restraints weight = 7020.369| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.32 r_work: 0.4077 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6246 Z= 0.129 Angle : 0.521 6.542 8508 Z= 0.274 Chirality : 0.043 0.138 984 Planarity : 0.004 0.041 1080 Dihedral : 3.745 35.859 857 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.48 % Allowed : 18.96 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.31), residues: 797 helix: 2.03 (0.29), residues: 337 sheet: 0.81 (0.47), residues: 116 loop : -0.22 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 277 TYR 0.020 0.002 TYR B 112 PHE 0.019 0.002 PHE B 494 TRP 0.012 0.001 TRP B 143 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 6243) covalent geometry : angle 0.52025 / 0.27 ( 8502) SS BOND : bond 0.01393 / 0.73 ( 3) SS BOND : angle 1.16783 / 0.74 ( 6) hydrogen bonds : bond 0.03666 / 2.41 ( 352) hydrogen bonds : angle 4.35685 / 2.96 ( 981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.135 Fit side-chains REVERT: A 223 ASP cc_start: 0.7125 (m-30) cc_final: 0.6876 (m-30) REVERT: A 233 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7220 (pp) REVERT: B 9 TYR cc_start: 0.7190 (t80) cc_final: 0.6394 (t80) REVERT: B 111 ARG cc_start: 0.7437 (mtp85) cc_final: 0.7202 (mtp180) REVERT: B 135 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7200 (pt) REVERT: B 205 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6460 (mpp-170) REVERT: B 210 GLN cc_start: 0.7275 (mt0) cc_final: 0.6625 (mp10) REVERT: B 214 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: B 217 ASP cc_start: 0.6228 (m-30) cc_final: 0.5841 (m-30) REVERT: B 329 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5914 (mm-30) REVERT: B 379 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.6496 (mp0) outliers start: 22 outliers final: 6 residues processed: 103 average time/residue: 0.3264 time to fit residues: 35.9102 Evaluate side-chains 89 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 436 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN B 289 ASN B 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.195637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174225 restraints weight = 6968.030| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.42 r_work: 0.3873 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6246 Z= 0.160 Angle : 0.554 6.235 8508 Z= 0.290 Chirality : 0.045 0.154 984 Planarity : 0.005 0.043 1080 Dihedral : 4.319 45.214 857 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.42 % Allowed : 20.22 % Favored : 75.36 % 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 are not related in a simple way. whole: 1.18 (0.31), residues: 797 helix: 1.92 (0.29), residues: 336 sheet: 0.82 (0.50), residues: 104 loop : -0.31 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 120 TYR 0.024 0.002 TYR B 112 PHE 0.017 0.002 PHE B 70 TRP 0.013 0.001 TRP B 433 HIS 0.004 0.001 HIS B 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 6243) covalent geometry : angle 0.55289 / 0.29 ( 8502) SS BOND : bond 0.01734 / 0.91 ( 3) SS BOND : angle 1.15645 / 0.71 ( 6) hydrogen bonds : bond 0.04804 / 3.19 ( 352) hydrogen bonds : angle 4.54980 / 3.10 ( 981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.203 Fit side-chains REVERT: A 223 ASP cc_start: 0.7260 (m-30) cc_final: 0.7047 (m-30) REVERT: A 233 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7296 (pp) REVERT: A 268 GLU cc_start: 0.8437 (tt0) cc_final: 0.8130 (tt0) REVERT: B 135 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7767 (pt) REVERT: B 205 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6659 (mpp-170) REVERT: B 214 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6386 (mm-40) REVERT: B 217 ASP cc_start: 0.6408 (m-30) cc_final: 0.5949 (m-30) REVERT: B 260 LEU cc_start: 0.7833 (mt) cc_final: 0.7476 (mm) REVERT: B 329 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6080 (mm-30) REVERT: B 344 ASN cc_start: 0.6323 (t0) cc_final: 0.5941 (t0) REVERT: B 346 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6854 (mp0) REVERT: B 379 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: B 381 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7365 (mmtp) REVERT: B 389 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6710 (mt) outliers start: 28 outliers final: 8 residues processed: 105 average time/residue: 0.2985 time to fit residues: 33.6033 Evaluate side-chains 89 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 381 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 436 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 78 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN B 163 GLN B 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.199337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.176698 restraints weight = 7009.553| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.40 r_work: 0.3874 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6246 Z= 0.116 Angle : 0.475 5.146 8508 Z= 0.249 Chirality : 0.042 0.140 984 Planarity : 0.003 0.032 1080 Dihedral : 4.154 47.174 857 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.79 % Allowed : 22.12 % Favored : 74.09 % 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 are not related in a simple way. whole: 1.47 (0.31), residues: 797 helix: 2.40 (0.29), residues: 330 sheet: 0.85 (0.50), residues: 104 loop : -0.31 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.023 0.001 TYR B 112 PHE 0.011 0.001 PHE B 253 TRP 0.008 0.001 TRP B 433 HIS 0.003 0.001 HIS B 530 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 6243) covalent geometry : angle 0.47472 / 0.25 ( 8502) SS BOND : bond 0.00201 / 0.09 ( 3) SS BOND : angle 0.73366 / 0.47 ( 6) hydrogen bonds : bond 0.04063 / 2.68 ( 352) hydrogen bonds : angle 4.25733 / 2.90 ( 981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.147 Fit side-chains REVERT: A 233 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7155 (pp) REVERT: A 268 GLU cc_start: 0.8433 (tt0) cc_final: 0.8127 (tt0) REVERT: B 135 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7812 (pt) REVERT: B 208 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6650 (tt) REVERT: B 217 ASP cc_start: 0.6196 (m-30) cc_final: 0.5731 (m-30) REVERT: B 260 LEU cc_start: 0.7700 (mt) cc_final: 0.7358 (mm) REVERT: B 329 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5764 (mm-30) REVERT: B 344 ASN cc_start: 0.6363 (t0) cc_final: 0.6003 (t0) REVERT: B 346 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6799 (mp0) REVERT: B 379 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: B 389 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6378 (mt) outliers start: 24 outliers final: 9 residues processed: 102 average time/residue: 0.3328 time to fit residues: 36.2431 Evaluate side-chains 96 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN ** B 289 ASN ** 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 = 0.4031 r_free = 0.4031 target = 0.185388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162791 restraints weight = 7060.360| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.48 r_work: 0.3763 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6246 Z= 0.182 Angle : 0.563 5.624 8508 Z= 0.296 Chirality : 0.045 0.158 984 Planarity : 0.004 0.036 1080 Dihedral : 4.704 54.963 857 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.11 % Allowed : 21.96 % Favored : 73.93 % 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 are not related in a simple way. whole: 1.05 (0.31), residues: 797 helix: 1.88 (0.29), residues: 336 sheet: 0.69 (0.50), residues: 109 loop : -0.44 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 111 TYR 0.026 0.002 TYR B 112 PHE 0.025 0.002 PHE B 494 TRP 0.010 0.002 TRP B 433 HIS 0.003 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 6243) covalent geometry : angle 0.56232 / 0.30 ( 8502) SS BOND : bond 0.00489 / 0.23 ( 3) SS BOND : angle 0.93685 / 0.55 ( 6) hydrogen bonds : bond 0.05396 / 3.56 ( 352) hydrogen bonds : angle 4.72793 / 3.23 ( 981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.136 Fit side-chains REVERT: A 130 GLU cc_start: 0.7352 (tt0) cc_final: 0.7069 (mt-10) REVERT: A 233 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7470 (pp) REVERT: A 268 GLU cc_start: 0.8498 (tt0) cc_final: 0.8196 (tt0) REVERT: B 135 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7852 (pt) REVERT: B 170 ASP cc_start: 0.8088 (t70) cc_final: 0.7710 (t0) REVERT: B 192 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7064 (tt) REVERT: B 205 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6591 (mpp-170) REVERT: B 208 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6681 (tt) REVERT: B 260 LEU cc_start: 0.7997 (mt) cc_final: 0.7660 (mm) REVERT: B 329 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5742 (mp0) REVERT: B 344 ASN cc_start: 0.6655 (t0) cc_final: 0.6387 (t0) REVERT: B 379 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: B 389 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6700 (mt) outliers start: 26 outliers final: 13 residues processed: 100 average time/residue: 0.3193 time to fit residues: 33.9894 Evaluate side-chains 97 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN ** B 289 ASN ** 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 = 0.4064 r_free = 0.4064 target = 0.188965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165694 restraints weight = 6993.879| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.39 r_work: 0.3828 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6246 Z= 0.110 Angle : 0.476 5.518 8508 Z= 0.247 Chirality : 0.042 0.141 984 Planarity : 0.003 0.032 1080 Dihedral : 4.378 51.971 857 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.48 % Allowed : 22.91 % Favored : 73.62 % 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 are not related in a simple way. whole: 1.33 (0.31), residues: 797 helix: 2.19 (0.29), residues: 338 sheet: 0.77 (0.51), residues: 104 loop : -0.37 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.022 0.001 TYR B 112 PHE 0.014 0.001 PHE B 494 TRP 0.008 0.001 TRP B 433 HIS 0.002 0.000 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6243) covalent geometry : angle 0.47599 / 0.25 ( 8502) SS BOND : bond 0.00231 / 0.11 ( 3) SS BOND : angle 0.67178 / 0.42 ( 6) hydrogen bonds : bond 0.04312 / 2.85 ( 352) hydrogen bonds : angle 4.34900 / 2.97 ( 981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.138 Fit side-chains REVERT: A 233 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7379 (pp) REVERT: A 268 GLU cc_start: 0.8485 (tt0) cc_final: 0.8169 (tt0) REVERT: B 135 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7880 (pt) REVERT: B 170 ASP cc_start: 0.8064 (t70) cc_final: 0.7645 (t0) REVERT: B 192 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6975 (tt) REVERT: B 217 ASP cc_start: 0.6268 (m-30) cc_final: 0.5733 (m-30) REVERT: B 260 LEU cc_start: 0.7831 (mt) cc_final: 0.7530 (mm) REVERT: B 329 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5574 (mp0) REVERT: B 379 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: B 389 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6484 (mt) REVERT: B 455 TYR cc_start: 0.8038 (p90) cc_final: 0.7802 (p90) outliers start: 22 outliers final: 10 residues processed: 92 average time/residue: 0.2798 time to fit residues: 27.5956 Evaluate side-chains 89 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 0.0010 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.187383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163863 restraints weight = 6982.473| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.37 r_work: 0.3870 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6246 Z= 0.130 Angle : 0.499 5.428 8508 Z= 0.258 Chirality : 0.043 0.142 984 Planarity : 0.004 0.032 1080 Dihedral : 4.433 52.563 857 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.79 % Allowed : 22.12 % Favored : 74.09 % 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 are not related in a simple way. whole: 1.26 (0.31), residues: 797 helix: 2.17 (0.29), residues: 338 sheet: 0.73 (0.51), residues: 104 loop : -0.42 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 111 TYR 0.025 0.001 TYR B 112 PHE 0.013 0.001 PHE B 494 TRP 0.008 0.001 TRP B 433 HIS 0.002 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6243) covalent geometry : angle 0.49912 / 0.26 ( 8502) SS BOND : bond 0.00322 / 0.16 ( 3) SS BOND : angle 0.69511 / 0.42 ( 6) hydrogen bonds : bond 0.04540 / 3.00 ( 352) hydrogen bonds : angle 4.40637 / 3.00 ( 981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.159 Fit side-chains REVERT: A 130 GLU cc_start: 0.7410 (tt0) cc_final: 0.7164 (mt-10) REVERT: A 233 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7501 (pp) REVERT: A 268 GLU cc_start: 0.8490 (tt0) cc_final: 0.8177 (tt0) REVERT: B 135 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7806 (pt) REVERT: B 170 ASP cc_start: 0.8019 (t70) cc_final: 0.7620 (t0) REVERT: B 192 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7111 (tt) REVERT: B 260 LEU cc_start: 0.7843 (mt) cc_final: 0.7572 (mm) REVERT: B 329 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5659 (mp0) REVERT: B 346 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: B 379 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: B 389 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6640 (mt) outliers start: 24 outliers final: 12 residues processed: 92 average time/residue: 0.3036 time to fit residues: 29.9943 Evaluate side-chains 94 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 75 optimal weight: 0.0870 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN ** B 289 ASN ** 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 = 0.4134 r_free = 0.4134 target = 0.195713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.173232 restraints weight = 6912.280| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.36 r_work: 0.3892 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6246 Z= 0.115 Angle : 0.477 5.874 8508 Z= 0.247 Chirality : 0.042 0.140 984 Planarity : 0.003 0.031 1080 Dihedral : 4.351 51.555 857 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.48 % Allowed : 22.27 % Favored : 74.25 % 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 are not related in a simple way. whole: 1.34 (0.31), residues: 797 helix: 2.24 (0.29), residues: 338 sheet: 0.75 (0.51), residues: 104 loop : -0.38 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 111 TYR 0.024 0.001 TYR B 112 PHE 0.012 0.001 PHE B 494 TRP 0.008 0.001 TRP B 433 HIS 0.002 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6243) covalent geometry : angle 0.47675 / 0.25 ( 8502) SS BOND : bond 0.00254 / 0.12 ( 3) SS BOND : angle 0.61768 / 0.38 ( 6) hydrogen bonds : bond 0.04275 / 2.83 ( 352) hydrogen bonds : angle 4.30658 / 2.94 ( 981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.133 Fit side-chains REVERT: A 130 GLU cc_start: 0.7406 (tt0) cc_final: 0.7086 (mt-10) REVERT: A 233 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7523 (pp) REVERT: A 268 GLU cc_start: 0.8511 (tt0) cc_final: 0.8186 (tt0) REVERT: B 110 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7474 (tm) REVERT: B 135 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7734 (pt) REVERT: B 170 ASP cc_start: 0.8024 (t70) cc_final: 0.7630 (t0) REVERT: B 192 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7026 (tt) REVERT: B 217 ASP cc_start: 0.6344 (m-30) cc_final: 0.5814 (m-30) REVERT: B 260 LEU cc_start: 0.7793 (mt) cc_final: 0.7524 (mm) REVERT: B 329 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5662 (mp0) REVERT: B 379 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: B 389 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6628 (mt) outliers start: 22 outliers final: 12 residues processed: 94 average time/residue: 0.3140 time to fit residues: 31.5527 Evaluate side-chains 93 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 0.0020 chunk 64 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN ** B 289 ASN ** 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 = 0.4073 r_free = 0.4073 target = 0.189890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.168504 restraints weight = 7100.712| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.40 r_work: 0.3823 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6246 Z= 0.109 Angle : 0.479 6.289 8508 Z= 0.246 Chirality : 0.042 0.141 984 Planarity : 0.003 0.032 1080 Dihedral : 4.310 50.265 857 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.32 % Allowed : 22.59 % Favored : 74.09 % 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 are not related in a simple way. whole: 1.41 (0.31), residues: 797 helix: 2.30 (0.29), residues: 338 sheet: 0.78 (0.50), residues: 104 loop : -0.36 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 111 TYR 0.024 0.001 TYR B 112 PHE 0.036 0.001 PHE B 494 TRP 0.008 0.001 TRP A 204 HIS 0.001 0.000 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6243) covalent geometry : angle 0.47933 / 0.25 ( 8502) SS BOND : bond 0.00232 / 0.11 ( 3) SS BOND : angle 0.55048 / 0.33 ( 6) hydrogen bonds : bond 0.04126 / 2.73 ( 352) hydrogen bonds : angle 4.25672 / 2.90 ( 981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.134 Fit side-chains REVERT: A 130 GLU cc_start: 0.7414 (tt0) cc_final: 0.7072 (mt-10) REVERT: A 233 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7520 (pp) REVERT: A 268 GLU cc_start: 0.8500 (tt0) cc_final: 0.8181 (tt0) REVERT: B 110 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7511 (tm) REVERT: B 135 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7738 (pt) REVERT: B 170 ASP cc_start: 0.8077 (t70) cc_final: 0.7685 (t0) REVERT: B 192 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7056 (tt) REVERT: B 217 ASP cc_start: 0.6297 (m-30) cc_final: 0.5849 (m-30) REVERT: B 260 LEU cc_start: 0.7804 (mt) cc_final: 0.7532 (mm) REVERT: B 329 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5614 (mp0) REVERT: B 346 GLU cc_start: 0.6497 (mp0) cc_final: 0.6275 (mp0) REVERT: B 389 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6585 (mt) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.2916 time to fit residues: 30.3327 Evaluate side-chains 95 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN ** B 289 ASN ** 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 = 0.4064 r_free = 0.4064 target = 0.189017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165612 restraints weight = 7014.515| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.39 r_work: 0.3824 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6246 Z= 0.118 Angle : 0.483 5.763 8508 Z= 0.248 Chirality : 0.042 0.141 984 Planarity : 0.003 0.031 1080 Dihedral : 4.310 50.210 857 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.16 % Allowed : 22.75 % Favored : 74.09 % 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 are not related in a simple way. whole: 1.37 (0.31), residues: 797 helix: 2.25 (0.29), residues: 338 sheet: 0.77 (0.51), residues: 104 loop : -0.35 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 205 TYR 0.024 0.002 TYR B 112 PHE 0.036 0.001 PHE B 494 TRP 0.008 0.001 TRP A 204 HIS 0.002 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6243) covalent geometry : angle 0.48310 / 0.25 ( 8502) SS BOND : bond 0.00223 / 0.11 ( 3) SS BOND : angle 0.62560 / 0.37 ( 6) hydrogen bonds : bond 0.04223 / 2.79 ( 352) hydrogen bonds : angle 4.27827 / 2.92 ( 981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.145 Fit side-chains REVERT: A 130 GLU cc_start: 0.7391 (tt0) cc_final: 0.7022 (mt-10) REVERT: A 233 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7425 (pp) REVERT: A 268 GLU cc_start: 0.8456 (tt0) cc_final: 0.8122 (tt0) REVERT: B 110 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7584 (tm) REVERT: B 135 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7748 (pt) REVERT: B 170 ASP cc_start: 0.8084 (t70) cc_final: 0.7684 (t0) REVERT: B 192 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7048 (tt) REVERT: B 217 ASP cc_start: 0.6224 (m-30) cc_final: 0.5773 (m-30) REVERT: B 260 LEU cc_start: 0.7706 (mt) cc_final: 0.7429 (mm) REVERT: B 329 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5530 (mp0) REVERT: B 389 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6499 (mt) outliers start: 20 outliers final: 12 residues processed: 91 average time/residue: 0.2840 time to fit residues: 27.8818 Evaluate side-chains 94 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 528 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN ** B 289 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.183899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160189 restraints weight = 7004.753| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.37 r_work: 0.3771 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6246 Z= 0.199 Angle : 0.569 6.810 8508 Z= 0.297 Chirality : 0.045 0.153 984 Planarity : 0.004 0.036 1080 Dihedral : 4.756 56.682 857 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.48 % Allowed : 22.59 % Favored : 73.93 % 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 are not related in a simple way. whole: 1.01 (0.31), residues: 797 helix: 1.80 (0.28), residues: 337 sheet: 0.62 (0.48), residues: 119 loop : -0.43 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 205 TYR 0.023 0.002 TYR B 112 PHE 0.041 0.002 PHE B 494 TRP 0.014 0.002 TRP B 29 HIS 0.004 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 6243) covalent geometry : angle 0.56905 / 0.30 ( 8502) SS BOND : bond 0.00585 / 0.28 ( 3) SS BOND : angle 0.98566 / 0.58 ( 6) hydrogen bonds : bond 0.05390 / 3.55 ( 352) hydrogen bonds : angle 4.69149 / 3.21 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.18 seconds wall clock time: 30 minutes 53.88 seconds (1853.88 seconds total)