Starting phenix.real_space_refine on Sat May 10 19:49:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx2_37898/05_2025/8wx2_37898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx2_37898/05_2025/8wx2_37898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wx2_37898/05_2025/8wx2_37898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx2_37898/05_2025/8wx2_37898.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx2_37898/05_2025/8wx2_37898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx2_37898/05_2025/8wx2_37898.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.047 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 36 5.16 5 C 4528 2.51 5 N 1110 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6800 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3400 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Restraints were copied for chains: B Time building chain proxies: 5.90, per 1000 atoms: 0.87 Number of scatterers: 6800 At special positions: 0 Unit cell: (128.65, 88.81, 81.34, 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 36 16.00 O 1126 8.00 N 1110 7.00 C 4528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 536 " 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: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 30 through 63 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.913A pdb=" N GLN A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 98 removed outlier: 3.555A pdb=" N VAL A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 100 through 123 removed outlier: 3.601A pdb=" N VAL A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 123 through 131 removed outlier: 3.730A pdb=" N ARG A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 191 Processing helix chain 'A' and resid 191 through 224 removed outlier: 3.774A pdb=" N ILE A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 247 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 304 through 322 removed outlier: 3.700A pdb=" N PHE A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Proline residue: A 318 - end of helix Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.826A pdb=" N TYR A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 393 removed outlier: 3.811A pdb=" N LEU A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.537A pdb=" N LEU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 3.643A pdb=" N TYR A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 491 through 517 removed outlier: 3.765A pdb=" N MET A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.541A pdb=" N GLU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 63 Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.913A pdb=" N GLN B 71 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 98 removed outlier: 3.555A pdb=" N VAL B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 100 through 123 removed outlier: 3.602A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 123 through 131 removed outlier: 3.730A pdb=" N ARG B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 191 Processing helix chain 'B' and resid 191 through 224 removed outlier: 3.774A pdb=" N ILE B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 247 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 304 through 322 removed outlier: 3.700A pdb=" N PHE B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Proline residue: B 318 - end of helix Processing helix chain 'B' and resid 322 through 343 removed outlier: 3.827A pdb=" N TYR B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 393 removed outlier: 3.811A pdb=" N LEU B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 387 " --> pdb=" O VAL B 383 " (cutoff:3.500A) Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.537A pdb=" N LEU B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 439 removed outlier: 3.644A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 460 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 491 through 517 removed outlier: 3.764A pdb=" N MET B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 537 through 564 removed outlier: 3.540A pdb=" N GLU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.47: 1782 1.47 - 1.59: 3062 1.59 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6982 Sorted by residual: bond pdb=" C ALA A 487 " pdb=" N PRO A 488 " ideal model delta sigma weight residual 1.334 1.369 -0.036 2.34e-02 1.83e+03 2.31e+00 bond pdb=" C ALA B 487 " pdb=" N PRO B 488 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.17e+00 bond pdb=" C LEU B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.99e-01 bond pdb=" C LEU A 519 " pdb=" N PRO A 520 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.36e-01 bond pdb=" CA THR B 248 " pdb=" C THR B 248 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.63e-01 ... (remaining 6977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 9274 1.57 - 3.14: 162 3.14 - 4.70: 55 4.70 - 6.27: 19 6.27 - 7.84: 12 Bond angle restraints: 9522 Sorted by residual: angle pdb=" N PRO A 351 " pdb=" CA PRO A 351 " pdb=" CB PRO A 351 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" N PRO B 351 " pdb=" CA PRO B 351 " pdb=" CB PRO B 351 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N ALA A 487 " pdb=" CA ALA A 487 " pdb=" C ALA A 487 " ideal model delta sigma weight residual 109.81 117.65 -7.84 2.21e+00 2.05e-01 1.26e+01 angle pdb=" N ALA B 487 " pdb=" CA ALA B 487 " pdb=" C ALA B 487 " ideal model delta sigma weight residual 109.81 117.60 -7.79 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N ARG B 74 " pdb=" CA ARG B 74 " pdb=" CB ARG B 74 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 ... (remaining 9517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 3528 14.95 - 29.91: 338 29.91 - 44.86: 128 44.86 - 59.81: 38 59.81 - 74.77: 4 Dihedral angle restraints: 4036 sinusoidal: 1510 harmonic: 2526 Sorted by residual: dihedral pdb=" CA ALA B 487 " pdb=" C ALA B 487 " pdb=" N PRO B 488 " pdb=" CA PRO B 488 " ideal model delta harmonic sigma weight residual -180.00 -135.20 -44.80 0 5.00e+00 4.00e-02 8.03e+01 dihedral pdb=" CA ALA A 487 " pdb=" C ALA A 487 " pdb=" N PRO A 488 " pdb=" CA PRO A 488 " ideal model delta harmonic sigma weight residual -180.00 -135.27 -44.73 0 5.00e+00 4.00e-02 8.00e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 157 " pdb=" CB CYS B 157 " ideal model delta sinusoidal sigma weight residual -86.00 -28.54 -57.46 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 4033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 917 0.049 - 0.098: 166 0.098 - 0.147: 25 0.147 - 0.196: 0 0.196 - 0.245: 2 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA PRO B 351 " pdb=" N PRO B 351 " pdb=" C PRO B 351 " pdb=" CB PRO B 351 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO A 351 " pdb=" N PRO A 351 " pdb=" C PRO A 351 " pdb=" CB PRO A 351 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO B 488 " pdb=" N PRO B 488 " pdb=" C PRO B 488 " pdb=" CB PRO B 488 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1107 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 487 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO A 488 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 488 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 488 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 487 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 488 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 488 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 488 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 118 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 119 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.026 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 184 2.72 - 3.26: 7458 3.26 - 3.81: 11484 3.81 - 4.35: 13588 4.35 - 4.90: 22303 Nonbonded interactions: 55017 Sorted by model distance: nonbonded pdb=" N ASN A 66 " pdb=" OD1 ASN A 66 " model vdw 2.171 3.120 nonbonded pdb=" N ASN B 66 " pdb=" OD1 ASN B 66 " model vdw 2.171 3.120 nonbonded pdb=" O PHE B 65 " pdb=" N THR B 68 " model vdw 2.206 3.120 nonbonded pdb=" O PHE A 65 " pdb=" N THR A 68 " model vdw 2.206 3.120 nonbonded pdb=" O VAL B 514 " pdb=" OG SER B 518 " model vdw 2.329 3.040 ... (remaining 55012 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.080 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 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 0.036 6986 Z= 0.124 Angle : 0.646 7.841 9530 Z= 0.357 Chirality : 0.038 0.245 1110 Planarity : 0.005 0.074 1172 Dihedral : 14.514 74.766 2400 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.51 % Favored : 93.02 % Rotamer: Outliers : 1.99 % Allowed : 14.25 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.26), residues: 860 helix: -0.96 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -3.01 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 67 HIS 0.001 0.000 HIS B 434 PHE 0.011 0.001 PHE A 65 TYR 0.013 0.001 TYR B 59 ARG 0.001 0.000 ARG B 489 Details of bonding type rmsd hydrogen bonds : bond 0.18655 ( 532) hydrogen bonds : angle 6.74385 ( 1566) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.81986 ( 8) covalent geometry : bond 0.00233 ( 6982) covalent geometry : angle 0.64602 ( 9522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5625 (mtm-85) cc_final: 0.5291 (mtp180) REVERT: A 460 TRP cc_start: 0.5111 (m-90) cc_final: 0.4845 (m-10) outliers start: 14 outliers final: 8 residues processed: 169 average time/residue: 0.1732 time to fit residues: 39.4773 Evaluate side-chains 117 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 79 optimal weight: 0.0030 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.165555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.143885 restraints weight = 17266.273| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.93 r_work: 0.4193 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6986 Z= 0.165 Angle : 0.763 9.925 9530 Z= 0.371 Chirality : 0.042 0.158 1110 Planarity : 0.006 0.074 1172 Dihedral : 6.681 59.332 950 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.27 % Allowed : 18.80 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.28), residues: 860 helix: 0.26 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.84 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 558 HIS 0.006 0.002 HIS B 434 PHE 0.023 0.001 PHE A 244 TYR 0.025 0.001 TYR A 59 ARG 0.003 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 532) hydrogen bonds : angle 4.75298 ( 1566) SS BOND : bond 0.00067 ( 4) SS BOND : angle 0.55926 ( 8) covalent geometry : bond 0.00343 ( 6982) covalent geometry : angle 0.76351 ( 9522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.6636 (t80) cc_final: 0.6105 (t80) REVERT: A 374 TRP cc_start: 0.5806 (t60) cc_final: 0.5331 (t60) REVERT: A 460 TRP cc_start: 0.5216 (m-90) cc_final: 0.4512 (m100) REVERT: B 460 TRP cc_start: 0.5256 (m-90) cc_final: 0.4954 (m-10) outliers start: 30 outliers final: 14 residues processed: 142 average time/residue: 0.1578 time to fit residues: 31.1623 Evaluate side-chains 123 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 29 optimal weight: 0.0270 chunk 20 optimal weight: 0.0170 chunk 65 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.0570 chunk 76 optimal weight: 0.4980 chunk 41 optimal weight: 0.4980 chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 0.0870 overall best weight: 0.1172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.166412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.144822 restraints weight = 17653.686| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 3.05 r_work: 0.4196 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6986 Z= 0.144 Angle : 0.739 11.906 9530 Z= 0.352 Chirality : 0.041 0.156 1110 Planarity : 0.006 0.072 1172 Dihedral : 6.440 58.237 948 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.13 % Allowed : 21.08 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 860 helix: 0.62 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -3.27 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 204 HIS 0.006 0.001 HIS B 434 PHE 0.027 0.001 PHE A 202 TYR 0.014 0.001 TYR A 59 ARG 0.004 0.000 ARG A 537 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 532) hydrogen bonds : angle 4.41550 ( 1566) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.61789 ( 8) covalent geometry : bond 0.00290 ( 6982) covalent geometry : angle 0.73940 ( 9522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.5849 (t80) cc_final: 0.5534 (t80) REVERT: A 219 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: A 374 TRP cc_start: 0.5820 (t60) cc_final: 0.5351 (t60) REVERT: A 460 TRP cc_start: 0.5156 (m-90) cc_final: 0.4533 (m100) REVERT: A 486 GLU cc_start: 0.5210 (pm20) cc_final: 0.4846 (mp0) REVERT: B 74 ARG cc_start: 0.3203 (OUTLIER) cc_final: -0.0046 (ttt180) REVERT: B 198 PHE cc_start: 0.6581 (t80) cc_final: 0.6054 (t80) REVERT: B 219 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: B 460 TRP cc_start: 0.5157 (m-90) cc_final: 0.4895 (m-10) REVERT: B 486 GLU cc_start: 0.5759 (mm-30) cc_final: 0.5475 (mm-30) outliers start: 29 outliers final: 12 residues processed: 132 average time/residue: 0.1418 time to fit residues: 26.6781 Evaluate side-chains 116 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.0470 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.164124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.141936 restraints weight = 17648.512| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 3.04 r_work: 0.4156 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6986 Z= 0.142 Angle : 0.740 12.005 9530 Z= 0.349 Chirality : 0.041 0.189 1110 Planarity : 0.006 0.073 1172 Dihedral : 5.730 44.139 944 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.56 % Allowed : 21.37 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 860 helix: 0.94 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -3.14 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.004 0.001 HIS A 434 PHE 0.017 0.001 PHE B 244 TYR 0.021 0.001 TYR B 563 ARG 0.004 0.000 ARG B 537 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 532) hydrogen bonds : angle 4.23549 ( 1566) SS BOND : bond 0.00073 ( 4) SS BOND : angle 0.54911 ( 8) covalent geometry : bond 0.00306 ( 6982) covalent geometry : angle 0.74058 ( 9522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.5911 (t80) cc_final: 0.5672 (t80) REVERT: A 219 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: A 460 TRP cc_start: 0.5291 (m-90) cc_final: 0.4671 (m100) REVERT: B 74 ARG cc_start: 0.3101 (OUTLIER) cc_final: 0.0030 (ttt180) REVERT: B 101 TYR cc_start: 0.5740 (t80) cc_final: 0.5480 (t80) REVERT: B 460 TRP cc_start: 0.5176 (m-90) cc_final: 0.4512 (m100) outliers start: 32 outliers final: 15 residues processed: 128 average time/residue: 0.1859 time to fit residues: 32.1029 Evaluate side-chains 110 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.163193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.140610 restraints weight = 17398.239| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 3.11 r_work: 0.4135 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6986 Z= 0.143 Angle : 0.765 12.963 9530 Z= 0.360 Chirality : 0.042 0.173 1110 Planarity : 0.005 0.072 1172 Dihedral : 5.595 44.240 942 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.42 % Allowed : 21.94 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.29), residues: 860 helix: 1.19 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -3.22 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 374 HIS 0.002 0.000 HIS A 434 PHE 0.015 0.001 PHE B 244 TYR 0.013 0.001 TYR A 484 ARG 0.007 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 532) hydrogen bonds : angle 4.15962 ( 1566) SS BOND : bond 0.00464 ( 4) SS BOND : angle 3.15068 ( 8) covalent geometry : bond 0.00305 ( 6982) covalent geometry : angle 0.75955 ( 9522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: A 460 TRP cc_start: 0.5336 (m-90) cc_final: 0.4670 (m100) REVERT: B 74 ARG cc_start: 0.2960 (OUTLIER) cc_final: 0.0008 (ttt180) REVERT: B 101 TYR cc_start: 0.5841 (t80) cc_final: 0.5625 (t80) REVERT: B 219 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: B 460 TRP cc_start: 0.5271 (m-90) cc_final: 0.4879 (m-10) outliers start: 31 outliers final: 19 residues processed: 121 average time/residue: 0.1502 time to fit residues: 25.7789 Evaluate side-chains 115 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.162344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.139544 restraints weight = 17520.505| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.08 r_work: 0.4124 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6986 Z= 0.149 Angle : 0.759 12.965 9530 Z= 0.359 Chirality : 0.044 0.238 1110 Planarity : 0.005 0.070 1172 Dihedral : 5.528 44.084 942 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.56 % Allowed : 23.08 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 860 helix: 1.29 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.62 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 374 HIS 0.001 0.000 HIS B 434 PHE 0.020 0.001 PHE A 310 TYR 0.010 0.001 TYR B 59 ARG 0.005 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 532) hydrogen bonds : angle 4.15125 ( 1566) SS BOND : bond 0.00228 ( 4) SS BOND : angle 2.01038 ( 8) covalent geometry : bond 0.00327 ( 6982) covalent geometry : angle 0.75689 ( 9522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7250 (t80) cc_final: 0.6986 (t80) REVERT: A 219 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: A 460 TRP cc_start: 0.5436 (m-90) cc_final: 0.4805 (m100) REVERT: B 74 ARG cc_start: 0.3026 (OUTLIER) cc_final: 0.0057 (ttt180) REVERT: B 198 PHE cc_start: 0.6545 (t80) cc_final: 0.6044 (t80) REVERT: B 219 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: B 460 TRP cc_start: 0.5375 (m-90) cc_final: 0.4708 (m100) outliers start: 32 outliers final: 19 residues processed: 118 average time/residue: 0.1586 time to fit residues: 26.1284 Evaluate side-chains 114 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.162261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.139429 restraints weight = 17103.322| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 3.06 r_work: 0.4117 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6986 Z= 0.144 Angle : 0.759 13.792 9530 Z= 0.360 Chirality : 0.043 0.249 1110 Planarity : 0.005 0.070 1172 Dihedral : 5.434 44.268 942 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.13 % Allowed : 23.08 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 860 helix: 1.38 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.70 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.002 0.000 HIS A 437 PHE 0.022 0.001 PHE A 310 TYR 0.018 0.001 TYR A 59 ARG 0.006 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 532) hydrogen bonds : angle 4.12942 ( 1566) SS BOND : bond 0.00276 ( 4) SS BOND : angle 1.44658 ( 8) covalent geometry : bond 0.00307 ( 6982) covalent geometry : angle 0.75776 ( 9522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7266 (t80) cc_final: 0.7006 (t80) REVERT: A 219 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6946 (m-80) REVERT: A 460 TRP cc_start: 0.5458 (m-90) cc_final: 0.4872 (m100) REVERT: B 74 ARG cc_start: 0.3256 (OUTLIER) cc_final: 0.0253 (ttt180) REVERT: B 198 PHE cc_start: 0.6591 (t80) cc_final: 0.6028 (t80) REVERT: B 219 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: B 460 TRP cc_start: 0.5378 (m-90) cc_final: 0.4773 (m100) outliers start: 29 outliers final: 22 residues processed: 119 average time/residue: 0.1680 time to fit residues: 27.5189 Evaluate side-chains 114 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.161800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.138664 restraints weight = 17358.996| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.07 r_work: 0.4109 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6986 Z= 0.153 Angle : 0.759 13.615 9530 Z= 0.365 Chirality : 0.044 0.274 1110 Planarity : 0.005 0.069 1172 Dihedral : 5.440 43.983 942 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.56 % Allowed : 23.93 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.30), residues: 860 helix: 1.40 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.56 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.002 0.000 HIS A 437 PHE 0.037 0.002 PHE B 202 TYR 0.011 0.001 TYR B 59 ARG 0.004 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 532) hydrogen bonds : angle 4.16595 ( 1566) SS BOND : bond 0.00091 ( 4) SS BOND : angle 1.28104 ( 8) covalent geometry : bond 0.00338 ( 6982) covalent geometry : angle 0.75812 ( 9522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7268 (t80) cc_final: 0.6983 (t80) REVERT: A 219 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: A 460 TRP cc_start: 0.5484 (m-90) cc_final: 0.4904 (m100) REVERT: B 74 ARG cc_start: 0.3238 (OUTLIER) cc_final: 0.0287 (ttt180) REVERT: B 79 PHE cc_start: 0.7605 (t80) cc_final: 0.7321 (t80) REVERT: B 219 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: B 460 TRP cc_start: 0.5426 (m-90) cc_final: 0.4823 (m100) outliers start: 25 outliers final: 20 residues processed: 111 average time/residue: 0.1500 time to fit residues: 23.7280 Evaluate side-chains 109 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.162182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.139121 restraints weight = 17378.445| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 3.11 r_work: 0.4118 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6986 Z= 0.147 Angle : 0.770 13.946 9530 Z= 0.366 Chirality : 0.044 0.220 1110 Planarity : 0.005 0.070 1172 Dihedral : 5.450 44.438 942 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.70 % Allowed : 24.36 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.30), residues: 860 helix: 1.42 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.51 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 558 HIS 0.002 0.000 HIS A 437 PHE 0.026 0.001 PHE A 310 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.001 ARG A 562 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 532) hydrogen bonds : angle 4.17298 ( 1566) SS BOND : bond 0.00096 ( 4) SS BOND : angle 1.18990 ( 8) covalent geometry : bond 0.00323 ( 6982) covalent geometry : angle 0.76986 ( 9522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7258 (t80) cc_final: 0.7000 (t80) REVERT: A 198 PHE cc_start: 0.6720 (t80) cc_final: 0.6202 (t80) REVERT: A 219 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: A 242 PHE cc_start: 0.7698 (m-10) cc_final: 0.7371 (m-10) REVERT: A 460 TRP cc_start: 0.5450 (m-90) cc_final: 0.4884 (m100) REVERT: B 74 ARG cc_start: 0.3082 (OUTLIER) cc_final: 0.0257 (ttt180) REVERT: B 79 PHE cc_start: 0.7606 (t80) cc_final: 0.7353 (t80) REVERT: B 198 PHE cc_start: 0.6492 (t80) cc_final: 0.5957 (t80) REVERT: B 219 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: B 460 TRP cc_start: 0.5396 (m-90) cc_final: 0.4774 (m100) outliers start: 26 outliers final: 21 residues processed: 117 average time/residue: 0.1531 time to fit residues: 24.9934 Evaluate side-chains 110 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.160922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.137675 restraints weight = 17690.905| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.08 r_work: 0.4093 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6986 Z= 0.159 Angle : 0.783 13.156 9530 Z= 0.373 Chirality : 0.046 0.312 1110 Planarity : 0.005 0.068 1172 Dihedral : 5.434 43.632 942 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.70 % Allowed : 24.22 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.30), residues: 860 helix: 1.35 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.47 (0.44), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 558 HIS 0.002 0.000 HIS A 437 PHE 0.027 0.002 PHE A 310 TYR 0.010 0.001 TYR B 59 ARG 0.005 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 532) hydrogen bonds : angle 4.19591 ( 1566) SS BOND : bond 0.00076 ( 4) SS BOND : angle 1.17327 ( 8) covalent geometry : bond 0.00354 ( 6982) covalent geometry : angle 0.78234 ( 9522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7301 (t80) cc_final: 0.7027 (t80) REVERT: A 198 PHE cc_start: 0.6701 (t80) cc_final: 0.6178 (t80) REVERT: A 219 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: A 460 TRP cc_start: 0.5575 (m-90) cc_final: 0.4973 (m100) REVERT: B 74 ARG cc_start: 0.3143 (OUTLIER) cc_final: 0.0292 (ttt180) REVERT: B 79 PHE cc_start: 0.7604 (t80) cc_final: 0.7361 (t80) REVERT: B 219 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: B 460 TRP cc_start: 0.5463 (m-90) cc_final: 0.4848 (m100) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.1503 time to fit residues: 23.7954 Evaluate side-chains 109 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 76 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.160701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.137606 restraints weight = 17544.547| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.02 r_work: 0.4097 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6986 Z= 0.155 Angle : 0.798 14.148 9530 Z= 0.378 Chirality : 0.046 0.321 1110 Planarity : 0.006 0.096 1172 Dihedral : 5.470 44.118 942 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.28 % Allowed : 24.79 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.30), residues: 860 helix: 1.29 (0.20), residues: 730 sheet: None (None), residues: 0 loop : -3.74 (0.45), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 558 HIS 0.002 0.000 HIS A 437 PHE 0.027 0.002 PHE A 310 TYR 0.016 0.001 TYR B 484 ARG 0.005 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 532) hydrogen bonds : angle 4.23253 ( 1566) SS BOND : bond 0.00076 ( 4) SS BOND : angle 1.14946 ( 8) covalent geometry : bond 0.00342 ( 6982) covalent geometry : angle 0.79723 ( 9522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.18 seconds wall clock time: 57 minutes 42.34 seconds (3462.34 seconds total)