Starting phenix.real_space_refine on Tue Mar 11 22:48:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx2_37898/03_2025/8wx2_37898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx2_37898/03_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_37898/03_2025/8wx2_37898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx2_37898/03_2025/8wx2_37898.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx2_37898/03_2025/8wx2_37898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx2_37898/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.33, per 1000 atoms: 0.93 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 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: 0.73 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: 2.03 Time building geometry restraints manager: 2.15 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: 0.04 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: 1.490 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.210 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- 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 6982 Z= 0.146 Angle : 0.646 7.841 9522 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 *********************** 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 : 0.626 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: 39.5726 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 : 0.747 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.143886 restraints weight = 17266.277| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.93 r_work: 0.4194 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 6982 Z= 0.220 Angle : 0.764 9.925 9522 Z= 0.372 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 *********************** 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 : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.6636 (t80) cc_final: 0.6104 (t80) REVERT: A 374 TRP cc_start: 0.5805 (t60) cc_final: 0.5333 (t60) REVERT: A 460 TRP cc_start: 0.5209 (m-90) cc_final: 0.4510 (m100) REVERT: B 460 TRP cc_start: 0.5251 (m-90) cc_final: 0.4960 (m-10) outliers start: 30 outliers final: 14 residues processed: 142 average time/residue: 0.1662 time to fit residues: 33.0079 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 : 0.735 ------------------------------------------------------------------------------- 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: 0.9980 chunk 64 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS B 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.164237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.141846 restraints weight = 17606.249| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 3.06 r_work: 0.4152 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6982 Z= 0.196 Angle : 0.740 11.705 9522 Z= 0.356 Chirality : 0.042 0.158 1110 Planarity : 0.006 0.076 1172 Dihedral : 6.460 57.883 948 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.85 % Allowed : 20.51 % Favored : 75.64 % 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: -0.14 (0.29), residues: 860 helix: 0.59 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -3.39 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 558 HIS 0.005 0.001 HIS B 434 PHE 0.025 0.002 PHE A 202 TYR 0.015 0.001 TYR A 59 ARG 0.004 0.000 ARG A 537 *********************** 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 137 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.3132 (OUTLIER) cc_final: -0.0037 (ttt180) REVERT: A 101 TYR cc_start: 0.5864 (t80) cc_final: 0.5634 (t80) REVERT: A 219 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: A 374 TRP cc_start: 0.5895 (t60) cc_final: 0.5392 (t60) REVERT: A 460 TRP cc_start: 0.5299 (m-90) cc_final: 0.4642 (m100) REVERT: A 486 GLU cc_start: 0.5293 (pm20) cc_final: 0.4886 (mp0) REVERT: B 74 ARG cc_start: 0.3120 (OUTLIER) cc_final: -0.0063 (ttt180) REVERT: B 198 PHE cc_start: 0.6641 (t80) cc_final: 0.6111 (t80) REVERT: B 460 TRP cc_start: 0.5223 (m-90) cc_final: 0.4530 (m100) outliers start: 27 outliers final: 14 residues processed: 122 average time/residue: 0.1523 time to fit residues: 26.3907 Evaluate side-chains 114 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 104 VAL 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 526 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.162516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.139617 restraints weight = 17587.310| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 3.07 r_work: 0.4121 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6982 Z= 0.205 Angle : 0.746 12.375 9522 Z= 0.352 Chirality : 0.041 0.199 1110 Planarity : 0.006 0.076 1172 Dihedral : 5.947 59.722 945 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.13 % Allowed : 20.09 % 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: 0.22 (0.29), residues: 860 helix: 0.84 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -3.42 (0.48), residues: 138 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 0.018 0.001 PHE B 244 TYR 0.023 0.001 TYR B 59 ARG 0.004 0.000 ARG B 537 *********************** 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 143 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: A 460 TRP cc_start: 0.5417 (m-90) cc_final: 0.4768 (m100) REVERT: B 74 ARG cc_start: 0.3236 (OUTLIER) cc_final: -0.0050 (ttt180) REVERT: B 460 TRP cc_start: 0.5329 (m-90) cc_final: 0.4633 (m100) outliers start: 36 outliers final: 17 residues processed: 130 average time/residue: 0.1867 time to fit residues: 32.5858 Evaluate side-chains 110 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 87 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.161341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.138421 restraints weight = 17373.066| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.98 r_work: 0.4110 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6982 Z= 0.209 Angle : 0.761 12.615 9522 Z= 0.360 Chirality : 0.042 0.172 1110 Planarity : 0.005 0.074 1172 Dihedral : 5.644 45.396 942 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 4.27 % Allowed : 21.51 % Favored : 74.22 % 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: 0.56 (0.29), residues: 860 helix: 1.11 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -3.20 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.003 0.001 HIS A 434 PHE 0.020 0.001 PHE B 244 TYR 0.014 0.001 TYR B 484 ARG 0.010 0.001 ARG A 46 *********************** 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 132 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: A 460 TRP cc_start: 0.5486 (m-90) cc_final: 0.4838 (m100) REVERT: B 74 ARG cc_start: 0.3090 (OUTLIER) cc_final: -0.0095 (ttt180) REVERT: B 219 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: B 460 TRP cc_start: 0.5468 (m-90) cc_final: 0.4771 (m100) outliers start: 30 outliers final: 18 residues processed: 117 average time/residue: 0.1555 time to fit residues: 25.7605 Evaluate side-chains 112 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 72 optimal weight: 0.0170 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.161076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.137892 restraints weight = 17515.659| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.08 r_work: 0.4097 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6982 Z= 0.203 Angle : 0.754 13.186 9522 Z= 0.357 Chirality : 0.044 0.257 1110 Planarity : 0.005 0.076 1172 Dihedral : 5.526 43.483 942 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.99 % Allowed : 23.50 % 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: 0.68 (0.29), residues: 860 helix: 1.22 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -3.58 (0.46), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.001 0.000 HIS A 437 PHE 0.021 0.001 PHE B 310 TYR 0.011 0.001 TYR B 484 ARG 0.006 0.001 ARG B 537 *********************** 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 132 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: A 460 TRP cc_start: 0.5510 (m-90) cc_final: 0.4901 (m100) REVERT: B 74 ARG cc_start: 0.2983 (OUTLIER) cc_final: -0.0092 (ttt180) REVERT: B 198 PHE cc_start: 0.6667 (t80) cc_final: 0.6227 (t80) REVERT: B 219 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: B 460 TRP cc_start: 0.5514 (m-90) cc_final: 0.4855 (m100) outliers start: 28 outliers final: 19 residues processed: 123 average time/residue: 0.1751 time to fit residues: 29.7693 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 66 ASN 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 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 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: 6.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.160203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.137029 restraints weight = 17096.366| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 3.01 r_work: 0.4088 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6982 Z= 0.212 Angle : 0.761 13.608 9522 Z= 0.362 Chirality : 0.044 0.278 1110 Planarity : 0.005 0.077 1172 Dihedral : 5.509 45.900 942 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.13 % Allowed : 24.22 % Favored : 71.65 % 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: 0.83 (0.29), residues: 860 helix: 1.32 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.57 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.003 0.001 HIS A 434 PHE 0.022 0.001 PHE A 310 TYR 0.010 0.001 TYR B 484 ARG 0.006 0.000 ARG B 537 *********************** 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 127 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7393 (t80) cc_final: 0.6987 (t80) REVERT: A 219 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: A 460 TRP cc_start: 0.5528 (m-90) cc_final: 0.4960 (m100) REVERT: B 74 ARG cc_start: 0.3064 (OUTLIER) cc_final: -0.0016 (ttt180) REVERT: B 219 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6662 (m-80) REVERT: B 460 TRP cc_start: 0.5515 (m-90) cc_final: 0.4892 (m100) outliers start: 29 outliers final: 20 residues processed: 123 average time/residue: 0.1596 time to fit residues: 27.5841 Evaluate side-chains 112 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 111 TYR Chi-restraints excluded: chain A residue 165 LEU 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 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 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: 0.9990 chunk 12 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN B 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.159275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.135681 restraints weight = 17256.899| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 3.06 r_work: 0.4068 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6982 Z= 0.227 Angle : 0.770 11.719 9522 Z= 0.370 Chirality : 0.045 0.280 1110 Planarity : 0.006 0.094 1172 Dihedral : 5.455 45.012 942 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.85 % Allowed : 26.21 % Favored : 69.94 % 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 (0.29), residues: 860 helix: 1.32 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.51 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 558 HIS 0.014 0.001 HIS A 437 PHE 0.027 0.002 PHE A 202 TYR 0.017 0.001 TYR A 59 ARG 0.007 0.000 ARG B 537 *********************** 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 124 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: A 460 TRP cc_start: 0.5618 (m-90) cc_final: 0.5025 (m100) REVERT: B 74 ARG cc_start: 0.3162 (OUTLIER) cc_final: 0.0213 (ttt180) REVERT: B 460 TRP cc_start: 0.5587 (m-90) cc_final: 0.4981 (m100) REVERT: B 464 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7737 (tm-30) outliers start: 27 outliers final: 21 residues processed: 119 average time/residue: 0.1580 time to fit residues: 26.7603 Evaluate side-chains 117 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 165 LEU 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 389 LEU 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 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 464 GLN 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: 0.6980 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4549 r_free = 0.4549 target = 0.159852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.136730 restraints weight = 17258.870| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.94 r_work: 0.4089 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6982 Z= 0.210 Angle : 0.788 13.818 9522 Z= 0.373 Chirality : 0.045 0.275 1110 Planarity : 0.006 0.101 1172 Dihedral : 5.463 46.170 942 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.99 % Allowed : 26.64 % Favored : 69.37 % 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: 0.89 (0.30), residues: 860 helix: 1.36 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.47 (0.45), 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 434 PHE 0.026 0.002 PHE A 310 TYR 0.015 0.001 TYR A 484 ARG 0.007 0.000 ARG B 537 *********************** 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 126 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7525 (t80) cc_final: 0.7291 (t80) REVERT: A 460 TRP cc_start: 0.5561 (m-90) cc_final: 0.4972 (m100) REVERT: B 74 ARG cc_start: 0.3301 (OUTLIER) cc_final: 0.0301 (ttt180) REVERT: B 79 PHE cc_start: 0.7362 (t80) cc_final: 0.7123 (t80) REVERT: B 219 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: B 460 TRP cc_start: 0.5513 (m-90) cc_final: 0.4932 (m100) outliers start: 28 outliers final: 22 residues processed: 122 average time/residue: 0.1649 time to fit residues: 28.0849 Evaluate side-chains 114 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU 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 491 MET 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 65 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 62 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4555 r_free = 0.4555 target = 0.160375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.136910 restraints weight = 17583.510| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 3.11 r_work: 0.4082 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6982 Z= 0.211 Angle : 0.797 13.340 9522 Z= 0.377 Chirality : 0.046 0.352 1110 Planarity : 0.006 0.095 1172 Dihedral : 5.461 45.458 942 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.42 % Allowed : 26.35 % Favored : 70.23 % 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: 0.93 (0.30), residues: 860 helix: 1.39 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.44 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 204 HIS 0.001 0.000 HIS A 438 PHE 0.040 0.002 PHE A 202 TYR 0.012 0.001 TYR A 59 ARG 0.007 0.001 ARG B 537 ********************** 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 120 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7505 (t80) cc_final: 0.7280 (t80) REVERT: A 198 PHE cc_start: 0.6758 (t80) cc_final: 0.6217 (t80) REVERT: A 460 TRP cc_start: 0.5512 (m-90) cc_final: 0.4920 (m100) REVERT: B 74 ARG cc_start: 0.3154 (OUTLIER) cc_final: 0.0279 (ttt180) REVERT: B 79 PHE cc_start: 0.7373 (t80) cc_final: 0.7141 (t80) REVERT: B 198 PHE cc_start: 0.6927 (t80) cc_final: 0.6466 (t80) REVERT: B 219 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: B 460 TRP cc_start: 0.5492 (m-90) cc_final: 0.4898 (m100) outliers start: 24 outliers final: 21 residues processed: 116 average time/residue: 0.1605 time to fit residues: 26.2087 Evaluate side-chains 113 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU 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: 0.8980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 80 optimal weight: 4.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.160426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.137086 restraints weight = 17501.549| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 3.09 r_work: 0.4084 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6982 Z= 0.211 Angle : 0.803 13.697 9522 Z= 0.377 Chirality : 0.045 0.375 1110 Planarity : 0.006 0.098 1172 Dihedral : 5.451 45.768 942 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.28 % Allowed : 26.50 % Favored : 70.23 % 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: 1.01 (0.30), residues: 860 helix: 1.43 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -3.27 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.001 0.000 HIS A 438 PHE 0.027 0.002 PHE A 310 TYR 0.010 0.001 TYR A 59 ARG 0.007 0.001 ARG B 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.85 seconds wall clock time: 59 minutes 5.59 seconds (3545.59 seconds total)