Starting phenix.real_space_refine on Tue Jan 14 14:51:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx2_37898/01_2025/8wx2_37898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx2_37898/01_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_37898/01_2025/8wx2_37898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx2_37898/01_2025/8wx2_37898.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx2_37898/01_2025/8wx2_37898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx2_37898/01_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-5571/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: 5.78, per 1000 atoms: 0.85 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=2, 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 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: 1.68 Conformation dependent library (CDL) restraints added in 967.9 milliseconds 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: 0.53 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: 1.97 Time building geometry restraints manager: 1.96 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: 3527 14.95 - 29.91: 337 29.91 - 44.86: 126 44.86 - 59.81: 36 59.81 - 74.77: 4 Dihedral angle restraints: 4030 sinusoidal: 1504 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 A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual -86.00 -28.57 -57.43 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 4027 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: 2.03 - 2.61: 50 2.61 - 3.18: 6070 3.18 - 3.75: 11342 3.75 - 4.33: 14422 4.33 - 4.90: 23139 Nonbonded interactions: 55023 Sorted by model distance: nonbonded pdb=" SG CYS B 526 " pdb=" SG CYS B 536 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS B 131 " pdb=" SG CYS B 157 " model vdw 2.034 3.760 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 ... (remaining 55018 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.960 Find NCS groups from input model: 0.120 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- 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= 0.145 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 : 2.033 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 : 0.771 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: 0.1758 time to fit residues: 40.0855 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 : 0.750 ------------------------------------------------------------------------------- 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 ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.166240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.143892 restraints weight = 17380.689| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.03 r_work: 0.4186 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6982 Z= 0.209 Angle : 0.765 10.055 9522 Z= 0.371 Chirality : 0.042 0.149 1110 Planarity : 0.006 0.074 1172 Dihedral : 6.574 59.304 950 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.85 % Allowed : 18.95 % Favored : 77.21 % 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: 0.27 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.86 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 197 *********************** 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 151 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.6656 (t80) cc_final: 0.6122 (t80) REVERT: A 374 TRP cc_start: 0.5826 (t60) cc_final: 0.5345 (t60) REVERT: A 460 TRP cc_start: 0.5226 (m-90) cc_final: 0.4527 (m100) REVERT: B 460 TRP cc_start: 0.5266 (m-90) cc_final: 0.4964 (m-10) outliers start: 27 outliers final: 15 residues processed: 139 average time/residue: 0.1585 time to fit residues: 30.7343 Evaluate side-chains 128 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 319 VAL 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 332 GLN 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 20 optimal weight: 0.0000 chunk 65 optimal weight: 0.0030 chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 overall best weight: 0.1350 ------------------------------------------------------------------------------- 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 = 0.4620 r_free = 0.4620 target = 0.166382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.144907 restraints weight = 17466.810| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 3.00 r_work: 0.4198 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6982 Z= 0.183 Angle : 0.735 10.916 9522 Z= 0.352 Chirality : 0.041 0.154 1110 Planarity : 0.006 0.072 1172 Dihedral : 6.344 58.166 947 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.13 % Allowed : 20.51 % Favored : 75.36 % 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: -0.15 (0.29), residues: 860 helix: 0.61 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -3.31 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 204 HIS 0.005 0.001 HIS B 434 PHE 0.028 0.001 PHE A 202 TYR 0.014 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 149 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.5783 (t80) cc_final: 0.5504 (t80) REVERT: A 219 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6922 (m-80) REVERT: A 374 TRP cc_start: 0.5830 (t60) cc_final: 0.5363 (t60) REVERT: A 460 TRP cc_start: 0.5188 (m-90) cc_final: 0.4557 (m100) REVERT: A 486 GLU cc_start: 0.5285 (pm20) cc_final: 0.4926 (mp0) REVERT: B 74 ARG cc_start: 0.3117 (OUTLIER) cc_final: -0.0076 (ttt180) REVERT: B 198 PHE cc_start: 0.6555 (t80) cc_final: 0.6066 (t80) REVERT: B 219 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: B 429 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6724 (tm-30) REVERT: B 460 TRP cc_start: 0.5193 (m-90) cc_final: 0.4894 (m-10) outliers start: 29 outliers final: 11 residues processed: 134 average time/residue: 0.1556 time to fit residues: 29.2511 Evaluate side-chains 117 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.162646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.139801 restraints weight = 17478.848| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 3.04 r_work: 0.4123 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2580 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= 0.220 Angle : 0.756 11.574 9522 Z= 0.360 Chirality : 0.042 0.198 1110 Planarity : 0.006 0.074 1172 Dihedral : 5.670 44.661 943 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.84 % Allowed : 20.51 % Favored : 74.64 % 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: 0.25 (0.29), residues: 860 helix: 0.87 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -3.45 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 558 HIS 0.004 0.001 HIS A 434 PHE 0.017 0.001 PHE B 244 TYR 0.009 0.001 TYR A 203 ARG 0.004 0.001 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 141 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: A 460 TRP cc_start: 0.5453 (m-90) cc_final: 0.4811 (m100) REVERT: B 74 ARG cc_start: 0.3171 (OUTLIER) cc_final: -0.0069 (ttt180) REVERT: B 101 TYR cc_start: 0.5869 (t80) cc_final: 0.5648 (t80) REVERT: B 219 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: B 460 TRP cc_start: 0.5358 (m-90) cc_final: 0.4672 (m100) outliers start: 34 outliers final: 16 residues processed: 128 average time/residue: 0.1756 time to fit residues: 30.5451 Evaluate side-chains 115 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 319 VAL 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 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 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: 0.9980 chunk 87 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4536 r_free = 0.4536 target = 0.159146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.135355 restraints weight = 17222.470| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 3.06 r_work: 0.4062 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6982 Z= 0.265 Angle : 0.795 12.576 9522 Z= 0.383 Chirality : 0.044 0.197 1110 Planarity : 0.006 0.075 1172 Dihedral : 5.666 47.091 942 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 4.27 % Allowed : 22.79 % Favored : 72.93 % 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: 0.35 (0.29), residues: 860 helix: 0.95 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -3.54 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 558 HIS 0.003 0.001 HIS B 343 PHE 0.018 0.002 PHE A 244 TYR 0.019 0.002 TYR B 484 ARG 0.011 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 130 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TYR cc_start: 0.5803 (t80) cc_final: 0.5536 (t80) REVERT: A 198 PHE cc_start: 0.6744 (t80) cc_final: 0.6236 (t80) REVERT: A 460 TRP cc_start: 0.5679 (m-90) cc_final: 0.5010 (m100) REVERT: B 74 ARG cc_start: 0.3055 (OUTLIER) cc_final: -0.0135 (ttt180) REVERT: B 219 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: B 460 TRP cc_start: 0.5677 (m-90) cc_final: 0.4931 (m100) outliers start: 30 outliers final: 19 residues processed: 119 average time/residue: 0.1596 time to fit residues: 26.4210 Evaluate side-chains 110 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 370 ILE 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 332 GLN Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 438 HIS 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: 0.1980 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 50.0000 chunk 76 optimal weight: 7.9990 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 = 0.4545 r_free = 0.4545 target = 0.160040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.136878 restraints weight = 17365.281| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.07 r_work: 0.4086 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3196 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= 0.210 Angle : 0.773 13.046 9522 Z= 0.368 Chirality : 0.045 0.243 1110 Planarity : 0.005 0.076 1172 Dihedral : 5.551 43.970 942 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.13 % Allowed : 23.79 % 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: 0.60 (0.30), residues: 860 helix: 1.15 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -4.01 (0.45), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.003 0.001 HIS B 343 PHE 0.021 0.001 PHE A 310 TYR 0.019 0.002 TYR B 59 ARG 0.004 0.000 ARG A 46 *********************** 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 130 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 TRP cc_start: 0.5579 (m-90) cc_final: 0.4954 (m100) REVERT: B 74 ARG cc_start: 0.2890 (OUTLIER) cc_final: -0.0176 (ttt180) REVERT: B 198 PHE cc_start: 0.6803 (t80) cc_final: 0.6321 (t80) REVERT: B 460 TRP cc_start: 0.5518 (m-90) cc_final: 0.4843 (m100) outliers start: 29 outliers final: 21 residues processed: 122 average time/residue: 0.1656 time to fit residues: 27.7085 Evaluate side-chains 113 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 386 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 332 GLN Chi-restraints excluded: chain B residue 370 ILE 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 438 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 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** A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.160765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.137778 restraints weight = 16938.886| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 3.04 r_work: 0.4102 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6982 Z= 0.198 Angle : 0.766 13.491 9522 Z= 0.365 Chirality : 0.044 0.256 1110 Planarity : 0.005 0.077 1172 Dihedral : 5.498 45.575 942 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.85 % Allowed : 23.79 % 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: 0.83 (0.30), residues: 860 helix: 1.34 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.66 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 204 HIS 0.003 0.001 HIS B 343 PHE 0.030 0.001 PHE B 202 TYR 0.019 0.001 TYR A 59 ARG 0.004 0.000 ARG B 46 *********************** 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 132 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: A 460 TRP cc_start: 0.5569 (m-90) cc_final: 0.4978 (m100) REVERT: B 74 ARG cc_start: 0.2988 (OUTLIER) cc_final: -0.0009 (ttt180) REVERT: B 219 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: B 460 TRP cc_start: 0.5498 (m-90) cc_final: 0.4858 (m100) outliers start: 27 outliers final: 21 residues processed: 125 average time/residue: 0.1609 time to fit residues: 28.1869 Evaluate side-chains 118 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 386 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 332 GLN 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 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: 2.9990 chunk 48 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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 = 0.4550 r_free = 0.4550 target = 0.160110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.136981 restraints weight = 17169.666| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.95 r_work: 0.4096 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6982 Z= 0.222 Angle : 0.778 13.519 9522 Z= 0.373 Chirality : 0.044 0.246 1110 Planarity : 0.005 0.076 1172 Dihedral : 5.473 43.577 942 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.85 % Allowed : 25.21 % Favored : 70.94 % 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: 0.84 (0.30), residues: 860 helix: 1.29 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -3.74 (0.46), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.002 0.000 HIS B 343 PHE 0.023 0.002 PHE A 310 TYR 0.013 0.001 TYR A 484 ARG 0.004 0.000 ARG A 46 *********************** 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 127 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7341 (t80) cc_final: 0.6952 (t80) REVERT: A 460 TRP cc_start: 0.5569 (m-90) cc_final: 0.4985 (m100) REVERT: B 74 ARG cc_start: 0.3161 (OUTLIER) cc_final: 0.0159 (ttt180) REVERT: B 79 PHE cc_start: 0.7315 (t80) cc_final: 0.7071 (t80) REVERT: B 460 TRP cc_start: 0.5509 (m-90) cc_final: 0.4899 (m100) outliers start: 27 outliers final: 19 residues processed: 120 average time/residue: 0.1481 time to fit residues: 25.3580 Evaluate side-chains 112 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 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 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 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 332 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 58 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 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 = 0.4554 r_free = 0.4554 target = 0.160372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.137287 restraints weight = 17119.820| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.05 r_work: 0.4093 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6982 Z= 0.218 Angle : 0.798 14.001 9522 Z= 0.378 Chirality : 0.045 0.242 1110 Planarity : 0.006 0.098 1172 Dihedral : 5.536 46.380 942 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.42 % Allowed : 25.36 % Favored : 71.23 % 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: 0.85 (0.30), residues: 860 helix: 1.30 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -3.58 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 204 HIS 0.002 0.001 HIS B 343 PHE 0.040 0.002 PHE B 202 TYR 0.013 0.001 TYR B 484 ARG 0.006 0.000 ARG A 46 *********************** 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 119 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7355 (t80) cc_final: 0.7020 (t80) REVERT: A 460 TRP cc_start: 0.5563 (m-90) cc_final: 0.4966 (m100) REVERT: B 74 ARG cc_start: 0.3279 (OUTLIER) cc_final: 0.0269 (ttt180) REVERT: B 79 PHE cc_start: 0.7375 (t80) cc_final: 0.7109 (t80) REVERT: B 198 PHE cc_start: 0.6887 (t80) cc_final: 0.6332 (t80) REVERT: B 460 TRP cc_start: 0.5512 (m-90) cc_final: 0.4877 (m100) outliers start: 24 outliers final: 21 residues processed: 114 average time/residue: 0.1694 time to fit residues: 27.0269 Evaluate side-chains 113 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 236 CYS Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 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 236 CYS Chi-restraints excluded: chain B residue 332 GLN 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 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: 1.9990 chunk 40 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4535 r_free = 0.4535 target = 0.158714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.135027 restraints weight = 17497.981| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 3.10 r_work: 0.4065 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6982 Z= 0.242 Angle : 0.810 13.017 9522 Z= 0.386 Chirality : 0.046 0.240 1110 Planarity : 0.006 0.097 1172 Dihedral : 5.548 45.432 942 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.56 % Allowed : 25.07 % Favored : 71.37 % 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: 0.70 (0.30), residues: 860 helix: 1.23 (0.20), residues: 726 sheet: None (None), residues: 0 loop : -3.79 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 558 HIS 0.002 0.001 HIS B 343 PHE 0.025 0.002 PHE A 310 TYR 0.014 0.001 TYR B 484 ARG 0.005 0.000 ARG A 46 ********************** 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 125 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7481 (t80) cc_final: 0.7078 (t80) REVERT: A 460 TRP cc_start: 0.5661 (m-90) cc_final: 0.5042 (m100) REVERT: B 74 ARG cc_start: 0.3225 (OUTLIER) cc_final: 0.0277 (ttt180) REVERT: B 79 PHE cc_start: 0.7473 (t80) cc_final: 0.7148 (t80) REVERT: B 198 PHE cc_start: 0.6949 (t80) cc_final: 0.6428 (t80) REVERT: B 460 TRP cc_start: 0.5621 (m-90) cc_final: 0.4958 (m100) outliers start: 25 outliers final: 23 residues processed: 118 average time/residue: 0.1601 time to fit residues: 26.3894 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 : 0.759 ------------------------------------------------------------------------------- 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 236 CYS Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 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 236 CYS Chi-restraints excluded: chain B residue 332 GLN 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 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: 2.9990 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.0270 chunk 80 optimal weight: 0.1980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.160551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.137604 restraints weight = 17406.512| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.06 r_work: 0.4101 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3913 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 : 0.825 14.094 9522 Z= 0.389 Chirality : 0.045 0.241 1110 Planarity : 0.006 0.100 1172 Dihedral : 5.548 45.154 942 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.56 % Allowed : 26.07 % Favored : 70.37 % 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: 0.82 (0.30), residues: 860 helix: 1.30 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -3.59 (0.46), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 523 HIS 0.002 0.001 HIS B 343 PHE 0.029 0.002 PHE B 202 TYR 0.012 0.001 TYR B 484 ARG 0.006 0.001 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.26 seconds wall clock time: 55 minutes 52.69 seconds (3352.69 seconds total)