Starting phenix.real_space_refine on Sun Apr 27 07:53:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j2g_35949/04_2025/8j2g_35949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j2g_35949/04_2025/8j2g_35949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j2g_35949/04_2025/8j2g_35949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j2g_35949/04_2025/8j2g_35949.map" model { file = "/net/cci-nas-00/data/ceres_data/8j2g_35949/04_2025/8j2g_35949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j2g_35949/04_2025/8j2g_35949.cif" } resolution = 3.4 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= 0.010 sd= 0.143 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 42 5.16 5 C 3282 2.51 5 N 860 2.21 5 O 874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5058 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2529 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B Time building chain proxies: 4.42, per 1000 atoms: 0.87 Number of scatterers: 5058 At special positions: 0 Unit cell: (73.7, 67.1, 126.5, 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 42 16.00 O 874 8.00 N 860 7.00 C 3282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " 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: 1.28 Conformation dependent library (CDL) restraints added in 676.5 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 45.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 3.658A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.716A pdb=" N LEU A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 46 " --> pdb=" O HIS A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.905A pdb=" N GLU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.591A pdb=" N VAL A 84 " --> pdb=" O MET A 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 85' Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.859A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.540A pdb=" N VAL A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.963A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.521A pdb=" N LEU A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.628A pdb=" N LEU A 314 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.680A pdb=" N CYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.094A pdb=" N TYR A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.864A pdb=" N GLU A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.579A pdb=" N ASN A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.694A pdb=" N ARG A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'B' and resid 11 through 32 removed outlier: 3.659A pdb=" N LEU B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.716A pdb=" N LEU B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 46 " --> pdb=" O HIS B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.904A pdb=" N GLU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.592A pdb=" N VAL B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.858A pdb=" N ILE B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 removed outlier: 3.539A pdb=" N VAL B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.964A pdb=" N LEU B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.522A pdb=" N LEU B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.627A pdb=" N LEU B 314 " --> pdb=" O CYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.680A pdb=" N CYS B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 322 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 removed outlier: 4.093A pdb=" N TYR B 330 " --> pdb=" O CYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.864A pdb=" N GLU B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.580A pdb=" N ASN B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.694A pdb=" N ARG B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 376 removed outlier: 6.697A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 376 removed outlier: 6.697A pdb=" N VAL B 369 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS B 389 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 414 " --> pdb=" O ILE B 382 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 372 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: 1.42 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1588 1.34 - 1.46: 950 1.46 - 1.58: 2572 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 5172 Sorted by residual: bond pdb=" CA HIS B 251 " pdb=" C HIS B 251 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CA HIS A 251 " pdb=" C HIS A 251 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CB PRO A 318 " pdb=" CG PRO A 318 " ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.34e+00 bond pdb=" CB PRO B 318 " pdb=" CG PRO B 318 " ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.29e+00 bond pdb=" CB VAL B 248 " pdb=" CG1 VAL B 248 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 5167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 6688 2.37 - 4.73: 298 4.73 - 7.10: 38 7.10 - 9.46: 6 9.46 - 11.83: 4 Bond angle restraints: 7034 Sorted by residual: angle pdb=" N ARG B 246 " pdb=" CA ARG B 246 " pdb=" C ARG B 246 " ideal model delta sigma weight residual 114.64 102.81 11.83 1.52e+00 4.33e-01 6.06e+01 angle pdb=" N ARG A 246 " pdb=" CA ARG A 246 " pdb=" C ARG A 246 " ideal model delta sigma weight residual 114.64 102.86 11.78 1.52e+00 4.33e-01 6.01e+01 angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 114.12 108.34 5.78 1.39e+00 5.18e-01 1.73e+01 angle pdb=" N LEU B 45 " pdb=" CA LEU B 45 " pdb=" C LEU B 45 " ideal model delta sigma weight residual 114.12 108.39 5.73 1.39e+00 5.18e-01 1.70e+01 angle pdb=" C PHE A 134 " pdb=" N HIS A 135 " pdb=" CA HIS A 135 " ideal model delta sigma weight residual 120.82 126.73 -5.91 1.47e+00 4.63e-01 1.62e+01 ... (remaining 7029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.99: 2399 7.99 - 15.99: 455 15.99 - 23.98: 117 23.98 - 31.98: 39 31.98 - 39.97: 30 Dihedral angle restraints: 3040 sinusoidal: 1166 harmonic: 1874 Sorted by residual: dihedral pdb=" CA ASN B 299 " pdb=" C ASN B 299 " pdb=" N SER B 300 " pdb=" CA SER B 300 " ideal model delta harmonic sigma weight residual -180.00 -147.40 -32.60 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA ASN A 299 " pdb=" C ASN A 299 " pdb=" N SER A 300 " pdb=" CA SER A 300 " ideal model delta harmonic sigma weight residual -180.00 -147.46 -32.54 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA VAL B 128 " pdb=" C VAL B 128 " pdb=" N LEU B 129 " pdb=" CA LEU B 129 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 3037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 363 0.036 - 0.073: 335 0.073 - 0.109: 98 0.109 - 0.145: 27 0.145 - 0.182: 15 Chirality restraints: 838 Sorted by residual: chirality pdb=" CA PRO A 318 " pdb=" N PRO A 318 " pdb=" C PRO A 318 " pdb=" CB PRO A 318 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA PRO B 318 " pdb=" N PRO B 318 " pdb=" C PRO B 318 " pdb=" CB PRO B 318 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CG LEU B 35 " pdb=" CB LEU B 35 " pdb=" CD1 LEU B 35 " pdb=" CD2 LEU B 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 835 not shown) Planarity restraints: 878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 317 " 0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO B 318 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 317 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 318 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 333 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 334 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " 0.035 5.00e-02 4.00e+02 ... (remaining 875 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1797 2.88 - 3.39: 4412 3.39 - 3.89: 7453 3.89 - 4.40: 8331 4.40 - 4.90: 14363 Nonbonded interactions: 36356 Sorted by model distance: nonbonded pdb=" OE2 GLU B 109 " pdb=" NE1 TRP B 273 " model vdw 2.380 3.120 nonbonded pdb=" OE2 GLU A 109 " pdb=" NE1 TRP A 273 " model vdw 2.381 3.120 nonbonded pdb=" NE2 GLN B 376 " pdb=" O GLY B 379 " model vdw 2.382 3.120 nonbonded pdb=" NE2 GLN A 376 " pdb=" O GLY A 379 " model vdw 2.382 3.120 nonbonded pdb=" O GLU B 58 " pdb=" NH1 ARG B 62 " model vdw 2.390 3.120 ... (remaining 36351 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: 1.350 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.410 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.010 0.104 5174 Z= 0.395 Angle : 1.138 11.829 7038 Z= 0.625 Chirality : 0.057 0.182 838 Planarity : 0.008 0.072 878 Dihedral : 10.183 38.574 1818 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -6.39 (0.24), residues: 642 helix: -5.04 (0.09), residues: 350 sheet: -1.22 (0.89), residues: 46 loop : -3.27 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 375 HIS 0.008 0.002 HIS B 373 PHE 0.022 0.003 PHE A 407 TYR 0.012 0.003 TYR B 270 ARG 0.011 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.31674 ( 128) hydrogen bonds : angle 9.51772 ( 372) SS BOND : bond 0.00222 ( 2) SS BOND : angle 1.20899 ( 4) covalent geometry : bond 0.00958 ( 5172) covalent geometry : angle 1.13802 ( 7034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7886 (ttp-110) REVERT: A 99 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 64 THR cc_start: 0.8794 (p) cc_final: 0.8353 (m) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2176 time to fit residues: 28.8496 Evaluate side-chains 76 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 370 HIS A 409 ASN A 413 HIS B 251 HIS B 284 ASN B 370 HIS B 409 ASN B 413 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.191153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139626 restraints weight = 5617.661| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.62 r_work: 0.3485 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5174 Z= 0.150 Angle : 0.725 20.014 7038 Z= 0.350 Chirality : 0.042 0.141 838 Planarity : 0.006 0.054 878 Dihedral : 7.243 29.655 686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.91 % Allowed : 8.15 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -5.54 (0.26), residues: 642 helix: -4.25 (0.16), residues: 354 sheet: -1.36 (0.80), residues: 46 loop : -2.89 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 375 HIS 0.003 0.001 HIS B 373 PHE 0.012 0.001 PHE B 94 TYR 0.016 0.002 TYR B 270 ARG 0.002 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 128) hydrogen bonds : angle 5.56496 ( 372) SS BOND : bond 0.00174 ( 2) SS BOND : angle 1.06329 ( 4) covalent geometry : bond 0.00359 ( 5172) covalent geometry : angle 0.72487 ( 7034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.7891 (ttm-80) REVERT: A 44 MET cc_start: 0.8059 (mtp) cc_final: 0.7824 (mtt) REVERT: A 78 GLU cc_start: 0.8640 (pt0) cc_final: 0.8257 (pt0) REVERT: A 99 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 44 MET cc_start: 0.8230 (mtm) cc_final: 0.7995 (mtt) REVERT: B 78 GLU cc_start: 0.8553 (pt0) cc_final: 0.8200 (pt0) REVERT: B 80 MET cc_start: 0.8939 (ptm) cc_final: 0.8575 (ptm) REVERT: B 99 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7283 (tm-30) REVERT: B 371 GLU cc_start: 0.8299 (tp30) cc_final: 0.7937 (tp30) outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 0.1429 time to fit residues: 17.2045 Evaluate side-chains 74 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.182011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127162 restraints weight = 5636.422| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.82 r_work: 0.3313 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 5174 Z= 0.266 Angle : 0.815 21.664 7038 Z= 0.388 Chirality : 0.047 0.139 838 Planarity : 0.006 0.060 878 Dihedral : 7.396 29.233 686 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 1.81 % Allowed : 10.87 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -5.03 (0.28), residues: 642 helix: -3.81 (0.20), residues: 354 sheet: -1.15 (0.81), residues: 46 loop : -2.70 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 375 HIS 0.006 0.001 HIS A 373 PHE 0.015 0.002 PHE A 94 TYR 0.023 0.003 TYR B 270 ARG 0.003 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 128) hydrogen bonds : angle 5.16176 ( 372) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.84486 ( 4) covalent geometry : bond 0.00653 ( 5172) covalent geometry : angle 0.81505 ( 7034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.7974 (ttm-80) REVERT: A 44 MET cc_start: 0.8147 (mtp) cc_final: 0.7909 (mtt) REVERT: A 99 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 359 GLU cc_start: 0.7877 (mp0) cc_final: 0.7404 (mp0) REVERT: A 396 TYR cc_start: 0.7113 (t80) cc_final: 0.6824 (t80) REVERT: B 44 MET cc_start: 0.8459 (mtm) cc_final: 0.8216 (mtt) REVERT: B 99 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7203 (tm-30) outliers start: 10 outliers final: 8 residues processed: 83 average time/residue: 0.1686 time to fit residues: 19.6964 Evaluate side-chains 84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 332 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.192968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141119 restraints weight = 5790.346| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.66 r_work: 0.3497 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5174 Z= 0.088 Angle : 0.624 18.925 7038 Z= 0.297 Chirality : 0.040 0.135 838 Planarity : 0.004 0.036 878 Dihedral : 6.149 27.052 686 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.91 % Allowed : 11.59 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.63 (0.29), residues: 642 helix: -3.33 (0.22), residues: 362 sheet: -0.91 (0.79), residues: 46 loop : -2.77 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 375 HIS 0.002 0.001 HIS B 108 PHE 0.008 0.001 PHE A 94 TYR 0.015 0.002 TYR B 270 ARG 0.002 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.02688 ( 128) hydrogen bonds : angle 4.31294 ( 372) SS BOND : bond 0.00189 ( 2) SS BOND : angle 0.71579 ( 4) covalent geometry : bond 0.00203 ( 5172) covalent geometry : angle 0.62435 ( 7034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8410 (ttp-170) cc_final: 0.8020 (ttm-80) REVERT: A 20 MET cc_start: 0.7869 (ppp) cc_final: 0.7580 (ppp) REVERT: A 30 ARG cc_start: 0.7187 (tmt170) cc_final: 0.6664 (tmt170) REVERT: A 58 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7636 (mm-30) REVERT: A 78 GLU cc_start: 0.8666 (pt0) cc_final: 0.8298 (pt0) REVERT: A 99 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 10 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8504 (ttp-110) REVERT: B 30 ARG cc_start: 0.7120 (tmt170) cc_final: 0.6692 (tmt170) REVERT: B 44 MET cc_start: 0.8170 (mtm) cc_final: 0.7922 (mtt) REVERT: B 359 GLU cc_start: 0.7665 (mp0) cc_final: 0.7107 (mt-10) outliers start: 5 outliers final: 3 residues processed: 86 average time/residue: 0.2879 time to fit residues: 31.1747 Evaluate side-chains 69 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.0980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.187477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129191 restraints weight = 5566.237| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.86 r_work: 0.3398 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5174 Z= 0.137 Angle : 0.650 19.432 7038 Z= 0.306 Chirality : 0.042 0.134 838 Planarity : 0.004 0.034 878 Dihedral : 6.146 26.356 686 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.81 % Allowed : 12.50 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.18 (0.31), residues: 642 helix: -3.11 (0.23), residues: 352 sheet: -0.58 (0.80), residues: 46 loop : -2.40 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.003 0.001 HIS A 373 PHE 0.011 0.001 PHE A 94 TYR 0.014 0.001 TYR B 270 ARG 0.006 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 128) hydrogen bonds : angle 4.19597 ( 372) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.60714 ( 4) covalent geometry : bond 0.00332 ( 5172) covalent geometry : angle 0.65025 ( 7034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8156 (ttp-170) cc_final: 0.7773 (ttm-80) REVERT: A 30 ARG cc_start: 0.7256 (tmt170) cc_final: 0.6734 (tmt170) REVERT: A 78 GLU cc_start: 0.8706 (pt0) cc_final: 0.8239 (pt0) REVERT: A 99 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 359 GLU cc_start: 0.7821 (mp0) cc_final: 0.7558 (mp0) REVERT: B 30 ARG cc_start: 0.7120 (tmt170) cc_final: 0.6682 (tmt170) REVERT: B 44 MET cc_start: 0.8308 (mtm) cc_final: 0.8051 (mtt) REVERT: B 80 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8401 (ttm) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.1595 time to fit residues: 17.2670 Evaluate side-chains 76 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.190891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133069 restraints weight = 5463.472| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.82 r_work: 0.3447 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5174 Z= 0.093 Angle : 0.619 18.336 7038 Z= 0.286 Chirality : 0.040 0.133 838 Planarity : 0.004 0.031 878 Dihedral : 5.699 24.988 686 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.45 % Allowed : 14.31 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.85 (0.31), residues: 642 helix: -2.83 (0.25), residues: 352 sheet: -0.20 (0.81), residues: 46 loop : -2.34 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.002 0.001 HIS B 108 PHE 0.008 0.001 PHE A 94 TYR 0.012 0.001 TYR B 270 ARG 0.003 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.02533 ( 128) hydrogen bonds : angle 3.92699 ( 372) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.56986 ( 4) covalent geometry : bond 0.00221 ( 5172) covalent geometry : angle 0.61907 ( 7034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7749 (ttm-80) REVERT: A 20 MET cc_start: 0.7810 (ppp) cc_final: 0.7591 (ppp) REVERT: A 30 ARG cc_start: 0.7201 (tmt170) cc_final: 0.6775 (tmt170) REVERT: A 78 GLU cc_start: 0.8594 (pt0) cc_final: 0.8217 (pt0) REVERT: A 99 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 30 ARG cc_start: 0.7116 (tmt170) cc_final: 0.6730 (tmt170) REVERT: B 44 MET cc_start: 0.8091 (mtm) cc_final: 0.7884 (mtt) REVERT: B 78 GLU cc_start: 0.8627 (pt0) cc_final: 0.8280 (pt0) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.1658 time to fit residues: 15.9247 Evaluate side-chains 68 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 68 GLN B 127 ASN B 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.184423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125684 restraints weight = 5530.834| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.88 r_work: 0.3353 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5174 Z= 0.197 Angle : 0.698 19.887 7038 Z= 0.325 Chirality : 0.044 0.136 838 Planarity : 0.004 0.037 878 Dihedral : 6.189 24.603 686 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.90 % Allowed : 13.04 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.85 (0.31), residues: 642 helix: -2.89 (0.24), residues: 352 sheet: -0.26 (0.82), residues: 46 loop : -2.22 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.005 0.001 HIS B 43 PHE 0.013 0.001 PHE A 94 TYR 0.011 0.001 TYR B 270 ARG 0.004 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 128) hydrogen bonds : angle 4.21088 ( 372) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.55310 ( 4) covalent geometry : bond 0.00486 ( 5172) covalent geometry : angle 0.69782 ( 7034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7576 (ttm-80) REVERT: B 30 ARG cc_start: 0.7181 (tmt170) cc_final: 0.6908 (tmt170) REVERT: B 44 MET cc_start: 0.8350 (mtm) cc_final: 0.8088 (mtt) outliers start: 16 outliers final: 14 residues processed: 90 average time/residue: 0.1489 time to fit residues: 17.8655 Evaluate side-chains 85 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.189541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130802 restraints weight = 5595.876| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.93 r_work: 0.3431 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5174 Z= 0.101 Angle : 0.626 18.793 7038 Z= 0.293 Chirality : 0.040 0.131 838 Planarity : 0.004 0.031 878 Dihedral : 5.635 23.757 686 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.99 % Allowed : 14.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.63 (0.32), residues: 642 helix: -2.60 (0.25), residues: 356 sheet: 0.01 (0.83), residues: 46 loop : -2.32 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.002 0.001 HIS B 108 PHE 0.008 0.001 PHE A 94 TYR 0.009 0.001 TYR B 270 ARG 0.002 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.02586 ( 128) hydrogen bonds : angle 3.86042 ( 372) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.50390 ( 4) covalent geometry : bond 0.00245 ( 5172) covalent geometry : angle 0.62595 ( 7034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7834 (ttm-80) REVERT: A 30 ARG cc_start: 0.7064 (tmt170) cc_final: 0.6836 (tmt170) REVERT: A 78 GLU cc_start: 0.8706 (pt0) cc_final: 0.8312 (pt0) REVERT: A 381 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6492 (ttt90) REVERT: B 44 MET cc_start: 0.8150 (mtm) cc_final: 0.7928 (mtp) REVERT: B 78 GLU cc_start: 0.8666 (pt0) cc_final: 0.8309 (pt0) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.1959 time to fit residues: 19.4956 Evaluate side-chains 70 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 332 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 26 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.0060 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.192950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136497 restraints weight = 5469.696| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.75 r_work: 0.3494 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5174 Z= 0.085 Angle : 0.600 17.779 7038 Z= 0.281 Chirality : 0.040 0.131 838 Planarity : 0.003 0.032 878 Dihedral : 5.226 22.315 686 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.81 % Allowed : 15.40 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.40 (0.32), residues: 642 helix: -2.34 (0.26), residues: 362 sheet: 0.46 (0.84), residues: 46 loop : -2.44 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.002 0.000 HIS B 108 PHE 0.007 0.001 PHE A 94 TYR 0.007 0.001 TYR A 330 ARG 0.002 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.02197 ( 128) hydrogen bonds : angle 3.61086 ( 372) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.56164 ( 4) covalent geometry : bond 0.00199 ( 5172) covalent geometry : angle 0.60031 ( 7034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.7879 (ttm-80) REVERT: A 78 GLU cc_start: 0.8399 (pt0) cc_final: 0.8128 (pt0) REVERT: A 80 MET cc_start: 0.8611 (ttm) cc_final: 0.8294 (tpp) REVERT: A 381 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6552 (ttt90) REVERT: B 65 HIS cc_start: 0.8093 (m-70) cc_final: 0.7580 (t-90) REVERT: B 78 GLU cc_start: 0.8527 (pt0) cc_final: 0.8187 (pp20) REVERT: B 92 LEU cc_start: 0.8126 (tp) cc_final: 0.7910 (tt) REVERT: B 388 ILE cc_start: 0.7762 (mt) cc_final: 0.7389 (pt) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.1817 time to fit residues: 18.1399 Evaluate side-chains 65 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 45 optimal weight: 0.3980 chunk 8 optimal weight: 0.0030 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.194509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137691 restraints weight = 5433.387| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.76 r_work: 0.3503 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5174 Z= 0.085 Angle : 0.606 17.442 7038 Z= 0.279 Chirality : 0.040 0.132 838 Planarity : 0.003 0.032 878 Dihedral : 4.973 21.345 686 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.09 % Allowed : 16.67 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.13 (0.33), residues: 642 helix: -2.01 (0.27), residues: 360 sheet: 0.68 (0.83), residues: 46 loop : -2.56 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.000 HIS B 108 PHE 0.007 0.001 PHE A 94 TYR 0.012 0.001 TYR B 270 ARG 0.001 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.02065 ( 128) hydrogen bonds : angle 3.49017 ( 372) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.44770 ( 4) covalent geometry : bond 0.00201 ( 5172) covalent geometry : angle 0.60581 ( 7034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7865 (ttm-80) REVERT: A 78 GLU cc_start: 0.8383 (pt0) cc_final: 0.8161 (pt0) REVERT: A 80 MET cc_start: 0.8604 (ttm) cc_final: 0.8343 (tpp) REVERT: A 381 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6516 (ttt90) REVERT: B 65 HIS cc_start: 0.8121 (m-70) cc_final: 0.7633 (t-90) REVERT: B 78 GLU cc_start: 0.8535 (pt0) cc_final: 0.8207 (pt0) REVERT: B 92 LEU cc_start: 0.8145 (tp) cc_final: 0.7923 (tt) REVERT: B 388 ILE cc_start: 0.7705 (mt) cc_final: 0.7306 (pt) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1623 time to fit residues: 14.7532 Evaluate side-chains 66 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.190857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131606 restraints weight = 5546.157| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.92 r_work: 0.3434 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5174 Z= 0.116 Angle : 0.645 18.412 7038 Z= 0.294 Chirality : 0.041 0.134 838 Planarity : 0.003 0.032 878 Dihedral : 5.148 20.958 686 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.81 % Allowed : 16.49 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.77 (0.33), residues: 642 helix: -1.86 (0.27), residues: 350 sheet: 0.88 (0.85), residues: 46 loop : -2.15 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.003 0.001 HIS A 43 PHE 0.010 0.001 PHE A 94 TYR 0.013 0.001 TYR B 270 ARG 0.003 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.02604 ( 128) hydrogen bonds : angle 3.58774 ( 372) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.42174 ( 4) covalent geometry : bond 0.00287 ( 5172) covalent geometry : angle 0.64517 ( 7034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.09 seconds wall clock time: 66 minutes 2.69 seconds (3962.69 seconds total)