Starting phenix.real_space_refine on Thu Mar 6 05:19:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j2g_35949/03_2025/8j2g_35949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j2g_35949/03_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_35949/03_2025/8j2g_35949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j2g_35949/03_2025/8j2g_35949.map" model { file = "/net/cci-nas-00/data/ceres_data/8j2g_35949/03_2025/8j2g_35949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j2g_35949/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.06, per 1000 atoms: 0.80 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: 1.12 Conformation dependent library (CDL) restraints added in 603.4 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: 0.52 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: 1.00 Time building geometry restraints manager: 1.36 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- 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 5172 Z= 0.616 Angle : 1.138 11.829 7034 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 *********************** 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 : 0.920 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: 0.1826 time to fit residues: 23.5862 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 : 0.552 ------------------------------------------------------------------------------- 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 5172 Z= 0.233 Angle : 0.725 20.014 7034 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 *********************** 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 : 0.452 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: 0.1379 time to fit residues: 17.4391 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 : 0.827 ------------------------------------------------------------------------------- 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 5172 Z= 0.420 Angle : 0.815 21.664 7034 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 *********************** 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 : 0.561 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: 0.1876 time to fit residues: 21.2566 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 : 0.582 ------------------------------------------------------------------------------- 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 5172 Z= 0.133 Angle : 0.624 18.925 7034 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 *********************** 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 : 0.945 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: 0.2832 time to fit residues: 30.9841 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 : 0.641 ------------------------------------------------------------------------------- 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: 3.9990 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: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.185087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126555 restraints weight = 5615.951| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.87 r_work: 0.3362 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5172 Z= 0.284 Angle : 0.693 20.110 7034 Z= 0.326 Chirality : 0.043 0.134 838 Planarity : 0.005 0.039 878 Dihedral : 6.407 26.639 686 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.36 % Allowed : 12.50 % Favored : 85.14 % 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: -4.25 (0.31), residues: 642 helix: -3.19 (0.23), residues: 352 sheet: -0.68 (0.80), residues: 46 loop : -2.38 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.004 0.001 HIS B 373 PHE 0.012 0.001 PHE A 94 TYR 0.014 0.001 TYR B 270 ARG 0.006 0.000 ARG B 381 *********************** 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 91 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8165 (ttp-170) cc_final: 0.7810 (ttm-80) REVERT: A 99 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 359 GLU cc_start: 0.7851 (mp0) cc_final: 0.7610 (mp0) REVERT: A 396 TYR cc_start: 0.7215 (t80) cc_final: 0.6973 (t80) REVERT: B 44 MET cc_start: 0.8428 (mtm) cc_final: 0.8179 (mtt) REVERT: B 80 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8553 (ttm) outliers start: 13 outliers final: 11 residues processed: 89 average time/residue: 0.1521 time to fit residues: 18.2842 Evaluate side-chains 82 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 297 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 64 THR 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 332 THR 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: 3.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.185248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126593 restraints weight = 5568.129| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.89 r_work: 0.3367 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5172 Z= 0.252 Angle : 0.687 19.644 7034 Z= 0.318 Chirality : 0.043 0.133 838 Planarity : 0.004 0.034 878 Dihedral : 6.267 25.548 686 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.54 % Allowed : 13.59 % Favored : 83.88 % 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: -4.05 (0.31), residues: 642 helix: -3.04 (0.24), residues: 352 sheet: -0.44 (0.82), residues: 46 loop : -2.29 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.004 0.001 HIS B 43 PHE 0.012 0.001 PHE A 94 TYR 0.012 0.001 TYR B 270 ARG 0.004 0.000 ARG B 381 *********************** 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 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7577 (ttm-80) REVERT: A 30 ARG cc_start: 0.7119 (tmt170) cc_final: 0.6694 (tmt170) REVERT: A 78 GLU cc_start: 0.8678 (pt0) cc_final: 0.8225 (pt0) REVERT: B 30 ARG cc_start: 0.7123 (tmt170) cc_final: 0.6759 (tmt170) REVERT: B 44 MET cc_start: 0.8389 (mtm) cc_final: 0.8120 (mtt) outliers start: 14 outliers final: 12 residues processed: 87 average time/residue: 0.1898 time to fit residues: 21.7049 Evaluate side-chains 83 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.188429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130693 restraints weight = 5469.064| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.86 r_work: 0.3421 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5172 Z= 0.164 Angle : 0.640 19.100 7034 Z= 0.297 Chirality : 0.041 0.132 838 Planarity : 0.004 0.032 878 Dihedral : 5.768 24.431 686 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.99 % Allowed : 14.31 % Favored : 83.70 % 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: -3.81 (0.32), residues: 642 helix: -2.77 (0.25), residues: 356 sheet: -0.11 (0.83), residues: 46 loop : -2.35 (0.40), 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 43 PHE 0.009 0.001 PHE A 94 TYR 0.011 0.001 TYR B 270 ARG 0.002 0.000 ARG B 381 *********************** 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 84 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7603 (ttm-80) REVERT: A 30 ARG cc_start: 0.6965 (tmt170) cc_final: 0.6507 (tmt170) REVERT: A 78 GLU cc_start: 0.8693 (pt0) cc_final: 0.8235 (pt0) REVERT: A 381 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6498 (ttt90) REVERT: B 30 ARG cc_start: 0.6910 (tmt170) cc_final: 0.6422 (tmt170) REVERT: B 44 MET cc_start: 0.8181 (mtm) cc_final: 0.7876 (mtt) REVERT: B 359 GLU cc_start: 0.7245 (mp0) cc_final: 0.6838 (mt-10) REVERT: B 388 ILE cc_start: 0.7799 (mt) cc_final: 0.7354 (pt) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.2311 time to fit residues: 25.9100 Evaluate side-chains 75 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 381 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 0.0370 chunk 41 optimal weight: 0.0470 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.191421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133817 restraints weight = 5483.822| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.82 r_work: 0.3469 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5172 Z= 0.134 Angle : 0.603 17.968 7034 Z= 0.281 Chirality : 0.040 0.133 838 Planarity : 0.003 0.032 878 Dihedral : 5.394 23.235 686 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.36 % Allowed : 15.40 % 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: -3.62 (0.32), residues: 642 helix: -2.53 (0.25), residues: 362 sheet: 0.23 (0.84), residues: 46 loop : -2.48 (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 0.008 0.001 PHE A 94 TYR 0.011 0.001 TYR B 270 ARG 0.002 0.000 ARG A 6 *********************** 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 77 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7630 (ttp-110) REVERT: A 78 GLU cc_start: 0.8645 (pt0) cc_final: 0.8244 (pt0) REVERT: A 381 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6524 (ttt90) REVERT: B 44 MET cc_start: 0.8163 (mtm) cc_final: 0.7897 (mtt) REVERT: B 65 HIS cc_start: 0.8108 (m-70) cc_final: 0.7648 (t-90) REVERT: B 359 GLU cc_start: 0.7391 (mp0) cc_final: 0.6922 (mt-10) REVERT: B 388 ILE cc_start: 0.7782 (mt) cc_final: 0.7451 (pt) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.2099 time to fit residues: 22.1041 Evaluate side-chains 67 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 71 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.190158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131913 restraints weight = 5492.400| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.88 r_work: 0.3401 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5172 Z= 0.161 Angle : 0.617 18.457 7034 Z= 0.286 Chirality : 0.041 0.132 838 Planarity : 0.003 0.033 878 Dihedral : 5.376 22.651 686 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.81 % Allowed : 15.22 % Favored : 82.97 % 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: -3.20 (0.33), residues: 642 helix: -2.28 (0.26), residues: 352 sheet: 0.41 (0.83), residues: 46 loop : -2.16 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.001 HIS B 43 PHE 0.009 0.001 PHE A 94 TYR 0.009 0.001 TYR A 270 ARG 0.002 0.000 ARG B 381 *********************** 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 71 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8245 (ttp-170) cc_final: 0.7886 (ttm-80) REVERT: A 78 GLU cc_start: 0.8664 (pt0) cc_final: 0.8265 (pt0) REVERT: A 381 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6491 (ttt90) REVERT: B 44 MET cc_start: 0.8116 (mtm) cc_final: 0.7906 (mtt) REVERT: B 65 HIS cc_start: 0.8130 (m-70) cc_final: 0.7608 (t-90) REVERT: B 78 GLU cc_start: 0.8616 (pt0) cc_final: 0.8296 (pt0) REVERT: B 92 LEU cc_start: 0.8200 (tp) cc_final: 0.7956 (tt) REVERT: B 359 GLU cc_start: 0.7419 (mp0) cc_final: 0.6925 (mt-10) REVERT: B 388 ILE cc_start: 0.7642 (mt) cc_final: 0.7365 (pt) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.2161 time to fit residues: 20.3004 Evaluate side-chains 69 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 71 THR 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 71 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: 0.0020 chunk 48 optimal weight: 0.0770 chunk 42 optimal weight: 0.3980 chunk 51 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 overall best weight: 0.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 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 = 0.4318 r_free = 0.4318 target = 0.197672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141702 restraints weight = 5383.149| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.73 r_work: 0.3552 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5172 Z= 0.120 Angle : 0.590 16.378 7034 Z= 0.275 Chirality : 0.039 0.131 838 Planarity : 0.003 0.033 878 Dihedral : 4.835 21.175 686 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.91 % Allowed : 16.67 % Favored : 82.43 % 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: -3.08 (0.33), residues: 642 helix: -1.98 (0.26), residues: 362 sheet: 0.68 (0.81), residues: 46 loop : -2.51 (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 249 TYR 0.009 0.001 TYR B 270 ARG 0.002 0.000 ARG B 10 ********************** 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: 5 poor density : 63 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.7808 (ttm-80) REVERT: A 20 MET cc_start: 0.7630 (ppp) cc_final: 0.7402 (ppp) REVERT: A 80 MET cc_start: 0.8604 (ttm) cc_final: 0.8304 (tpp) REVERT: A 381 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6469 (ttt90) REVERT: B 20 MET cc_start: 0.7640 (ppp) cc_final: 0.7420 (ppp) REVERT: B 65 HIS cc_start: 0.8110 (m-70) cc_final: 0.7652 (t-90) REVERT: B 78 GLU cc_start: 0.8401 (pt0) cc_final: 0.8135 (pp20) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.1660 time to fit residues: 15.2068 Evaluate side-chains 64 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 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 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 = 0.4268 r_free = 0.4268 target = 0.192033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134196 restraints weight = 5545.957| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.77 r_work: 0.3459 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5172 Z= 0.162 Angle : 0.606 18.117 7034 Z= 0.280 Chirality : 0.041 0.131 838 Planarity : 0.003 0.034 878 Dihedral : 5.000 20.671 686 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.27 % Allowed : 16.49 % 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: -2.69 (0.33), residues: 642 helix: -1.76 (0.28), residues: 352 sheet: 0.87 (0.85), residues: 46 loop : -2.17 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 375 HIS 0.002 0.001 HIS A 373 PHE 0.010 0.001 PHE A 94 TYR 0.013 0.001 TYR B 270 ARG 0.004 0.000 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.49 seconds wall clock time: 64 minutes 8.05 seconds (3848.05 seconds total)