Starting phenix.real_space_refine on Wed Aug 5 03:24:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ene_19832/08_2026/9ene_19832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ene_19832/08_2026/9ene_19832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ene_19832/08_2026/9ene_19832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ene_19832/08_2026/9ene_19832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ene_19832/08_2026/9ene_19832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ene_19832/08_2026/9ene_19832.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 144 5.49 5 S 36 5.16 5 C 4824 2.51 5 N 1494 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8484 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2686 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 15, 'TRANS': 313} Chain breaks: 3 Chain: "B" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2686 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 15, 'TRANS': 313} Chain breaks: 3 Chain: "C" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 61} Chain: "D" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 61} Time building chain proxies: 1.81, per 1000 atoms: 0.21 Number of scatterers: 8484 At special positions: 0 Unit cell: (102.34, 152.22, 68.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 144 15.00 O 1986 8.00 N 1494 7.00 C 4824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.62 Conformation dependent library (CDL) restraints added in 176.3 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: 1248 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 34.5% alpha, 16.1% beta 44 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.590A pdb=" N ALA A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.513A pdb=" N SER A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN A 110 " --> pdb=" O GLN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 168 removed outlier: 3.655A pdb=" N ARG A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 214 through 217 removed outlier: 3.505A pdb=" N VAL A 217 " --> pdb=" O GLN A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 277 through 291 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.625A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 370 removed outlier: 3.944A pdb=" N LYS A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.720A pdb=" N ALA B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 88 through 100 removed outlier: 4.230A pdb=" N LYS B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 4.321A pdb=" N ASN B 110 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.749A pdb=" N ARG B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 214 through 217 removed outlier: 3.758A pdb=" N VAL B 217 " --> pdb=" O GLN B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 214 through 217' Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.557A pdb=" N CYS B 281 " --> pdb=" O HIS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.610A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 368 removed outlier: 3.510A pdb=" N GLU B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 Processing helix chain 'B' and resid 398 through 402 removed outlier: 4.398A pdb=" N ALA B 401 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.652A pdb=" N GLY A 61 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 removed outlier: 6.413A pdb=" N TYR A 71 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE A 124 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP A 326 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN A 126 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N LYS A 328 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 194 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N CYS A 327 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 192 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 269 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLN A 266 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL A 246 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU A 268 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA A 244 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 270 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.714A pdb=" N GLY B 61 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 174 removed outlier: 6.511A pdb=" N TYR B 71 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE B 124 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP B 326 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN B 126 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS B 328 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR B 194 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N CYS B 327 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU B 192 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 269 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 243 " --> pdb=" O THR B 270 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1020 1.27 - 1.40: 2627 1.40 - 1.54: 4958 1.54 - 1.67: 315 1.67 - 1.81: 58 Bond restraints: 8978 Sorted by residual: bond pdb=" C CYS A 226 " pdb=" O CYS A 226 " ideal model delta sigma weight residual 1.234 1.133 0.102 1.20e-02 6.94e+03 7.19e+01 bond pdb=" C CYS A 226 " pdb=" N LYS A 227 " ideal model delta sigma weight residual 1.334 1.389 -0.056 1.79e-02 3.12e+03 9.62e+00 bond pdb=" N VAL A 230 " pdb=" CA VAL A 230 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.57e+00 bond pdb=" N MET A 228 " pdb=" CA MET A 228 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.27e-02 6.20e+03 6.75e+00 bond pdb=" N LYS A 227 " pdb=" CA LYS A 227 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.55e+00 ... (remaining 8973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.56: 12838 5.56 - 11.13: 9 11.13 - 16.69: 1 16.69 - 22.26: 1 22.26 - 27.82: 1 Bond angle restraints: 12850 Sorted by residual: angle pdb=" O CYS A 226 " pdb=" C CYS A 226 " pdb=" N LYS A 227 " ideal model delta sigma weight residual 122.92 109.61 13.31 1.17e+00 7.31e-01 1.29e+02 angle pdb=" O3' A D 38 " pdb=" P U D 39 " pdb=" OP1 U D 39 " ideal model delta sigma weight residual 108.00 80.18 27.82 3.00e+00 1.11e-01 8.60e+01 angle pdb=" O3' A D 38 " pdb=" P U D 39 " pdb=" OP2 U D 39 " ideal model delta sigma weight residual 108.00 85.94 22.06 3.00e+00 1.11e-01 5.41e+01 angle pdb=" CA CYS A 226 " pdb=" C CYS A 226 " pdb=" N LYS A 227 " ideal model delta sigma weight residual 115.67 106.99 8.68 1.36e+00 5.41e-01 4.08e+01 angle pdb=" C1' C D 66 " pdb=" N1 C D 66 " pdb=" C2 C D 66 " ideal model delta sigma weight residual 118.80 123.95 -5.15 1.10e+00 8.26e-01 2.19e+01 ... (remaining 12845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.86: 4502 18.86 - 37.73: 603 37.73 - 56.59: 225 56.59 - 75.45: 239 75.45 - 94.32: 21 Dihedral angle restraints: 5590 sinusoidal: 3664 harmonic: 1926 Sorted by residual: dihedral pdb=" O4' U C 40 " pdb=" C1' U C 40 " pdb=" N1 U C 40 " pdb=" C2 U C 40 " ideal model delta sinusoidal sigma weight residual -128.00 -56.88 -71.12 1 1.70e+01 3.46e-03 2.25e+01 dihedral pdb=" O4' U D 40 " pdb=" C1' U D 40 " pdb=" N1 U D 40 " pdb=" C2 U D 40 " ideal model delta sinusoidal sigma weight residual -128.00 -60.45 -67.55 1 1.70e+01 3.46e-03 2.05e+01 dihedral pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N ILE B 69 " pdb=" CA ILE B 69 " ideal model delta harmonic sigma weight residual 180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 1519 0.401 - 0.801: 0 0.801 - 1.202: 0 1.202 - 1.602: 0 1.602 - 2.003: 1 Chirality restraints: 1520 Sorted by residual: chirality pdb=" P U D 39 " pdb=" OP1 U D 39 " pdb=" OP2 U D 39 " pdb=" O5' U D 39 " both_signs ideal model delta sigma weight residual True 2.41 0.41 2.00 2.00e-01 2.50e+01 1.00e+02 chirality pdb=" CA PHE A 320 " pdb=" N PHE A 320 " pdb=" C PHE A 320 " pdb=" CB PHE A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA PHE B 320 " pdb=" N PHE B 320 " pdb=" C PHE B 320 " pdb=" CB PHE B 320 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 1517 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 226 " 0.084 2.00e-02 2.50e+03 1.69e-01 2.87e+02 pdb=" C CYS A 226 " -0.292 2.00e-02 2.50e+03 pdb=" O CYS A 226 " 0.124 2.00e-02 2.50e+03 pdb=" N LYS A 227 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 18 " 0.025 2.00e-02 2.50e+03 1.07e-02 3.43e+00 pdb=" N9 G D 18 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G D 18 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G D 18 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G D 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G D 18 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G D 18 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G D 18 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G D 18 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G D 18 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G D 18 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G D 18 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 18 " -0.025 2.00e-02 2.50e+03 1.06e-02 3.40e+00 pdb=" N9 G C 18 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G C 18 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G C 18 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G C 18 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G C 18 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G C 18 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G C 18 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G C 18 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 18 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 18 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G C 18 " 0.003 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1664 2.77 - 3.30: 7418 3.30 - 3.83: 15035 3.83 - 4.37: 17014 4.37 - 4.90: 26709 Nonbonded interactions: 67840 Sorted by model distance: nonbonded pdb=" N7 G D 22 " pdb=" N2 G D 46 " model vdw 2.233 2.560 nonbonded pdb=" N7 G C 22 " pdb=" N2 G C 46 " model vdw 2.233 2.560 nonbonded pdb=" OH TYR B 197 " pdb=" O VAL B 318 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 197 " pdb=" O VAL A 318 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU A 294 " pdb=" OH TYR A 411 " model vdw 2.236 3.040 ... (remaining 67835 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.310 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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 : 0.004 0.102 8978 Z= 0.276 Angle : 0.772 27.822 12850 Z= 0.525 Chirality : 0.074 2.003 1520 Planarity : 0.006 0.169 1108 Dihedral : 22.563 94.318 4342 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.04 % Allowed : 25.43 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.32), residues: 642 helix: 1.27 (0.40), residues: 176 sheet: -0.57 (0.58), residues: 64 loop : -1.40 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 166 TYR 0.013 0.001 TYR A 276 PHE 0.017 0.001 PHE A 320 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.28 ( 8978) covalent geometry : angle 0.77217 / 0.53 (12850) hydrogen bonds : bond 0.18488 / 12.67 ( 303) hydrogen bonds : angle 5.01962 / 3.48 ( 692) *********************** 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 40 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.147 Fit side-chains REVERT: B 293 MET cc_start: 0.8314 (ptp) cc_final: 0.8060 (ptp) REVERT: B 361 MET cc_start: 0.9179 (ttm) cc_final: 0.8937 (ttm) outliers start: 6 outliers final: 1 residues processed: 37 average time/residue: 0.0914 time to fit residues: 4.6175 Evaluate side-chains 30 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 HIS A 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.085700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059507 restraints weight = 22761.954| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.58 r_work: 0.2907 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8978 Z= 0.148 Angle : 0.612 27.059 12850 Z= 0.301 Chirality : 0.062 1.976 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.445 93.726 3019 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.56 % Allowed : 25.43 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.32), residues: 642 helix: 1.05 (0.39), residues: 184 sheet: -0.55 (0.58), residues: 60 loop : -1.45 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.014 0.001 TYR A 276 PHE 0.018 0.001 PHE B 320 TRP 0.008 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 8978) covalent geometry : angle 0.61161 / 0.30 (12850) hydrogen bonds : bond 0.06791 / 4.56 ( 303) hydrogen bonds : angle 4.01864 / 2.83 ( 692) *********************** 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 38 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.233 Fit side-chains REVERT: B 293 MET cc_start: 0.8346 (ptp) cc_final: 0.8114 (ptp) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.0518 time to fit residues: 3.0705 Evaluate side-chains 34 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 300 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.085026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058694 restraints weight = 22829.915| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.59 r_work: 0.2888 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8978 Z= 0.201 Angle : 0.630 27.182 12850 Z= 0.307 Chirality : 0.063 1.973 1520 Planarity : 0.004 0.044 1108 Dihedral : 22.389 93.794 3018 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.94 % Allowed : 25.09 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.32), residues: 642 helix: 0.94 (0.39), residues: 184 sheet: -0.69 (0.59), residues: 60 loop : -1.47 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.012 0.002 TYR B 276 PHE 0.019 0.002 PHE A 320 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 8978) covalent geometry : angle 0.62976 / 0.31 (12850) hydrogen bonds : bond 0.06927 / 4.65 ( 303) hydrogen bonds : angle 3.94741 / 2.79 ( 692) *********************** 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 46 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.266 Fit side-chains REVERT: A 163 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8996 (mp) outliers start: 17 outliers final: 11 residues processed: 44 average time/residue: 0.0654 time to fit residues: 4.3458 Evaluate side-chains 40 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.085089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058446 restraints weight = 23105.875| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.60 r_work: 0.2878 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8978 Z= 0.201 Angle : 0.628 27.371 12850 Z= 0.306 Chirality : 0.063 1.974 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.323 93.539 3018 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 4.15 % Allowed : 24.05 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.32), residues: 642 helix: 0.94 (0.39), residues: 182 sheet: -0.72 (0.59), residues: 60 loop : -1.54 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 116 TYR 0.022 0.002 TYR A 276 PHE 0.019 0.002 PHE A 320 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 8978) covalent geometry : angle 0.62773 / 0.31 (12850) hydrogen bonds : bond 0.06718 / 4.49 ( 303) hydrogen bonds : angle 3.89156 / 2.75 ( 692) *********************** 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 52 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 28 time to evaluate : 0.171 Fit side-chains REVERT: A 163 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9000 (mp) outliers start: 24 outliers final: 18 residues processed: 51 average time/residue: 0.0607 time to fit residues: 4.7058 Evaluate side-chains 47 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.086588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060031 restraints weight = 23016.267| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.61 r_work: 0.2918 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8978 Z= 0.112 Angle : 0.572 27.207 12850 Z= 0.275 Chirality : 0.061 1.992 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.224 93.409 3018 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.29 % Allowed : 23.70 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.32), residues: 642 helix: 1.11 (0.40), residues: 182 sheet: -0.28 (0.60), residues: 60 loop : -1.39 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 116 TYR 0.016 0.001 TYR B 276 PHE 0.017 0.001 PHE A 320 TRP 0.008 0.001 TRP B 352 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8978) covalent geometry : angle 0.57234 / 0.27 (12850) hydrogen bonds : bond 0.05433 / 3.67 ( 303) hydrogen bonds : angle 3.66348 / 2.57 ( 692) *********************** 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 48 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 29 time to evaluate : 0.182 Fit side-chains REVERT: A 163 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8937 (mp) REVERT: A 257 ARG cc_start: 0.8243 (tmt170) cc_final: 0.7956 (tmt170) REVERT: B 293 MET cc_start: 0.8323 (ptp) cc_final: 0.8087 (ptp) outliers start: 19 outliers final: 10 residues processed: 46 average time/residue: 0.0711 time to fit residues: 4.7447 Evaluate side-chains 40 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060352 restraints weight = 22863.818| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.60 r_work: 0.2928 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8978 Z= 0.113 Angle : 0.573 27.136 12850 Z= 0.273 Chirality : 0.061 1.992 1520 Planarity : 0.004 0.041 1108 Dihedral : 22.177 93.539 3018 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.11 % Allowed : 24.57 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.33), residues: 642 helix: 1.13 (0.40), residues: 182 sheet: -0.11 (0.62), residues: 60 loop : -1.31 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 257 TYR 0.013 0.001 TYR A 276 PHE 0.017 0.001 PHE A 320 TRP 0.010 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8978) covalent geometry : angle 0.57255 / 0.27 (12850) hydrogen bonds : bond 0.05295 / 3.57 ( 303) hydrogen bonds : angle 3.59135 / 2.52 ( 692) *********************** 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 47 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.227 Fit side-chains REVERT: A 116 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8122 (ptp-170) REVERT: A 163 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8925 (mp) REVERT: A 257 ARG cc_start: 0.8265 (tmt170) cc_final: 0.7890 (tmt170) REVERT: B 257 ARG cc_start: 0.8382 (mmp80) cc_final: 0.8055 (mmp80) outliers start: 18 outliers final: 10 residues processed: 45 average time/residue: 0.0678 time to fit residues: 4.4410 Evaluate side-chains 40 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.0270 chunk 6 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.0470 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060127 restraints weight = 23158.476| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.62 r_work: 0.2924 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8978 Z= 0.128 Angle : 0.577 27.189 12850 Z= 0.275 Chirality : 0.061 1.989 1520 Planarity : 0.004 0.041 1108 Dihedral : 22.146 93.584 3018 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.94 % Allowed : 24.91 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.33), residues: 642 helix: 1.12 (0.40), residues: 182 sheet: -0.17 (0.62), residues: 60 loop : -1.27 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 257 TYR 0.014 0.001 TYR A 276 PHE 0.018 0.001 PHE A 320 TRP 0.008 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8978) covalent geometry : angle 0.57734 / 0.28 (12850) hydrogen bonds : bond 0.05371 / 3.62 ( 303) hydrogen bonds : angle 3.60495 / 2.53 ( 692) *********************** 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 47 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.197 Fit side-chains REVERT: A 163 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8943 (mp) REVERT: A 257 ARG cc_start: 0.8267 (tmt170) cc_final: 0.7930 (tmt170) REVERT: B 257 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8142 (mmp80) outliers start: 17 outliers final: 13 residues processed: 46 average time/residue: 0.0783 time to fit residues: 5.1460 Evaluate side-chains 43 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.085540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059154 restraints weight = 22883.945| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.57 r_work: 0.2888 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8978 Z= 0.205 Angle : 0.628 27.443 12850 Z= 0.303 Chirality : 0.063 1.972 1520 Planarity : 0.004 0.043 1108 Dihedral : 22.150 93.316 3018 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.63 % Allowed : 24.22 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.33), residues: 642 helix: 1.00 (0.40), residues: 182 sheet: -0.51 (0.61), residues: 60 loop : -1.36 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 257 TYR 0.019 0.002 TYR A 276 PHE 0.019 0.002 PHE B 320 TRP 0.007 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 ( 8978) covalent geometry : angle 0.62755 / 0.30 (12850) hydrogen bonds : bond 0.06380 / 4.26 ( 303) hydrogen bonds : angle 3.81270 / 2.67 ( 692) *********************** 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 50 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 29 time to evaluate : 0.250 Fit side-chains REVERT: A 163 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9009 (mp) REVERT: A 257 ARG cc_start: 0.8353 (tmt170) cc_final: 0.8019 (tmt170) REVERT: B 257 ARG cc_start: 0.8463 (mmp80) cc_final: 0.8233 (mmp80) REVERT: B 331 ASN cc_start: 0.8449 (m-40) cc_final: 0.8239 (p0) outliers start: 21 outliers final: 15 residues processed: 49 average time/residue: 0.0659 time to fit residues: 4.7729 Evaluate side-chains 45 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.085696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059097 restraints weight = 23114.931| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.59 r_work: 0.2895 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8978 Z= 0.186 Angle : 0.615 27.436 12850 Z= 0.297 Chirality : 0.063 1.984 1520 Planarity : 0.004 0.043 1108 Dihedral : 22.144 92.675 3018 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.94 % Allowed : 24.91 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.32), residues: 642 helix: 0.91 (0.39), residues: 182 sheet: -0.52 (0.61), residues: 60 loop : -1.37 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 257 TYR 0.018 0.002 TYR A 276 PHE 0.019 0.001 PHE A 320 TRP 0.007 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 8978) covalent geometry : angle 0.61544 / 0.30 (12850) hydrogen bonds : bond 0.06229 / 4.16 ( 303) hydrogen bonds : angle 3.76974 / 2.64 ( 692) *********************** 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 46 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.165 Fit side-chains REVERT: A 163 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9001 (mp) REVERT: A 257 ARG cc_start: 0.8309 (tmt170) cc_final: 0.7970 (tmt170) REVERT: B 257 ARG cc_start: 0.8479 (mmp80) cc_final: 0.8266 (mmp80) outliers start: 17 outliers final: 15 residues processed: 45 average time/residue: 0.0727 time to fit residues: 4.8886 Evaluate side-chains 45 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.086925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060690 restraints weight = 22865.198| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.58 r_work: 0.2927 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8978 Z= 0.114 Angle : 0.575 27.262 12850 Z= 0.274 Chirality : 0.061 1.995 1520 Planarity : 0.004 0.041 1108 Dihedral : 22.081 92.456 3018 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.25 % Allowed : 25.61 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.33), residues: 642 helix: 0.98 (0.40), residues: 182 sheet: -0.24 (0.61), residues: 60 loop : -1.31 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 257 TYR 0.014 0.001 TYR A 276 PHE 0.017 0.001 PHE A 320 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8978) covalent geometry : angle 0.57518 / 0.27 (12850) hydrogen bonds : bond 0.05267 / 3.54 ( 303) hydrogen bonds : angle 3.60634 / 2.51 ( 692) ********************** 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 43 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.144 Fit side-chains REVERT: A 163 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 257 ARG cc_start: 0.8285 (tmt170) cc_final: 0.7922 (tmt170) REVERT: B 257 ARG cc_start: 0.8455 (mmp80) cc_final: 0.8229 (mmp80) outliers start: 13 outliers final: 10 residues processed: 43 average time/residue: 0.0760 time to fit residues: 4.7958 Evaluate side-chains 41 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.086497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060071 restraints weight = 22894.609| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.60 r_work: 0.2915 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8978 Z= 0.146 Angle : 0.589 27.291 12850 Z= 0.282 Chirality : 0.062 1.990 1520 Planarity : 0.004 0.043 1108 Dihedral : 22.063 92.440 3018 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.60 % Allowed : 25.26 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.33), residues: 642 helix: 0.96 (0.39), residues: 182 sheet: -0.26 (0.61), residues: 60 loop : -1.28 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 257 TYR 0.017 0.001 TYR B 216 PHE 0.018 0.001 PHE A 320 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8978) covalent geometry : angle 0.58884 / 0.28 (12850) hydrogen bonds : bond 0.05607 / 3.75 ( 303) hydrogen bonds : angle 3.63111 / 2.54 ( 692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.13 seconds wall clock time: 28 minutes 23.51 seconds (1703.51 seconds total)