Starting phenix.real_space_refine on Thu Jul 2 10:45:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ene_19832/07_2026/9ene_19832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ene_19832/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ene_19832/07_2026/9ene_19832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ene_19832/07_2026/9ene_19832.map" model { file = "/net/cci-nas-00/data/ceres_data/9ene_19832/07_2026/9ene_19832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ene_19832/07_2026/9ene_19832.cif" } 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-dev-6108/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: 0.60 Conformation dependent library (CDL) restraints added in 370.4 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: 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: 0.90 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: 1.14 Time building geometry restraints manager: 0.82 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: 2.850 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.900 Find NCS groups from input model: 0.100 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.250 ------------------------------------------------------------------------------- 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= 0.263 Angle : 0.643 27.822 12850 Z= 0.404 Chirality : 0.063 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 0.00412 / 0.26 ( 8978) covalent geometry : angle 0.64252 / 0.40 (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 : 0.156 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: 0.0972 time to fit residues: 4.8555 Evaluate side-chains 31 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.085522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059310 restraints weight = 22752.735| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.59 r_work: 0.2902 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8978 Z= 0.167 Angle : 0.611 27.509 12850 Z= 0.303 Chirality : 0.062 1.997 1520 Planarity : 0.004 0.043 1108 Dihedral : 22.565 95.058 3019 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.73 % Allowed : 25.78 % Favored : 72.49 % 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: -0.92 (0.32), residues: 642 helix: 1.02 (0.39), residues: 184 sheet: -0.60 (0.58), residues: 60 loop : -1.48 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 116 TYR 0.015 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 0.00370 / 0.17 ( 8978) covalent geometry : angle 0.61106 / 0.30 (12850) hydrogen bonds : bond 0.06765 / 4.53 ( 303) hydrogen bonds : angle 4.03614 / 2.85 ( 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 40 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.191 Fit side-chains REVERT: B 293 MET cc_start: 0.8367 (ptp) cc_final: 0.8141 (ptp) outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 0.0734 time to fit residues: 4.1771 Evaluate side-chains 36 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.084675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058369 restraints weight = 22718.133| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.59 r_work: 0.2884 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8978 Z= 0.219 Angle : 0.629 27.770 12850 Z= 0.311 Chirality : 0.063 1.987 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.525 95.208 3018 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.63 % Allowed : 24.74 % Favored : 71.63 % 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: 0.96 (0.39), residues: 182 sheet: -0.77 (0.58), residues: 60 loop : -1.54 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 116 TYR 0.012 0.002 TYR B 276 PHE 0.020 0.002 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 0.00501 / 0.22 ( 8978) covalent geometry : angle 0.62901 / 0.31 (12850) hydrogen bonds : bond 0.07027 / 4.71 ( 303) hydrogen bonds : angle 3.97515 / 2.81 ( 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 51 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.251 Fit side-chains REVERT: A 163 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9001 (mp) REVERT: B 293 MET cc_start: 0.8376 (ptp) cc_final: 0.8136 (ptp) outliers start: 21 outliers final: 15 residues processed: 49 average time/residue: 0.0700 time to fit residues: 4.9886 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 VAL 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 357 VAL 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: 2.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.086006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059672 restraints weight = 22990.025| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.62 r_work: 0.2918 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8978 Z= 0.134 Angle : 0.579 27.604 12850 Z= 0.281 Chirality : 0.062 2.023 1520 Planarity : 0.004 0.043 1108 Dihedral : 22.433 95.199 3018 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.11 % Allowed : 25.09 % 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: -0.88 (0.32), residues: 642 helix: 1.06 (0.40), residues: 182 sheet: -0.43 (0.59), residues: 60 loop : -1.47 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.018 0.001 TYR A 276 PHE 0.018 0.001 PHE A 320 TRP 0.007 0.001 TRP B 352 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8978) covalent geometry : angle 0.57894 / 0.28 (12850) hydrogen bonds : bond 0.05782 / 3.89 ( 303) hydrogen bonds : angle 3.74340 / 2.63 ( 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 48 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.274 Fit side-chains REVERT: A 163 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8940 (mp) REVERT: B 293 MET cc_start: 0.8374 (ptp) cc_final: 0.8119 (ptp) outliers start: 18 outliers final: 10 residues processed: 48 average time/residue: 0.0946 time to fit residues: 6.5347 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 : 0.251 ------------------------------------------------------------------------------- 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 163 ILE Chi-restraints excluded: chain A residue 191 LEU 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 327 CYS Chi-restraints excluded: chain B residue 364 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.086147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059831 restraints weight = 23000.702| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.60 r_work: 0.2924 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8978 Z= 0.125 Angle : 0.570 27.521 12850 Z= 0.275 Chirality : 0.062 2.027 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.368 95.283 3018 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.29 % Allowed : 24.22 % Favored : 72.49 % 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: 1.14 (0.40), residues: 182 sheet: -0.25 (0.61), residues: 60 loop : -1.39 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 116 TYR 0.015 0.001 TYR B 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 0.00276 / 0.12 ( 8978) covalent geometry : angle 0.57011 / 0.27 (12850) hydrogen bonds : bond 0.05519 / 3.72 ( 303) hydrogen bonds : angle 3.64599 / 2.56 ( 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 49 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.246 Fit side-chains REVERT: A 116 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8125 (ptp-170) REVERT: A 163 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8942 (mp) REVERT: A 257 ARG cc_start: 0.8271 (tmt170) cc_final: 0.7986 (tmt170) outliers start: 19 outliers final: 12 residues processed: 48 average time/residue: 0.1014 time to fit residues: 6.7795 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 161 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU 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 228 MET Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 364 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.0020 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.087276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061158 restraints weight = 22584.163| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.59 r_work: 0.2950 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8978 Z= 0.098 Angle : 0.558 27.637 12850 Z= 0.265 Chirality : 0.062 2.041 1520 Planarity : 0.004 0.039 1108 Dihedral : 22.302 95.472 3018 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.29 % Allowed : 24.91 % 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: -0.60 (0.33), residues: 642 helix: 1.20 (0.40), residues: 182 sheet: -0.05 (0.62), residues: 60 loop : -1.28 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 257 TYR 0.013 0.001 TYR B 276 PHE 0.016 0.001 PHE A 320 TRP 0.012 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 8978) covalent geometry : angle 0.55824 / 0.27 (12850) hydrogen bonds : bond 0.04821 / 3.26 ( 303) hydrogen bonds : angle 3.52559 / 2.47 ( 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 48 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 29 time to evaluate : 0.254 Fit side-chains REVERT: A 116 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8114 (ptp-170) REVERT: A 163 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8916 (mp) REVERT: A 257 ARG cc_start: 0.8217 (tmt170) cc_final: 0.7858 (tmt170) REVERT: A 409 ARG cc_start: 0.7961 (ptt180) cc_final: 0.7734 (mtm180) REVERT: B 257 ARG cc_start: 0.8427 (mmp80) cc_final: 0.8128 (mmp80) outliers start: 19 outliers final: 11 residues processed: 46 average time/residue: 0.1205 time to fit residues: 7.4984 Evaluate side-chains 42 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain A residue 163 ILE 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 279 VAL 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: 0.0770 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.088392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.061817 restraints weight = 23102.633| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.72 r_work: 0.2914 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8978 Z= 0.086 Angle : 0.549 27.681 12850 Z= 0.259 Chirality : 0.061 2.025 1520 Planarity : 0.004 0.039 1108 Dihedral : 22.253 95.756 3018 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -0.46 (0.33), residues: 642 helix: 1.22 (0.40), residues: 182 sheet: 0.13 (0.64), residues: 60 loop : -1.16 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 257 TYR 0.015 0.001 TYR B 276 PHE 0.016 0.001 PHE A 320 TRP 0.009 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.09 ( 8978) covalent geometry : angle 0.54878 / 0.26 (12850) hydrogen bonds : bond 0.04382 / 2.98 ( 303) hydrogen bonds : angle 3.49063 / 2.42 ( 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: 15 poor density : 32 time to evaluate : 0.256 Fit side-chains REVERT: A 116 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7832 (ptp-170) REVERT: A 163 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8829 (mp) REVERT: A 257 ARG cc_start: 0.8228 (tmt170) cc_final: 0.7808 (tmt170) outliers start: 15 outliers final: 11 residues processed: 46 average time/residue: 0.1169 time to fit residues: 7.3270 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 : 0.255 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain A residue 163 ILE 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 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 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: 10.0000 chunk 58 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.087780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061471 restraints weight = 22568.507| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.68 r_work: 0.2932 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8978 Z= 0.105 Angle : 0.558 27.508 12850 Z= 0.263 Chirality : 0.061 2.013 1520 Planarity : 0.004 0.038 1108 Dihedral : 22.216 96.005 3018 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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: -0.45 (0.33), residues: 642 helix: 1.26 (0.40), residues: 182 sheet: 0.10 (0.63), residues: 60 loop : -1.16 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 257 TYR 0.014 0.001 TYR A 216 PHE 0.016 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 0.00232 / 0.10 ( 8978) covalent geometry : angle 0.55827 / 0.26 (12850) hydrogen bonds : bond 0.04576 / 3.09 ( 303) hydrogen bonds : angle 3.46989 / 2.42 ( 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 46 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.264 Fit side-chains REVERT: A 116 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8054 (ptp-170) REVERT: A 163 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8871 (mp) REVERT: A 257 ARG cc_start: 0.8224 (tmt170) cc_final: 0.7848 (tmt170) outliers start: 17 outliers final: 14 residues processed: 45 average time/residue: 0.1082 time to fit residues: 6.7981 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 : 0.267 ------------------------------------------------------------------------------- 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 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 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 327 CYS Chi-restraints excluded: chain B residue 364 SER 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: 4.9990 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 11.9990 chunk 77 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.087196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060746 restraints weight = 22770.264| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.69 r_work: 0.2914 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8978 Z= 0.127 Angle : 0.568 27.538 12850 Z= 0.269 Chirality : 0.062 2.016 1520 Planarity : 0.004 0.039 1108 Dihedral : 22.197 96.113 3018 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.29 % Allowed : 24.57 % 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: -0.48 (0.33), residues: 642 helix: 1.20 (0.40), residues: 182 sheet: -0.02 (0.63), residues: 60 loop : -1.15 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.015 0.001 TYR A 276 PHE 0.018 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 0.00285 / 0.13 ( 8978) covalent geometry : angle 0.56796 / 0.27 (12850) hydrogen bonds : bond 0.05026 / 3.38 ( 303) hydrogen bonds : angle 3.52556 / 2.46 ( 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 49 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.200 Fit side-chains REVERT: A 116 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8064 (ptp-170) REVERT: A 163 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8911 (mp) REVERT: A 257 ARG cc_start: 0.8266 (tmt170) cc_final: 0.7890 (tmt170) REVERT: A 409 ARG cc_start: 0.7686 (mtm180) cc_final: 0.7445 (mtm-85) outliers start: 19 outliers final: 16 residues processed: 48 average time/residue: 0.1022 time to fit residues: 6.8140 Evaluate side-chains 48 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 116 ARG 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 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 Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 408 MET 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: 0.0070 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 overall best weight: 2.3804 ------------------------------------------------------------------------------- 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 = 0.086508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.059759 restraints weight = 22642.232| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.71 r_work: 0.2879 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8978 Z= 0.208 Angle : 0.621 27.544 12850 Z= 0.303 Chirality : 0.063 1.994 1520 Planarity : 0.004 0.040 1108 Dihedral : 22.215 95.558 3018 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % 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: -0.72 (0.33), residues: 642 helix: 1.08 (0.40), residues: 182 sheet: -0.42 (0.61), residues: 60 loop : -1.29 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 116 TYR 0.020 0.002 TYR B 216 PHE 0.021 0.002 PHE A 320 TRP 0.006 0.001 TRP A 352 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 ( 8978) covalent geometry : angle 0.62126 / 0.30 (12850) hydrogen bonds : bond 0.06255 / 4.17 ( 303) hydrogen bonds : angle 3.71139 / 2.61 ( 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 46 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.244 Fit side-chains REVERT: A 116 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7992 (ptp-170) REVERT: A 163 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8963 (mp) REVERT: B 331 ASN cc_start: 0.8490 (m-40) cc_final: 0.8233 (p0) outliers start: 17 outliers final: 14 residues processed: 45 average time/residue: 0.0927 time to fit residues: 5.9995 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 : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.087023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.060330 restraints weight = 22812.486| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.66 r_work: 0.2914 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8978 Z= 0.122 Angle : 0.575 27.472 12850 Z= 0.276 Chirality : 0.062 2.026 1520 Planarity : 0.004 0.038 1108 Dihedral : 22.200 95.536 3018 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.11 % Allowed : 24.91 % 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: -0.68 (0.33), residues: 642 helix: 1.04 (0.40), residues: 182 sheet: -0.27 (0.61), residues: 60 loop : -1.25 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.015 0.001 TYR A 276 PHE 0.017 0.001 PHE A 320 TRP 0.006 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8978) covalent geometry : angle 0.57521 / 0.28 (12850) hydrogen bonds : bond 0.05284 / 3.55 ( 303) hydrogen bonds : angle 3.59165 / 2.51 ( 692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.78 seconds wall clock time: 32 minutes 21.19 seconds (1941.19 seconds total)