Starting phenix.real_space_refine on Wed Jan 15 12:43:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ene_19832/01_2025/9ene_19832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ene_19832/01_2025/9ene_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_19832/01_2025/9ene_19832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ene_19832/01_2025/9ene_19832.map" model { file = "/net/cci-nas-00/data/ceres_data/9ene_19832/01_2025/9ene_19832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ene_19832/01_2025/9ene_19832.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.64, per 1000 atoms: 0.66 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: 2.25 Conformation dependent library (CDL) restraints added in 682.5 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 3.45 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: 3.01 Time building geometry restraints manager: 2.56 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=" O3' A D 38 " pdb=" P U D 39 " pdb=" O5' U D 39 " ideal model delta sigma weight residual 104.00 98.05 5.95 1.50e+00 4.44e-01 1.57e+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: 0.03 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: 2.950 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.290 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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= 0.271 Angle : 0.642 27.822 12850 Z= 0.321 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (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 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE A 320 TYR 0.013 0.001 TYR A 276 ARG 0.001 0.000 ARG B 166 *********************** 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 : 0.722 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: 0.2649 time to fit residues: 13.4102 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 : 0.696 ------------------------------------------------------------------------------- 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 65 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 266 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.086544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060466 restraints weight = 22839.038| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.60 r_work: 0.2934 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0898 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= 0.173 Angle : 0.600 27.751 12850 Z= 0.278 Chirality : 0.062 2.026 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.420 95.482 3019 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.38 % Allowed : 25.43 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.33), residues: 642 helix: 1.16 (0.39), residues: 184 sheet: -0.47 (0.59), residues: 60 loop : -1.35 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE B 320 TYR 0.011 0.001 TYR B 276 ARG 0.004 0.000 ARG B 116 *********************** 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 39 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.688 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 39 average time/residue: 0.2225 time to fit residues: 12.4314 Evaluate side-chains 35 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.084930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.058364 restraints weight = 23203.524| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.60 r_work: 0.2873 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0985 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= 0.334 Angle : 0.657 27.765 12850 Z= 0.311 Chirality : 0.063 2.003 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.387 95.156 3018 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.42 % Allowed : 25.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.32), residues: 642 helix: 0.98 (0.39), residues: 184 sheet: -0.77 (0.59), residues: 60 loop : -1.47 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.019 0.002 PHE A 320 TYR 0.020 0.002 TYR A 276 ARG 0.007 0.001 ARG B 257 *********************** 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 44 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.652 Fit side-chains REVERT: A 163 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9032 (mp) REVERT: B 257 ARG cc_start: 0.8515 (mmp80) cc_final: 0.8282 (mmp80) outliers start: 14 outliers final: 8 residues processed: 42 average time/residue: 0.2478 time to fit residues: 14.3339 Evaluate side-chains 39 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 408 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.085919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059377 restraints weight = 22902.339| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.60 r_work: 0.2901 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8978 Z= 0.228 Angle : 0.609 27.719 12850 Z= 0.283 Chirality : 0.062 2.023 1520 Planarity : 0.004 0.043 1108 Dihedral : 22.289 94.516 3018 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.77 % Allowed : 25.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.32), residues: 642 helix: 1.13 (0.39), residues: 182 sheet: -0.57 (0.60), residues: 60 loop : -1.44 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.018 0.001 PHE A 320 TYR 0.014 0.001 TYR A 276 ARG 0.005 0.000 ARG B 257 *********************** 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 46 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.669 Fit side-chains REVERT: A 163 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9004 (mp) outliers start: 16 outliers final: 10 residues processed: 45 average time/residue: 0.2317 time to fit residues: 14.5240 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 : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 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 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 46 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.084343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057652 restraints weight = 23026.129| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.64 r_work: 0.2851 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 8978 Z= 0.389 Angle : 0.683 28.119 12850 Z= 0.326 Chirality : 0.064 1.995 1520 Planarity : 0.005 0.047 1108 Dihedral : 22.372 96.498 3018 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.33 % Allowed : 23.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.32), residues: 642 helix: 0.82 (0.39), residues: 182 sheet: -0.98 (0.57), residues: 64 loop : -1.52 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.003 0.001 HIS A 112 PHE 0.021 0.002 PHE A 320 TYR 0.018 0.002 TYR A 276 ARG 0.006 0.001 ARG B 257 *********************** 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 55 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 30 time to evaluate : 0.724 Fit side-chains REVERT: A 163 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9044 (mp) REVERT: B 293 MET cc_start: 0.8353 (ptp) cc_final: 0.8096 (ptp) outliers start: 25 outliers final: 19 residues processed: 53 average time/residue: 0.1839 time to fit residues: 14.4299 Evaluate side-chains 49 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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 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 217 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.086289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059714 restraints weight = 22790.755| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.61 r_work: 0.2910 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8978 Z= 0.193 Angle : 0.599 27.627 12850 Z= 0.278 Chirality : 0.062 2.034 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.234 94.338 3018 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.60 % Allowed : 25.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.33), residues: 642 helix: 1.03 (0.40), residues: 182 sheet: -0.47 (0.61), residues: 60 loop : -1.41 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.002 0.001 HIS A 360 PHE 0.017 0.001 PHE B 320 TYR 0.012 0.001 TYR B 276 ARG 0.005 0.000 ARG B 257 *********************** 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 45 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.698 Fit side-chains REVERT: A 116 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7796 (ptp-170) REVERT: A 163 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8995 (mp) REVERT: B 293 MET cc_start: 0.8315 (ptp) cc_final: 0.8080 (ptp) outliers start: 15 outliers final: 9 residues processed: 45 average time/residue: 0.2048 time to fit residues: 13.1008 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 : 0.687 ------------------------------------------------------------------------------- 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 217 VAL 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 327 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.087830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.061495 restraints weight = 22965.705| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.59 r_work: 0.2954 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8978 Z= 0.140 Angle : 0.575 28.291 12850 Z= 0.260 Chirality : 0.061 2.013 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.119 93.565 3018 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.08 % Allowed : 26.64 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.33), residues: 642 helix: 1.12 (0.40), residues: 184 sheet: -0.12 (0.63), residues: 60 loop : -1.25 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.017 0.001 PHE A 320 TYR 0.012 0.001 TYR B 276 ARG 0.005 0.000 ARG B 257 *********************** 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 43 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.776 Fit side-chains REVERT: A 116 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7743 (ptp-170) REVERT: A 163 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8949 (mp) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.2422 time to fit residues: 14.4216 Evaluate side-chains 42 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.085137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.058513 restraints weight = 23141.573| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.63 r_work: 0.2873 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8978 Z= 0.339 Angle : 0.654 27.874 12850 Z= 0.309 Chirality : 0.063 1.995 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.223 96.379 3018 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.29 % Allowed : 25.26 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.33), residues: 642 helix: 0.91 (0.40), residues: 182 sheet: -0.48 (0.61), residues: 60 loop : -1.43 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 PHE 0.020 0.002 PHE A 320 TYR 0.020 0.002 TYR A 216 ARG 0.005 0.000 ARG B 116 *********************** 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 48 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 29 time to evaluate : 0.752 Fit side-chains REVERT: A 116 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8112 (ptp-170) REVERT: A 163 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9007 (mp) outliers start: 19 outliers final: 14 residues processed: 48 average time/residue: 0.2193 time to fit residues: 15.1296 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 : 0.755 ------------------------------------------------------------------------------- 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 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 286 LEU Chi-restraints excluded: chain B residue 327 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.0170 chunk 65 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.086320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059934 restraints weight = 23048.723| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.59 r_work: 0.2909 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1409 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= 0.215 Angle : 0.604 27.682 12850 Z= 0.280 Chirality : 0.062 2.025 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.162 95.018 3018 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.94 % Allowed : 25.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.33), residues: 642 helix: 0.92 (0.40), residues: 182 sheet: -0.35 (0.62), residues: 60 loop : -1.36 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 PHE 0.018 0.001 PHE A 320 TYR 0.013 0.001 TYR B 276 ARG 0.004 0.000 ARG B 116 *********************** 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 : 0.810 Fit side-chains REVERT: A 116 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7857 (ptp-170) REVERT: A 163 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8987 (mp) REVERT: A 257 ARG cc_start: 0.8401 (tmt170) cc_final: 0.8135 (tmt170) outliers start: 17 outliers final: 12 residues processed: 46 average time/residue: 0.2199 time to fit residues: 14.4230 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 : 0.730 ------------------------------------------------------------------------------- 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 286 LEU 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 38 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.060278 restraints weight = 22750.987| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.57 r_work: 0.2922 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8978 Z= 0.192 Angle : 0.597 27.580 12850 Z= 0.276 Chirality : 0.062 2.030 1520 Planarity : 0.004 0.043 1108 Dihedral : 22.127 94.661 3018 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.42 % Allowed : 26.12 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.33), residues: 642 helix: 1.01 (0.40), residues: 182 sheet: -0.28 (0.62), residues: 60 loop : -1.33 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.018 0.001 PHE A 320 TYR 0.017 0.001 TYR B 276 ARG 0.005 0.000 ARG B 116 ********************** 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: 14 poor density : 29 time to evaluate : 0.734 Fit side-chains REVERT: A 116 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7810 (ptp-170) REVERT: A 163 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8988 (mp) outliers start: 14 outliers final: 11 residues processed: 43 average time/residue: 0.2221 time to fit residues: 13.5802 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 : 0.719 ------------------------------------------------------------------------------- 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 327 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.086321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059743 restraints weight = 23056.885| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.68 r_work: 0.2899 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1493 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= 0.216 Angle : 0.605 27.738 12850 Z= 0.280 Chirality : 0.062 2.000 1520 Planarity : 0.004 0.043 1108 Dihedral : 22.115 94.948 3018 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.77 % Allowed : 25.78 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.33), residues: 642 helix: 1.06 (0.40), residues: 182 sheet: -0.32 (0.62), residues: 60 loop : -1.34 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 PHE 0.018 0.001 PHE A 320 TYR 0.016 0.001 TYR B 276 ARG 0.005 0.000 ARG B 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.67 seconds wall clock time: 69 minutes 55.92 seconds (4195.92 seconds total)