Starting phenix.real_space_refine on Wed Sep 17 11:28:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ene_19832/09_2025/9ene_19832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ene_19832/09_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_19832/09_2025/9ene_19832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ene_19832/09_2025/9ene_19832.map" model { file = "/net/cci-nas-00/data/ceres_data/9ene_19832/09_2025/9ene_19832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ene_19832/09_2025/9ene_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 2.02, per 1000 atoms: 0.24 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: 0.82 Conformation dependent library (CDL) restraints added in 142.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 34.5% alpha, 16.1% beta 44 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 1.15 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: 1.24 Time building geometry restraints manager: 1.06 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: 0.01 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: 3.430 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.370 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.350 ------------------------------------------------------------------------------- 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= 0.208 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00412 ( 8978) covalent geometry : angle 0.64249 (12850) hydrogen bonds : bond 0.18488 ( 303) hydrogen bonds : angle 5.01962 ( 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 : 0.226 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: 0.1249 time to fit residues: 6.3539 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 : 0.235 ------------------------------------------------------------------------------- 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: 7.9990 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... 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 = 0.3661 r_free = 0.3661 target = 0.085568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059335 restraints weight = 22750.119| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.61 r_work: 0.2902 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8978 Z= 0.172 Angle : 0.625 27.779 12850 Z= 0.293 Chirality : 0.063 2.017 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.451 95.517 3019 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.73 % Allowed : 25.61 % Favored : 72.66 % 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 aren not related in a simple way. whole: -0.87 (0.33), residues: 642 helix: 1.05 (0.39), residues: 184 sheet: -0.67 (0.59), residues: 60 loop : -1.42 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.014 0.001 TYR A 276 PHE 0.018 0.001 PHE A 320 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8978) covalent geometry : angle 0.62515 (12850) hydrogen bonds : bond 0.06005 ( 303) hydrogen bonds : angle 3.88482 ( 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 41 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.170 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 41 average time/residue: 0.1160 time to fit residues: 6.2967 Evaluate side-chains 36 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 249 VAL 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 74 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 18 optimal weight: 0.0470 chunk 64 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.084756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.058202 restraints weight = 22894.112| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.59 r_work: 0.2866 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8978 Z= 0.235 Angle : 0.661 27.804 12850 Z= 0.313 Chirality : 0.063 2.000 1520 Planarity : 0.004 0.046 1108 Dihedral : 22.396 95.134 3018 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.81 % Allowed : 24.05 % 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 aren not related in a simple way. whole: -1.04 (0.32), residues: 642 helix: 0.97 (0.39), residues: 182 sheet: -0.83 (0.59), residues: 60 loop : -1.54 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 257 TYR 0.019 0.002 TYR A 276 PHE 0.019 0.002 PHE A 320 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 8978) covalent geometry : angle 0.66054 (12850) hydrogen bonds : bond 0.06762 ( 303) hydrogen bonds : angle 3.93418 ( 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 52 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 30 time to evaluate : 0.250 Fit side-chains REVERT: A 163 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9049 (mp) REVERT: B 257 ARG cc_start: 0.8471 (mmp80) cc_final: 0.8233 (mmp80) outliers start: 22 outliers final: 14 residues processed: 50 average time/residue: 0.0996 time to fit residues: 6.9632 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 : 0.247 ------------------------------------------------------------------------------- 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 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 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 300 ASP Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 0.0070 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.087732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.061423 restraints weight = 22925.558| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.61 r_work: 0.2951 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1303 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= 0.099 Angle : 0.574 27.765 12850 Z= 0.261 Chirality : 0.062 2.038 1520 Planarity : 0.004 0.038 1108 Dihedral : 22.223 94.544 3018 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.56 % Allowed : 26.30 % 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 aren not related in a simple way. whole: -0.64 (0.33), residues: 642 helix: 1.25 (0.40), residues: 184 sheet: -0.29 (0.61), residues: 60 loop : -1.33 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 257 TYR 0.011 0.001 TYR B 276 PHE 0.016 0.001 PHE B 320 TRP 0.008 0.001 TRP B 352 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8978) covalent geometry : angle 0.57449 (12850) hydrogen bonds : bond 0.04443 ( 303) hydrogen bonds : angle 3.48733 ( 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 39 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.251 Fit side-chains REVERT: A 163 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8952 (mp) REVERT: A 257 ARG cc_start: 0.8270 (tmt170) cc_final: 0.7973 (tmt170) REVERT: B 257 ARG cc_start: 0.8490 (mmp80) cc_final: 0.8200 (mmp80) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 0.0948 time to fit residues: 5.3197 Evaluate side-chains 33 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 73 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.086014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059356 restraints weight = 23079.962| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.60 r_work: 0.2902 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8978 Z= 0.175 Angle : 0.609 27.892 12850 Z= 0.283 Chirality : 0.063 2.030 1520 Planarity : 0.004 0.045 1108 Dihedral : 22.236 94.726 3018 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.77 % Allowed : 24.74 % 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 aren not related in a simple way. whole: -0.74 (0.33), residues: 642 helix: 1.18 (0.40), residues: 182 sheet: -0.37 (0.62), residues: 60 loop : -1.39 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 257 TYR 0.013 0.001 TYR A 276 PHE 0.019 0.001 PHE A 320 TRP 0.007 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8978) covalent geometry : angle 0.60932 (12850) hydrogen bonds : bond 0.05607 ( 303) hydrogen bonds : angle 3.66815 ( 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 46 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.242 Fit side-chains REVERT: A 116 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7695 (ptp-170) REVERT: A 163 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9030 (mp) REVERT: B 257 ARG cc_start: 0.8509 (mmp80) cc_final: 0.8306 (mmp80) outliers start: 16 outliers final: 9 residues processed: 44 average time/residue: 0.0959 time to fit residues: 6.0263 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 : 0.227 ------------------------------------------------------------------------------- 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 163 ILE Chi-restraints excluded: chain A residue 191 LEU 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 279 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 overall best weight: 1.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3680 r_free = 0.3680 target = 0.087506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060948 restraints weight = 22724.646| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.58 r_work: 0.2928 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8978 Z= 0.121 Angle : 0.582 27.687 12850 Z= 0.266 Chirality : 0.062 2.047 1520 Planarity : 0.004 0.040 1108 Dihedral : 22.164 94.444 3018 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.42 % Allowed : 25.95 % 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 aren not related in a simple way. whole: -0.62 (0.33), residues: 642 helix: 1.24 (0.40), residues: 182 sheet: -0.21 (0.62), residues: 60 loop : -1.29 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 257 TYR 0.012 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 covalent geometry : bond 0.00266 ( 8978) covalent geometry : angle 0.58155 (12850) hydrogen bonds : bond 0.04884 ( 303) hydrogen bonds : angle 3.52364 ( 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 43 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.251 Fit side-chains REVERT: A 116 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7704 (ptp-170) REVERT: A 163 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8986 (mp) REVERT: A 257 ARG cc_start: 0.8260 (tmt170) cc_final: 0.8045 (tmt170) outliers start: 14 outliers final: 10 residues processed: 41 average time/residue: 0.0903 time to fit residues: 5.2083 Evaluate side-chains 40 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 46 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 0.0670 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.088402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.061801 restraints weight = 23150.360| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.68 r_work: 0.2949 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8978 Z= 0.099 Angle : 0.567 27.632 12850 Z= 0.256 Chirality : 0.062 2.054 1520 Planarity : 0.004 0.040 1108 Dihedral : 22.075 95.213 3018 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.25 % Allowed : 26.64 % Favored : 71.11 % 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 aren not related in a simple way. whole: -0.50 (0.33), residues: 642 helix: 1.25 (0.40), residues: 184 sheet: -0.39 (0.58), residues: 70 loop : -1.15 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 257 TYR 0.012 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 covalent geometry : bond 0.00214 ( 8978) covalent geometry : angle 0.56688 (12850) hydrogen bonds : bond 0.04264 ( 303) hydrogen bonds : angle 3.41189 ( 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 45 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.251 Fit side-chains REVERT: A 116 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7710 (ptp-170) REVERT: A 163 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8942 (mp) REVERT: A 257 ARG cc_start: 0.8264 (tmt170) cc_final: 0.7984 (tmt170) outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.1057 time to fit residues: 6.4520 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE 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 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 279 VAL Chi-restraints excluded: chain B residue 327 CYS 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: 1.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.085931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059191 restraints weight = 22743.783| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.64 r_work: 0.2893 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8978 Z= 0.181 Angle : 0.616 27.939 12850 Z= 0.286 Chirality : 0.063 2.035 1520 Planarity : 0.004 0.042 1108 Dihedral : 22.113 95.646 3018 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.94 % Allowed : 26.12 % Favored : 70.93 % 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 aren not related in a simple way. whole: -0.63 (0.33), residues: 642 helix: 1.23 (0.40), residues: 182 sheet: -0.24 (0.62), residues: 60 loop : -1.30 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 257 TYR 0.013 0.002 TYR B 216 PHE 0.019 0.001 PHE A 320 TRP 0.006 0.001 TRP B 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8978) covalent geometry : angle 0.61632 (12850) hydrogen bonds : bond 0.05679 ( 303) hydrogen bonds : angle 3.61918 ( 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 47 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 163 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9004 (mp) REVERT: A 409 ARG cc_start: 0.7664 (mtm180) cc_final: 0.7418 (mtm-85) outliers start: 17 outliers final: 14 residues processed: 45 average time/residue: 0.0856 time to fit residues: 5.5177 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 : 0.181 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 72 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.084071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.057260 restraints weight = 23176.009| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.64 r_work: 0.2843 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 8978 Z= 0.306 Angle : 0.711 28.540 12850 Z= 0.341 Chirality : 0.065 2.021 1520 Planarity : 0.005 0.046 1108 Dihedral : 22.319 97.107 3018 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.94 % Allowed : 26.12 % Favored : 70.93 % 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 aren not related in a simple way. whole: -1.10 (0.32), residues: 642 helix: 0.76 (0.39), residues: 182 sheet: -0.92 (0.57), residues: 64 loop : -1.48 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 63 TYR 0.020 0.002 TYR B 216 PHE 0.021 0.002 PHE A 320 TRP 0.006 0.001 TRP B 74 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00699 ( 8978) covalent geometry : angle 0.71131 (12850) hydrogen bonds : bond 0.07469 ( 303) hydrogen bonds : angle 3.97296 ( 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 45 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 28 time to evaluate : 0.167 Fit side-chains REVERT: B 293 MET cc_start: 0.8359 (ptp) cc_final: 0.8108 (ptp) outliers start: 17 outliers final: 13 residues processed: 44 average time/residue: 0.0784 time to fit residues: 5.1190 Evaluate side-chains 41 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain 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 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: 3.9990 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.087115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.060768 restraints weight = 22625.576| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.64 r_work: 0.2928 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8978 Z= 0.103 Angle : 0.581 27.343 12850 Z= 0.267 Chirality : 0.062 2.060 1520 Planarity : 0.004 0.044 1108 Dihedral : 22.114 95.318 3018 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.21 % Allowed : 27.85 % Favored : 70.93 % 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 aren not related in a simple way. whole: -0.73 (0.33), residues: 642 helix: 1.07 (0.40), residues: 182 sheet: -0.54 (0.57), residues: 70 loop : -1.28 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 257 TYR 0.012 0.001 TYR B 276 PHE 0.017 0.001 PHE A 320 TRP 0.010 0.001 TRP B 352 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8978) covalent geometry : angle 0.58127 (12850) hydrogen bonds : bond 0.04627 ( 303) hydrogen bonds : angle 3.46081 ( 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 36 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.262 Fit side-chains REVERT: A 163 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8965 (mp) REVERT: A 409 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7415 (mtm-85) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.1062 time to fit residues: 5.5172 Evaluate side-chains 36 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.087174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060618 restraints weight = 22819.728| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.64 r_work: 0.2928 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1659 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= 0.112 Angle : 0.582 27.659 12850 Z= 0.265 Chirality : 0.062 2.058 1520 Planarity : 0.004 0.044 1108 Dihedral : 22.049 94.894 3018 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.38 % Allowed : 27.85 % Favored : 70.76 % 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 aren not related in a simple way. whole: -0.56 (0.33), residues: 642 helix: 1.21 (0.40), residues: 182 sheet: -0.43 (0.58), residues: 70 loop : -1.19 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 280 TYR 0.013 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 covalent geometry : bond 0.00248 ( 8978) covalent geometry : angle 0.58176 (12850) hydrogen bonds : bond 0.04642 ( 303) hydrogen bonds : angle 3.43895 ( 692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.55 seconds wall clock time: 34 minutes 12.26 seconds (2052.26 seconds total)