Starting phenix.real_space_refine on Thu Jul 2 10:52:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l5y_62848/07_2026/9l5y_62848.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l5y_62848/07_2026/9l5y_62848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l5y_62848/07_2026/9l5y_62848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l5y_62848/07_2026/9l5y_62848.map" model { file = "/net/cci-nas-00/data/ceres_data/9l5y_62848/07_2026/9l5y_62848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l5y_62848/07_2026/9l5y_62848.cif" } resolution = 3.81 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= 0.013 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 34 5.49 5 S 12 5.16 5 C 5039 2.51 5 N 1443 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8123 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3691 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 440} Chain breaks: 2 Chain: "B" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3702 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 19, 'TRANS': 441} Chain breaks: 1 Chain: "D" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 386 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain breaks: 1 Chain: "F" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 344 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna3p': 15} Chain breaks: 1 Time building chain proxies: 1.57, per 1000 atoms: 0.19 Number of scatterers: 8123 At special positions: 0 Unit cell: (175.497, 99.736, 68.089, 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 12 16.00 P 34 15.00 O 1595 8.00 N 1443 7.00 C 5039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 345.3 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 3 sheets defined 67.9% alpha, 4.6% beta 12 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.970A pdb=" N SER A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.799A pdb=" N ALA A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.542A pdb=" N MET A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 238 through 251 removed outlier: 5.034A pdb=" N ASN A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN A 247 " --> pdb=" O ARG A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.864A pdb=" N ARG A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.555A pdb=" N TYR A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.506A pdb=" N SER A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 355 Processing helix chain 'A' and resid 369 through 372 removed outlier: 3.684A pdb=" N THR A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.610A pdb=" N ALA A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 36 through 39 removed outlier: 3.529A pdb=" N PHE B 39 " --> pdb=" O SER B 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 39' Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.557A pdb=" N VAL B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.543A pdb=" N THR B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 133 removed outlier: 3.625A pdb=" N GLU B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.617A pdb=" N ASP B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.508A pdb=" N HIS B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.620A pdb=" N SER B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 209 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 225 through 236 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 238 through 251 removed outlier: 5.192A pdb=" N ASN B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN B 247 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 251 " --> pdb=" O ASN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 255 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.532A pdb=" N TYR B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 338 through 355 removed outlier: 3.560A pdb=" N ALA B 342 " --> pdb=" O HIS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.586A pdb=" N ALA B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 466 through 477 removed outlier: 4.063A pdb=" N VAL B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 4.486A pdb=" N PHE B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.710A pdb=" N THR A 317 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TRP A 359 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE A 319 " --> pdb=" O TRP A 359 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE A 361 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL A 321 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 414 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 411 " --> pdb=" O HIS A 440 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE A 442 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE A 413 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 439 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 365 through 367 removed outlier: 6.660A pdb=" N THR B 317 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TRP B 359 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N PHE B 319 " --> pdb=" O TRP B 359 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE B 361 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL B 321 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 411 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 414 through 415 386 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2466 1.34 - 1.45: 1383 1.45 - 1.57: 4430 1.57 - 1.69: 64 1.69 - 1.81: 24 Bond restraints: 8367 Sorted by residual: bond pdb=" CG GLN B 366 " pdb=" CD GLN B 366 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.38e+00 bond pdb=" CB ARG A 184 " pdb=" CG ARG A 184 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CA ILE B 413 " pdb=" CB ILE B 413 " ideal model delta sigma weight residual 1.531 1.543 -0.012 1.11e-02 8.12e+03 1.21e+00 bond pdb=" N9 G D 11 " pdb=" C4 G D 11 " ideal model delta sigma weight residual 1.375 1.384 -0.009 8.00e-03 1.56e+04 1.13e+00 bond pdb=" C2 C F 10 " pdb=" N3 C F 10 " ideal model delta sigma weight residual 1.353 1.361 -0.008 8.00e-03 1.56e+04 1.13e+00 ... (remaining 8362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 11307 2.62 - 5.25: 150 5.25 - 7.87: 22 7.87 - 10.49: 5 10.49 - 13.12: 2 Bond angle restraints: 11486 Sorted by residual: angle pdb=" CA MET B 327 " pdb=" CB MET B 327 " pdb=" CG MET B 327 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" N ALA B 362 " pdb=" CA ALA B 362 " pdb=" C ALA B 362 " ideal model delta sigma weight residual 112.72 107.16 5.56 1.28e+00 6.10e-01 1.89e+01 angle pdb=" CA ARG B 105 " pdb=" CB ARG B 105 " pdb=" CG ARG B 105 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA LEU B 187 " pdb=" CB LEU B 187 " pdb=" CG LEU B 187 " ideal model delta sigma weight residual 116.30 129.42 -13.12 3.50e+00 8.16e-02 1.40e+01 angle pdb=" CA GLU A 183 " pdb=" CB GLU A 183 " pdb=" CG GLU A 183 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 ... (remaining 11481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4235 17.94 - 35.89: 577 35.89 - 53.83: 173 53.83 - 71.78: 65 71.78 - 89.72: 27 Dihedral angle restraints: 5077 sinusoidal: 2403 harmonic: 2674 Sorted by residual: dihedral pdb=" CA HIS A 338 " pdb=" C HIS A 338 " pdb=" N MET A 339 " pdb=" CA MET A 339 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA LEU B 304 " pdb=" C LEU B 304 " pdb=" N GLU B 305 " pdb=" CA GLU B 305 " ideal model delta harmonic sigma weight residual 180.00 155.08 24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE B 361 " pdb=" C PHE B 361 " pdb=" N ALA B 362 " pdb=" CA ALA B 362 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 812 0.031 - 0.062: 336 0.062 - 0.093: 98 0.093 - 0.123: 43 0.123 - 0.154: 14 Chirality restraints: 1303 Sorted by residual: chirality pdb=" CG LEU A 38 " pdb=" CB LEU A 38 " pdb=" CD1 LEU A 38 " pdb=" CD2 LEU A 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA PRO A 423 " pdb=" N PRO A 423 " pdb=" C PRO A 423 " pdb=" CB PRO A 423 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CG LEU B 126 " pdb=" CB LEU B 126 " pdb=" CD1 LEU B 126 " pdb=" CD2 LEU B 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1300 not shown) Planarity restraints: 1333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 366 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" CD GLN B 366 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN B 366 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN B 366 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 463 " 0.011 2.00e-02 2.50e+03 1.19e-02 3.53e+00 pdb=" CG TRP A 463 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 463 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 463 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 463 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 463 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 463 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 463 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 463 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 463 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 89 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ALA B 89 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA B 89 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 90 " -0.011 2.00e-02 2.50e+03 ... (remaining 1330 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3378 2.93 - 3.42: 8956 3.42 - 3.92: 14649 3.92 - 4.41: 16291 4.41 - 4.90: 24517 Nonbonded interactions: 67791 Sorted by model distance: nonbonded pdb=" O ASN B 99 " pdb=" OD1 ASN B 99 " model vdw 2.438 3.040 nonbonded pdb=" O SER B 405 " pdb=" OG SER B 405 " model vdw 2.468 3.040 nonbonded pdb=" N1 A F 12 " pdb=" O6 G F 51 " model vdw 2.502 2.496 nonbonded pdb=" OD1 ASN B 99 " pdb=" OE2 GLU B 103 " model vdw 2.519 3.040 nonbonded pdb=" O SER A 405 " pdb=" OG SER A 405 " model vdw 2.556 3.040 ... (remaining 67786 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 25 through 117 or resid 119 through 492)) } ncs_group { reference = (chain 'D' and resid 8 through 55) selection = chain 'F' } 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 group one per residue 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: 2.050 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.090 Find NCS groups from input model: 0.120 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 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 : 0.003 0.046 8367 Z= 0.160 Angle : 0.769 13.119 11486 Z= 0.441 Chirality : 0.041 0.154 1303 Planarity : 0.005 0.056 1333 Dihedral : 19.336 89.721 3351 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.56 % Allowed : 28.34 % Favored : 68.11 % 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 are not related in a simple way. whole: -0.80 (0.27), residues: 911 helix: 0.03 (0.22), residues: 547 sheet: -2.58 (0.61), residues: 62 loop : -0.86 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 105 TYR 0.024 0.002 TYR B 128 PHE 0.020 0.002 PHE A 56 TRP 0.032 0.002 TRP A 463 HIS 0.012 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 ( 8367) covalent geometry : angle 0.76921 / 0.44 (11486) hydrogen bonds : bond 0.12874 / 8.84 ( 417) hydrogen bonds : angle 6.44303 / 4.51 ( 1186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.7152 (t0) cc_final: 0.6817 (t0) REVERT: B 77 TYR cc_start: 0.5035 (OUTLIER) cc_final: 0.2495 (p90) REVERT: B 99 ASN cc_start: 0.8087 (t0) cc_final: 0.7772 (t0) REVERT: B 105 ARG cc_start: 0.6959 (tpt90) cc_final: 0.6672 (tpt90) REVERT: B 137 ARG cc_start: 0.7442 (mmp80) cc_final: 0.6270 (tpp80) REVERT: B 209 MET cc_start: -0.0028 (OUTLIER) cc_final: -0.1101 (tpt) REVERT: B 472 GLU cc_start: 0.5150 (tm-30) cc_final: 0.4695 (tt0) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.1052 time to fit residues: 18.5849 Evaluate side-chains 123 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS B 99 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.241077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.209810 restraints weight = 16267.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.214726 restraints weight = 11433.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.217746 restraints weight = 8311.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.218277 restraints weight = 6248.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.218849 restraints weight = 6394.059| |-----------------------------------------------------------------------------| r_work (final): 0.4928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5194 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8367 Z= 0.157 Angle : 0.670 11.273 11486 Z= 0.339 Chirality : 0.041 0.319 1303 Planarity : 0.005 0.051 1333 Dihedral : 16.027 86.481 1596 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.99 % Allowed : 23.25 % Favored : 69.76 % 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 are not related in a simple way. whole: -0.74 (0.28), residues: 911 helix: 0.09 (0.22), residues: 558 sheet: -2.90 (0.56), residues: 62 loop : -0.80 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 104 TYR 0.024 0.002 TYR B 128 PHE 0.034 0.002 PHE A 39 TRP 0.014 0.002 TRP A 273 HIS 0.008 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 8367) covalent geometry : angle 0.67012 / 0.34 (11486) hydrogen bonds : bond 0.04697 / 3.27 ( 417) hydrogen bonds : angle 5.44195 / 3.87 ( 1186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 101 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.7153 (mmm160) cc_final: 0.5789 (tpp-160) REVERT: A 203 LYS cc_start: 0.7344 (ptmm) cc_final: 0.6949 (mmtm) REVERT: A 237 ASN cc_start: 0.7165 (t0) cc_final: 0.6741 (m-40) REVERT: A 424 TRP cc_start: 0.2254 (OUTLIER) cc_final: -0.0187 (m-90) REVERT: B 203 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7326 (ptmm) REVERT: B 209 MET cc_start: 0.0074 (OUTLIER) cc_final: -0.0546 (tpp) REVERT: B 452 PHE cc_start: 0.6537 (t80) cc_final: 0.6296 (t80) outliers start: 55 outliers final: 32 residues processed: 140 average time/residue: 0.0991 time to fit residues: 18.7859 Evaluate side-chains 121 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 75 optimal weight: 0.0370 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.0470 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.232268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.196200 restraints weight = 15094.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.202017 restraints weight = 9683.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.206196 restraints weight = 6896.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.208839 restraints weight = 5289.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.211368 restraints weight = 4346.577| |-----------------------------------------------------------------------------| r_work (final): 0.4939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8367 Z= 0.126 Angle : 0.632 14.691 11486 Z= 0.315 Chirality : 0.039 0.261 1303 Planarity : 0.004 0.057 1333 Dihedral : 15.854 90.823 1587 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.84 % Allowed : 24.02 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.28), residues: 911 helix: 0.09 (0.22), residues: 561 sheet: -2.69 (0.57), residues: 64 loop : -0.77 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 105 TYR 0.019 0.002 TYR B 280 PHE 0.032 0.002 PHE A 39 TRP 0.012 0.001 TRP A 273 HIS 0.008 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8367) covalent geometry : angle 0.63191 / 0.32 (11486) hydrogen bonds : bond 0.04374 / 2.99 ( 417) hydrogen bonds : angle 5.18195 / 3.69 ( 1186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.6417 (mm) cc_final: 0.5971 (tt) REVERT: A 137 ARG cc_start: 0.7222 (mmm160) cc_final: 0.6992 (mmm-85) REVERT: A 186 LEU cc_start: 0.8171 (mt) cc_final: 0.7417 (tp) REVERT: A 203 LYS cc_start: 0.7368 (ptmm) cc_final: 0.7066 (mmtm) REVERT: A 237 ASN cc_start: 0.7151 (t0) cc_final: 0.6909 (t0) REVERT: A 424 TRP cc_start: 0.2293 (OUTLIER) cc_final: -0.0243 (m-90) REVERT: B 77 TYR cc_start: 0.4804 (OUTLIER) cc_final: 0.2276 (p90) REVERT: B 209 MET cc_start: 0.0124 (ppp) cc_final: -0.0477 (tpp) outliers start: 46 outliers final: 33 residues processed: 135 average time/residue: 0.0975 time to fit residues: 17.8854 Evaluate side-chains 132 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 20 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN A 251 HIS B 87 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.228839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.194825 restraints weight = 15501.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.200907 restraints weight = 9770.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.203827 restraints weight = 6582.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.207482 restraints weight = 5082.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.208066 restraints weight = 4552.004| |-----------------------------------------------------------------------------| r_work (final): 0.4900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5185 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8367 Z= 0.157 Angle : 0.651 12.724 11486 Z= 0.322 Chirality : 0.043 0.454 1303 Planarity : 0.004 0.057 1333 Dihedral : 15.777 94.672 1581 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.31 % Favored : 97.59 % Rotamer: Outliers : 6.35 % Allowed : 24.65 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.28), residues: 911 helix: 0.06 (0.22), residues: 562 sheet: -2.91 (0.55), residues: 64 loop : -0.75 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 105 TYR 0.022 0.002 TYR B 377 PHE 0.033 0.002 PHE A 39 TRP 0.011 0.002 TRP A 463 HIS 0.007 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8367) covalent geometry : angle 0.65142 / 0.32 (11486) hydrogen bonds : bond 0.04256 / 2.91 ( 417) hydrogen bonds : angle 5.14688 / 3.68 ( 1186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.7377 (ptmm) cc_final: 0.7053 (mmtm) REVERT: A 237 ASN cc_start: 0.7378 (t0) cc_final: 0.7089 (t0) REVERT: A 288 GLU cc_start: 0.4769 (OUTLIER) cc_final: 0.3889 (tt0) REVERT: A 358 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6826 (tm) REVERT: A 366 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: A 422 MET cc_start: 0.2026 (tpt) cc_final: 0.1478 (tpp) REVERT: A 424 TRP cc_start: 0.2382 (OUTLIER) cc_final: -0.0163 (m-90) REVERT: B 209 MET cc_start: 0.0197 (ppp) cc_final: -0.0432 (tpp) outliers start: 50 outliers final: 35 residues processed: 130 average time/residue: 0.1053 time to fit residues: 18.1686 Evaluate side-chains 126 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.239906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.209334 restraints weight = 16668.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.214089 restraints weight = 11017.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.216749 restraints weight = 7736.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.218999 restraints weight = 6051.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.219730 restraints weight = 5873.463| |-----------------------------------------------------------------------------| r_work (final): 0.4919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8367 Z= 0.128 Angle : 0.631 14.239 11486 Z= 0.311 Chirality : 0.041 0.365 1303 Planarity : 0.004 0.064 1333 Dihedral : 15.741 95.900 1579 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.52 % Favored : 97.37 % Rotamer: Outliers : 6.10 % Allowed : 24.40 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.28), residues: 911 helix: 0.11 (0.22), residues: 563 sheet: -2.83 (0.56), residues: 64 loop : -0.66 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 105 TYR 0.015 0.002 TYR B 280 PHE 0.031 0.002 PHE A 39 TRP 0.016 0.001 TRP A 463 HIS 0.011 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8367) covalent geometry : angle 0.63094 / 0.31 (11486) hydrogen bonds : bond 0.03983 / 2.74 ( 417) hydrogen bonds : angle 4.99556 / 3.58 ( 1186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.7403 (ptmm) cc_final: 0.7141 (mmtm) REVERT: A 237 ASN cc_start: 0.7419 (t0) cc_final: 0.7106 (t0) REVERT: A 358 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6719 (tm) REVERT: A 366 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: A 424 TRP cc_start: 0.2243 (OUTLIER) cc_final: -0.0289 (m-90) REVERT: B 77 TYR cc_start: 0.4971 (OUTLIER) cc_final: 0.2517 (p90) REVERT: B 209 MET cc_start: 0.0171 (OUTLIER) cc_final: -0.0350 (tpp) REVERT: B 305 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: B 377 TYR cc_start: 0.6378 (t80) cc_final: 0.6093 (t80) REVERT: B 424 TRP cc_start: 0.2971 (OUTLIER) cc_final: 0.0640 (m-90) outliers start: 48 outliers final: 32 residues processed: 128 average time/residue: 0.1187 time to fit residues: 19.9804 Evaluate side-chains 124 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.0050 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.245229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.216011 restraints weight = 16057.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.220171 restraints weight = 11146.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.223234 restraints weight = 8358.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.225370 restraints weight = 6652.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.227191 restraints weight = 5578.662| |-----------------------------------------------------------------------------| r_work (final): 0.5090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5148 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8367 Z= 0.122 Angle : 0.641 14.754 11486 Z= 0.315 Chirality : 0.041 0.377 1303 Planarity : 0.005 0.069 1333 Dihedral : 15.679 95.003 1578 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.41 % Favored : 97.48 % Rotamer: Outliers : 4.45 % Allowed : 26.56 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.28), residues: 911 helix: 0.15 (0.22), residues: 562 sheet: -2.73 (0.57), residues: 64 loop : -0.61 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 105 TYR 0.026 0.002 TYR A 128 PHE 0.032 0.002 PHE A 39 TRP 0.020 0.001 TRP A 463 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8367) covalent geometry : angle 0.64147 / 0.32 (11486) hydrogen bonds : bond 0.03901 / 2.71 ( 417) hydrogen bonds : angle 4.96585 / 3.57 ( 1186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.5663 (mm) cc_final: 0.5259 (tt) REVERT: A 237 ASN cc_start: 0.6940 (t0) cc_final: 0.6671 (t0) REVERT: A 358 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6569 (tm) REVERT: A 424 TRP cc_start: 0.2661 (OUTLIER) cc_final: -0.0038 (m-90) REVERT: B 77 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.2729 (p90) REVERT: B 114 LYS cc_start: 0.6981 (mmtp) cc_final: 0.6702 (mptt) REVERT: B 186 LEU cc_start: 0.8218 (mm) cc_final: 0.7718 (mm) REVERT: B 209 MET cc_start: 0.0181 (OUTLIER) cc_final: -0.0322 (tpp) REVERT: B 424 TRP cc_start: 0.3300 (OUTLIER) cc_final: 0.0766 (m-90) outliers start: 35 outliers final: 29 residues processed: 125 average time/residue: 0.1033 time to fit residues: 17.3242 Evaluate side-chains 126 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.243181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.213203 restraints weight = 16159.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.217311 restraints weight = 11349.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.220380 restraints weight = 8586.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.222296 restraints weight = 6846.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.224336 restraints weight = 5785.224| |-----------------------------------------------------------------------------| r_work (final): 0.5065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5215 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8367 Z= 0.136 Angle : 0.653 14.475 11486 Z= 0.322 Chirality : 0.041 0.372 1303 Planarity : 0.005 0.081 1333 Dihedral : 15.638 95.395 1575 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.31 % Favored : 97.59 % Rotamer: Outliers : 5.59 % Allowed : 26.56 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.28), residues: 911 helix: 0.13 (0.21), residues: 563 sheet: -2.80 (0.56), residues: 64 loop : -0.68 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 105 TYR 0.024 0.002 TYR A 128 PHE 0.034 0.002 PHE A 39 TRP 0.021 0.001 TRP A 463 HIS 0.006 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8367) covalent geometry : angle 0.65308 / 0.32 (11486) hydrogen bonds : bond 0.03871 / 2.68 ( 417) hydrogen bonds : angle 4.96883 / 3.58 ( 1186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.7039 (mmtm) cc_final: 0.6152 (mmmt) REVERT: A 237 ASN cc_start: 0.6836 (t0) cc_final: 0.6438 (t0) REVERT: A 288 GLU cc_start: 0.4828 (OUTLIER) cc_final: 0.3954 (tt0) REVERT: A 358 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6777 (tm) REVERT: A 366 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: A 424 TRP cc_start: 0.2658 (OUTLIER) cc_final: 0.0011 (m-90) REVERT: B 77 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.3170 (p90) REVERT: B 186 LEU cc_start: 0.8225 (mm) cc_final: 0.7733 (mm) REVERT: B 209 MET cc_start: 0.0211 (OUTLIER) cc_final: -0.0275 (tpp) REVERT: B 424 TRP cc_start: 0.3548 (OUTLIER) cc_final: 0.0971 (m-90) REVERT: B 472 GLU cc_start: 0.4717 (tm-30) cc_final: 0.4377 (tt0) outliers start: 44 outliers final: 32 residues processed: 123 average time/residue: 0.1033 time to fit residues: 17.0955 Evaluate side-chains 124 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 56 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 HIS A 251 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.243325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.215403 restraints weight = 16643.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.218283 restraints weight = 12233.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.222492 restraints weight = 8887.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.223382 restraints weight = 6983.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.224918 restraints weight = 5948.354| |-----------------------------------------------------------------------------| r_work (final): 0.5072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5192 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8367 Z= 0.127 Angle : 0.663 14.322 11486 Z= 0.326 Chirality : 0.041 0.367 1303 Planarity : 0.005 0.093 1333 Dihedral : 15.464 94.668 1572 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.52 % Favored : 97.37 % Rotamer: Outliers : 5.21 % Allowed : 27.19 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.28), residues: 911 helix: 0.21 (0.22), residues: 556 sheet: -2.80 (0.56), residues: 64 loop : -0.62 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 105 TYR 0.028 0.002 TYR A 128 PHE 0.034 0.002 PHE A 39 TRP 0.027 0.001 TRP A 463 HIS 0.014 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8367) covalent geometry : angle 0.66271 / 0.33 (11486) hydrogen bonds : bond 0.03894 / 2.69 ( 417) hydrogen bonds : angle 4.96534 / 3.57 ( 1186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.6898 (mmtm) cc_final: 0.5996 (mmmt) REVERT: A 358 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6660 (tm) REVERT: A 366 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: A 424 TRP cc_start: 0.2585 (OUTLIER) cc_final: -0.0063 (m-90) REVERT: B 77 TYR cc_start: 0.5387 (OUTLIER) cc_final: 0.3004 (p90) REVERT: B 186 LEU cc_start: 0.8177 (mm) cc_final: 0.7732 (mm) REVERT: B 209 MET cc_start: 0.0237 (OUTLIER) cc_final: -0.0242 (tpp) REVERT: B 422 MET cc_start: 0.1390 (tpp) cc_final: 0.0708 (tmm) REVERT: B 424 TRP cc_start: 0.3258 (OUTLIER) cc_final: 0.1309 (m-90) outliers start: 41 outliers final: 32 residues processed: 119 average time/residue: 0.1036 time to fit residues: 16.4039 Evaluate side-chains 124 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 HIS A 251 HIS B 256 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.243097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.213404 restraints weight = 16164.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.217311 restraints weight = 11401.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.220367 restraints weight = 8649.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.222514 restraints weight = 6932.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.224328 restraints weight = 5811.010| |-----------------------------------------------------------------------------| r_work (final): 0.5068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5212 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8367 Z= 0.143 Angle : 0.677 14.257 11486 Z= 0.338 Chirality : 0.041 0.377 1303 Planarity : 0.005 0.108 1333 Dihedral : 15.414 93.309 1570 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.52 % Favored : 97.26 % Rotamer: Outliers : 5.08 % Allowed : 27.06 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.28), residues: 911 helix: 0.24 (0.22), residues: 553 sheet: -2.82 (0.56), residues: 64 loop : -0.62 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 105 TYR 0.026 0.002 TYR A 128 PHE 0.035 0.002 PHE A 39 TRP 0.023 0.002 TRP A 463 HIS 0.023 0.002 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8367) covalent geometry : angle 0.67728 / 0.34 (11486) hydrogen bonds : bond 0.03906 / 2.70 ( 417) hydrogen bonds : angle 4.97768 / 3.59 ( 1186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.6890 (mmtm) cc_final: 0.6084 (mmmt) REVERT: A 288 GLU cc_start: 0.4901 (OUTLIER) cc_final: 0.4025 (tt0) REVERT: A 358 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6744 (tm) REVERT: A 424 TRP cc_start: 0.2709 (OUTLIER) cc_final: -0.0014 (m-90) REVERT: B 77 TYR cc_start: 0.5480 (OUTLIER) cc_final: 0.3095 (p90) REVERT: B 85 ARG cc_start: 0.5246 (mmm-85) cc_final: 0.4002 (ppt170) REVERT: B 186 LEU cc_start: 0.8200 (mm) cc_final: 0.7803 (mm) REVERT: B 209 MET cc_start: 0.0225 (OUTLIER) cc_final: -0.0250 (tpp) REVERT: B 424 TRP cc_start: 0.3429 (OUTLIER) cc_final: 0.1658 (m-90) REVERT: B 472 GLU cc_start: 0.4590 (tm-30) cc_final: 0.4150 (tt0) outliers start: 40 outliers final: 30 residues processed: 115 average time/residue: 0.1023 time to fit residues: 15.8868 Evaluate side-chains 121 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 0.0970 chunk 92 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 HIS A 251 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5253 r_free = 0.5253 target = 0.243761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.216481 restraints weight = 16516.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.219546 restraints weight = 11344.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.222982 restraints weight = 8682.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.223653 restraints weight = 6880.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.224211 restraints weight = 6214.037| |-----------------------------------------------------------------------------| r_work (final): 0.5068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5190 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8367 Z= 0.129 Angle : 0.689 14.606 11486 Z= 0.343 Chirality : 0.042 0.360 1303 Planarity : 0.005 0.098 1333 Dihedral : 15.380 91.703 1570 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.31 % Favored : 97.59 % Rotamer: Outliers : 3.94 % Allowed : 27.95 % Favored : 68.11 % 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 are not related in a simple way. whole: -0.48 (0.28), residues: 911 helix: 0.28 (0.22), residues: 554 sheet: -2.74 (0.57), residues: 64 loop : -0.64 (0.39), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 105 TYR 0.024 0.002 TYR A 128 PHE 0.034 0.002 PHE A 39 TRP 0.025 0.001 TRP A 463 HIS 0.013 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8367) covalent geometry : angle 0.68900 / 0.34 (11486) hydrogen bonds : bond 0.03840 / 2.69 ( 417) hydrogen bonds : angle 4.92318 / 3.55 ( 1186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.6730 (mmtm) cc_final: 0.6013 (mmmt) REVERT: A 424 TRP cc_start: 0.2603 (OUTLIER) cc_final: -0.0040 (m-90) REVERT: B 85 ARG cc_start: 0.5001 (mmm-85) cc_final: 0.3831 (ppt170) REVERT: B 186 LEU cc_start: 0.8116 (mm) cc_final: 0.7724 (mm) REVERT: B 209 MET cc_start: 0.0066 (OUTLIER) cc_final: -0.0338 (tpp) REVERT: B 422 MET cc_start: 0.0908 (tpp) cc_final: 0.0263 (tmm) REVERT: B 472 GLU cc_start: 0.4525 (tm-30) cc_final: 0.4261 (tt0) outliers start: 31 outliers final: 26 residues processed: 112 average time/residue: 0.1018 time to fit residues: 15.2530 Evaluate side-chains 112 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 89 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 47 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 HIS A 251 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5228 r_free = 0.5228 target = 0.237597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.204367 restraints weight = 15559.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.209546 restraints weight = 10386.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.213168 restraints weight = 7560.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.215827 restraints weight = 5895.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.217789 restraints weight = 4848.084| |-----------------------------------------------------------------------------| r_work (final): 0.5078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5176 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8367 Z= 0.126 Angle : 0.690 14.879 11486 Z= 0.339 Chirality : 0.043 0.523 1303 Planarity : 0.005 0.110 1333 Dihedral : 15.270 88.463 1566 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 4.57 % Allowed : 27.95 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.28), residues: 911 helix: 0.26 (0.22), residues: 557 sheet: -2.72 (0.56), residues: 64 loop : -0.72 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 105 TYR 0.022 0.002 TYR A 128 PHE 0.035 0.002 PHE A 39 TRP 0.037 0.002 TRP A 463 HIS 0.018 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8367) covalent geometry : angle 0.69035 / 0.34 (11486) hydrogen bonds : bond 0.03753 / 2.60 ( 417) hydrogen bonds : angle 4.87159 / 3.50 ( 1186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1531.21 seconds wall clock time: 27 minutes 12.40 seconds (1632.40 seconds total)