Starting phenix.real_space_refine on Wed Aug 5 01:05:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ifk_35419/08_2026/8ifk_35419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifk_35419/08_2026/8ifk_35419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2026/8ifk_35419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2026/8ifk_35419.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2026/8ifk_35419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2026/8ifk_35419.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2026/8ifk_35419.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ifk_35419/08_2026/8ifk_35419.cif" } resolution = 2.54 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= 0.227 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: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 4808 2.51 5 N 1280 2.21 5 O 1481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7632 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3475 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 14, 'TRANS': 399} Chain breaks: 2 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3300 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 24, 'TRANS': 384} Chain breaks: 6 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.24 Number of scatterers: 7632 At special positions: 0 Unit cell: (75.9, 86.9, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 41 15.00 Mg 1 11.99 O 1481 8.00 N 1280 7.00 C 4808 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: 0.67 Conformation dependent library (CDL) restraints added in 329.4 milliseconds 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 38.5% alpha, 17.9% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.908A pdb=" N PHE A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.428A pdb=" N LYS A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.034A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.665A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.698A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.851A pdb=" N GLU A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.564A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.676A pdb=" N LYS B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 115 through 129 removed outlier: 4.215A pdb=" N ALA B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 375 Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 5.924A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE A 95 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 319 through 324 removed outlier: 4.340A pdb=" N TYR B 280 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE B 443 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR B 6 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 314 removed outlier: 6.574A pdb=" N LEU A 402 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.704A pdb=" N SER B 41 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LYS B 94 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 43 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL B 141 " --> pdb=" O LEU B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 425 through 426 272 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1143 1.30 - 1.43: 2327 1.43 - 1.56: 4319 1.56 - 1.69: 80 1.69 - 1.81: 32 Bond restraints: 7901 Sorted by residual: bond pdb=" C PRO B 319 " pdb=" O PRO B 319 " ideal model delta sigma weight residual 1.234 1.178 0.056 1.14e-02 7.69e+03 2.38e+01 bond pdb=" C VAL B 278 " pdb=" O VAL B 278 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.11e-02 8.12e+03 1.86e+01 bond pdb=" C GLU B 436 " pdb=" O GLU B 436 " ideal model delta sigma weight residual 1.242 1.202 0.039 1.00e-02 1.00e+04 1.56e+01 bond pdb=" C MET B 435 " pdb=" O MET B 435 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.23e-02 6.61e+03 1.52e+01 bond pdb=" C TYR A 210 " pdb=" O TYR A 210 " ideal model delta sigma weight residual 1.235 1.194 0.042 1.13e-02 7.83e+03 1.37e+01 ... (remaining 7896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10386 1.74 - 3.47: 377 3.47 - 5.21: 64 5.21 - 6.94: 19 6.94 - 8.68: 7 Bond angle restraints: 10853 Sorted by residual: angle pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" O TYR A 210 " ideal model delta sigma weight residual 120.33 113.09 7.24 1.08e+00 8.57e-01 4.49e+01 angle pdb=" C ILE A 208 " pdb=" N ARG A 209 " pdb=" CA ARG A 209 " ideal model delta sigma weight residual 121.24 112.72 8.52 1.44e+00 4.82e-01 3.50e+01 angle pdb=" C PRO B 438 " pdb=" CA PRO B 438 " pdb=" CB PRO B 438 " ideal model delta sigma weight residual 111.21 103.77 7.44 1.33e+00 5.65e-01 3.13e+01 angle pdb=" C ARG A 54 " pdb=" CA ARG A 54 " pdb=" CB ARG A 54 " ideal model delta sigma weight residual 110.90 102.22 8.68 1.58e+00 4.01e-01 3.02e+01 angle pdb=" CA LYS B 211 " pdb=" C LYS B 211 " pdb=" O LYS B 211 " ideal model delta sigma weight residual 120.55 114.74 5.81 1.06e+00 8.90e-01 3.00e+01 ... (remaining 10848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3793 17.68 - 35.35: 562 35.35 - 53.03: 206 53.03 - 70.70: 80 70.70 - 88.38: 24 Dihedral angle restraints: 4665 sinusoidal: 2250 harmonic: 2415 Sorted by residual: dihedral pdb=" C4' A C 1 " pdb=" C3' A C 1 " pdb=" C2' A C 1 " pdb=" C1' A C 1 " ideal model delta sinusoidal sigma weight residual 36.34 -36.58 72.92 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' G C 20 " pdb=" C3' G C 20 " pdb=" C2' G C 20 " pdb=" C1' G C 20 " ideal model delta sinusoidal sigma weight residual 36.34 -36.01 72.36 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" O4' G C 20 " pdb=" C4' G C 20 " pdb=" C3' G C 20 " pdb=" C2' G C 20 " ideal model delta sinusoidal sigma weight residual -35.15 25.03 -60.18 1 4.00e+00 6.25e-02 3.02e+02 ... (remaining 4662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 977 0.063 - 0.126: 163 0.126 - 0.189: 20 0.189 - 0.252: 25 0.252 - 0.314: 7 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA ILE B 274 " pdb=" N ILE B 274 " pdb=" C ILE B 274 " pdb=" CB ILE B 274 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ARG A 209 " pdb=" N ARG A 209 " pdb=" C ARG A 209 " pdb=" CB ARG A 209 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' A C 1 " pdb=" C4' A C 1 " pdb=" O3' A C 1 " pdb=" C2' A C 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1189 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 437 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C VAL B 437 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL B 437 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO B 438 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 49 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE A 49 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE A 49 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A 50 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 321 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.21e+00 pdb=" C TYR B 321 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR B 321 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN B 322 " -0.016 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 36 2.38 - 3.01: 4009 3.01 - 3.64: 12781 3.64 - 4.27: 20625 4.27 - 4.90: 32431 Nonbonded interactions: 69882 Sorted by model distance: nonbonded pdb=" O TYR B 321 " pdb=" OD1 ASN B 322 " model vdw 1.744 3.040 nonbonded pdb=" O ILE B 507 " pdb="MG MG B 601 " model vdw 1.831 2.170 nonbonded pdb=" OP2 A C 1 " pdb="MG MG B 601 " model vdw 1.963 2.170 nonbonded pdb=" ND2 ASN B 468 " pdb="MG MG B 601 " model vdw 2.020 2.250 nonbonded pdb=" NH1 ARG B 275 " pdb=" OD2 ASP B 458 " model vdw 2.075 3.120 ... (remaining 69877 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.650 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.005 0.056 7901 Z= 0.311 Angle : 0.775 8.679 10853 Z= 0.503 Chirality : 0.060 0.314 1192 Planarity : 0.006 0.076 1218 Dihedral : 20.464 88.377 3099 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.35 % Allowed : 24.32 % Favored : 71.33 % 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: -0.23 (0.28), residues: 803 helix: 0.58 (0.31), residues: 281 sheet: -0.37 (0.36), residues: 171 loop : -0.50 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 250 TYR 0.028 0.002 TYR A 210 PHE 0.012 0.002 PHE A 343 TRP 0.034 0.002 TRP B 320 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.31 ( 7901) covalent geometry : angle 0.77546 / 0.50 (10853) hydrogen bonds : bond 0.12223 / 8.30 ( 312) hydrogen bonds : angle 5.77242 / 4.15 ( 830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.266 Fit side-chains REVERT: A 50 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6395 (tm-30) REVERT: B 270 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7832 (ptpp) outliers start: 32 outliers final: 26 residues processed: 134 average time/residue: 0.4918 time to fit residues: 69.4790 Evaluate side-chains 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 493 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 322 ASN B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153557 restraints weight = 7168.250| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.29 r_work: 0.3756 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7901 Z= 0.164 Angle : 0.699 12.469 10853 Z= 0.352 Chirality : 0.056 0.951 1192 Planarity : 0.005 0.047 1218 Dihedral : 16.765 72.485 1442 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.48 % Allowed : 22.69 % Favored : 72.83 % 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: -0.21 (0.28), residues: 803 helix: 0.60 (0.30), residues: 291 sheet: -0.47 (0.37), residues: 162 loop : -0.46 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 250 TYR 0.016 0.001 TYR A 210 PHE 0.013 0.001 PHE B 78 TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 7901) covalent geometry : angle 0.69906 / 0.35 (10853) hydrogen bonds : bond 0.04285 / 2.77 ( 312) hydrogen bonds : angle 5.09151 / 3.63 ( 830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.188 Fit side-chains REVERT: A 24 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6543 (mptm) REVERT: A 280 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7744 (mptp) REVERT: A 315 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8136 (mppt) REVERT: B 270 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.8010 (ptpt) REVERT: B 355 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7816 (tttp) outliers start: 33 outliers final: 14 residues processed: 134 average time/residue: 0.4678 time to fit residues: 66.4718 Evaluate side-chains 119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.174826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146174 restraints weight = 7089.537| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.28 r_work: 0.3673 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7901 Z= 0.262 Angle : 0.723 8.580 10853 Z= 0.366 Chirality : 0.054 0.501 1192 Planarity : 0.005 0.041 1218 Dihedral : 16.236 71.743 1403 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.35 % Allowed : 23.37 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.28), residues: 803 helix: 0.45 (0.30), residues: 290 sheet: -0.76 (0.36), residues: 176 loop : -0.63 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.013 0.002 TYR A 210 PHE 0.019 0.002 PHE A 343 TRP 0.024 0.003 TRP A 219 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.26 ( 7901) covalent geometry : angle 0.72265 / 0.37 (10853) hydrogen bonds : bond 0.04578 / 2.96 ( 312) hydrogen bonds : angle 5.23468 / 3.72 ( 830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.168 Fit side-chains REVERT: A 280 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7845 (mptp) REVERT: A 315 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8326 (mppt) REVERT: B 322 ASN cc_start: 0.6679 (OUTLIER) cc_final: 0.6333 (m-40) REVERT: B 355 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7861 (ttpp) outliers start: 32 outliers final: 14 residues processed: 130 average time/residue: 0.4687 time to fit residues: 64.4292 Evaluate side-chains 123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 389 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 0.0170 chunk 80 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN A 286 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.152609 restraints weight = 7183.092| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.29 r_work: 0.3746 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7901 Z= 0.141 Angle : 0.616 6.946 10853 Z= 0.313 Chirality : 0.048 0.318 1192 Planarity : 0.004 0.037 1218 Dihedral : 16.150 72.635 1396 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.48 % Allowed : 22.96 % Favored : 72.55 % 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: -0.33 (0.28), residues: 803 helix: 0.69 (0.30), residues: 290 sheet: -0.72 (0.37), residues: 168 loop : -0.62 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 71 TYR 0.011 0.001 TYR A 210 PHE 0.013 0.001 PHE A 343 TRP 0.022 0.002 TRP A 219 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7901) covalent geometry : angle 0.61571 / 0.31 (10853) hydrogen bonds : bond 0.03815 / 2.44 ( 312) hydrogen bonds : angle 4.97229 / 3.54 ( 830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.272 Fit side-chains REVERT: A 136 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6955 (mm-30) REVERT: B 322 ASN cc_start: 0.6455 (OUTLIER) cc_final: 0.6112 (m-40) REVERT: B 355 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7851 (ttpp) outliers start: 33 outliers final: 15 residues processed: 133 average time/residue: 0.4828 time to fit residues: 68.0104 Evaluate side-chains 123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 435 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.177989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149543 restraints weight = 7176.191| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.30 r_work: 0.3711 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7901 Z= 0.188 Angle : 0.634 7.495 10853 Z= 0.322 Chirality : 0.049 0.299 1192 Planarity : 0.004 0.042 1218 Dihedral : 15.995 71.994 1394 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.08 % Allowed : 23.37 % Favored : 72.55 % 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: -0.35 (0.28), residues: 803 helix: 0.69 (0.30), residues: 289 sheet: -0.82 (0.36), residues: 173 loop : -0.57 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 71 TYR 0.010 0.001 TYR A 210 PHE 0.017 0.002 PHE B 78 TRP 0.022 0.002 TRP A 219 HIS 0.002 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 7901) covalent geometry : angle 0.63410 / 0.32 (10853) hydrogen bonds : bond 0.03966 / 2.53 ( 312) hydrogen bonds : angle 4.99537 / 3.55 ( 830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.231 Fit side-chains REVERT: A 136 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6972 (mm-30) REVERT: A 280 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7707 (mptp) REVERT: A 315 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8537 (mppt) REVERT: B 355 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7819 (ttpp) outliers start: 30 outliers final: 12 residues processed: 127 average time/residue: 0.4503 time to fit residues: 60.5918 Evaluate side-chains 117 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 50 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.151688 restraints weight = 7146.353| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.29 r_work: 0.3737 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7901 Z= 0.152 Angle : 0.608 7.152 10853 Z= 0.307 Chirality : 0.048 0.266 1192 Planarity : 0.004 0.047 1218 Dihedral : 15.949 72.366 1391 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.80 % Allowed : 23.91 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.24 (0.28), residues: 803 helix: 0.77 (0.30), residues: 289 sheet: -0.71 (0.37), residues: 168 loop : -0.55 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 250 TYR 0.010 0.001 TYR A 210 PHE 0.014 0.002 PHE B 78 TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7901) covalent geometry : angle 0.60837 / 0.31 (10853) hydrogen bonds : bond 0.03703 / 2.36 ( 312) hydrogen bonds : angle 4.90715 / 3.50 ( 830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.229 Fit side-chains REVERT: A 136 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 280 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7606 (mptp) REVERT: A 315 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8545 (mppt) REVERT: B 322 ASN cc_start: 0.6474 (OUTLIER) cc_final: 0.6099 (m-40) REVERT: B 355 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7800 (ttpp) outliers start: 28 outliers final: 16 residues processed: 133 average time/residue: 0.4774 time to fit residues: 67.4067 Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 0.0030 chunk 25 optimal weight: 1.9990 overall best weight: 0.7570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.178848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150674 restraints weight = 7177.712| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.29 r_work: 0.3722 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7901 Z= 0.169 Angle : 0.616 7.308 10853 Z= 0.312 Chirality : 0.048 0.252 1192 Planarity : 0.004 0.051 1218 Dihedral : 15.937 72.109 1391 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.67 % Allowed : 24.05 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.24 (0.28), residues: 803 helix: 0.74 (0.30), residues: 290 sheet: -0.69 (0.37), residues: 168 loop : -0.52 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 71 TYR 0.010 0.001 TYR B 37 PHE 0.016 0.002 PHE B 78 TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 7901) covalent geometry : angle 0.61592 / 0.31 (10853) hydrogen bonds : bond 0.03747 / 2.40 ( 312) hydrogen bonds : angle 4.91724 / 3.50 ( 830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.188 Fit side-chains REVERT: A 136 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6915 (mm-30) REVERT: A 280 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7691 (mptp) REVERT: B 355 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7820 (ttpp) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 0.5262 time to fit residues: 71.1796 Evaluate side-chains 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 389 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 36 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.9115 > 50:) chunk 6 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.176204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147483 restraints weight = 7234.237| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.30 r_work: 0.3687 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 7901 Z= 0.220 Angle : 0.657 8.019 10853 Z= 0.332 Chirality : 0.050 0.279 1192 Planarity : 0.005 0.049 1218 Dihedral : 15.996 71.996 1391 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.67 % Allowed : 24.59 % Favored : 71.74 % 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: -0.35 (0.28), residues: 803 helix: 0.62 (0.30), residues: 290 sheet: -0.79 (0.37), residues: 173 loop : -0.52 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 250 TYR 0.012 0.002 TYR B 37 PHE 0.018 0.002 PHE B 78 TRP 0.021 0.002 TRP A 219 HIS 0.003 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 ( 7901) covalent geometry : angle 0.65745 / 0.33 (10853) hydrogen bonds : bond 0.04082 / 2.63 ( 312) hydrogen bonds : angle 5.03751 / 3.59 ( 830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.279 Fit side-chains REVERT: A 280 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7807 (mptp) REVERT: B 355 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7823 (ttpp) outliers start: 27 outliers final: 16 residues processed: 132 average time/residue: 0.4852 time to fit residues: 67.8850 Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 389 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.150124 restraints weight = 7147.843| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.30 r_work: 0.3719 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7901 Z= 0.173 Angle : 0.630 7.451 10853 Z= 0.318 Chirality : 0.048 0.257 1192 Planarity : 0.004 0.046 1218 Dihedral : 15.929 72.088 1391 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.26 % Allowed : 25.14 % Favored : 71.60 % 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: -0.27 (0.28), residues: 803 helix: 0.68 (0.30), residues: 290 sheet: -0.66 (0.37), residues: 168 loop : -0.53 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 250 TYR 0.010 0.001 TYR B 37 PHE 0.015 0.002 PHE B 78 TRP 0.021 0.002 TRP A 219 HIS 0.002 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 7901) covalent geometry : angle 0.62977 / 0.32 (10853) hydrogen bonds : bond 0.03778 / 2.41 ( 312) hydrogen bonds : angle 4.95745 / 3.53 ( 830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.178 Fit side-chains REVERT: A 71 ARG cc_start: 0.7004 (ttm110) cc_final: 0.6575 (mmm160) REVERT: A 280 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7723 (mptp) REVERT: A 352 LYS cc_start: 0.7434 (mmtm) cc_final: 0.7058 (mmmt) REVERT: B 355 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7813 (ttpp) outliers start: 24 outliers final: 16 residues processed: 129 average time/residue: 0.5075 time to fit residues: 69.3218 Evaluate side-chains 124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.178090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149499 restraints weight = 7195.062| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.30 r_work: 0.3716 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7901 Z= 0.184 Angle : 0.640 7.587 10853 Z= 0.324 Chirality : 0.049 0.254 1192 Planarity : 0.004 0.047 1218 Dihedral : 15.891 72.007 1391 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.72 % Allowed : 25.82 % Favored : 71.47 % 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: -0.26 (0.28), residues: 803 helix: 0.73 (0.30), residues: 285 sheet: -0.66 (0.37), residues: 168 loop : -0.55 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 250 TYR 0.011 0.001 TYR B 37 PHE 0.016 0.002 PHE B 78 TRP 0.024 0.002 TRP A 33 HIS 0.002 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 7901) covalent geometry : angle 0.63989 / 0.32 (10853) hydrogen bonds : bond 0.03815 / 2.45 ( 312) hydrogen bonds : angle 4.96329 / 3.53 ( 830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.328 Fit side-chains REVERT: A 157 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7438 (mp) REVERT: A 280 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7799 (mptp) REVERT: B 355 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7808 (ttpp) outliers start: 20 outliers final: 16 residues processed: 120 average time/residue: 0.4523 time to fit residues: 57.6799 Evaluate side-chains 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.180688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152538 restraints weight = 7135.091| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.29 r_work: 0.3743 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7901 Z= 0.149 Angle : 0.614 7.021 10853 Z= 0.311 Chirality : 0.047 0.260 1192 Planarity : 0.004 0.045 1218 Dihedral : 15.817 72.239 1391 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.72 % Allowed : 25.95 % Favored : 71.33 % 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: -0.16 (0.28), residues: 803 helix: 0.86 (0.31), residues: 284 sheet: -0.63 (0.37), residues: 168 loop : -0.53 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 71 TYR 0.012 0.001 TYR A 210 PHE 0.014 0.002 PHE A 343 TRP 0.023 0.002 TRP A 33 HIS 0.002 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 7901) covalent geometry : angle 0.61428 / 0.31 (10853) hydrogen bonds : bond 0.03556 / 2.28 ( 312) hydrogen bonds : angle 4.85430 / 3.46 ( 830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2622.38 seconds wall clock time: 45 minutes 18.50 seconds (2718.50 seconds total)