Starting phenix.real_space_refine on Tue Feb 3 19:20:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9og2_70450/02_2026/9og2_70450.cif Found real_map, /net/cci-nas-00/data/ceres_data/9og2_70450/02_2026/9og2_70450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9og2_70450/02_2026/9og2_70450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9og2_70450/02_2026/9og2_70450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9og2_70450/02_2026/9og2_70450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9og2_70450/02_2026/9og2_70450.map" } resolution = 2.8 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4038 2.51 5 N 1071 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6349 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2858 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 7, 'TRANS': 339} Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 1.42, per 1000 atoms: 0.22 Number of scatterers: 6349 At special positions: 0 Unit cell: (67.176, 95.166, 108.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1212 8.00 N 1071 7.00 C 4038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 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: 0.33 Conformation dependent library (CDL) restraints added in 363.2 milliseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 25.8% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 19 through 34 removed outlier: 4.161A pdb=" N ILE A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 63 removed outlier: 4.230A pdb=" N TYR A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.731A pdb=" N LYS A 71 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.830A pdb=" N ILE A 146 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 177 Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.716A pdb=" N PHE A 191 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.709A pdb=" N ASN A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.689A pdb=" N ILE A 328 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N HIS A 329 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 330 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.847A pdb=" N THR B 87 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.540A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.870A pdb=" N PHE E 83 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.740A pdb=" N THR A 268 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE A 269 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 318 removed outlier: 6.041A pdb=" N ILE A 313 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG A 282 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 315 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP A 290 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR A 283 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 288 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.302A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR B 33 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.302A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR B 33 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 88 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.655A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.156A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.156A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.580A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.512A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 50 " --> pdb=" O SER E 53 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.46 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: 2017 1.34 - 1.46: 1683 1.46 - 1.58: 2762 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 6506 Sorted by residual: bond pdb=" N ILE A 202 " pdb=" CA ILE A 202 " ideal model delta sigma weight residual 1.461 1.507 -0.046 1.31e-02 5.83e+03 1.21e+01 bond pdb=" C GLY D 65 " pdb=" N ARG D 66 " ideal model delta sigma weight residual 1.333 1.381 -0.049 1.52e-02 4.33e+03 1.03e+01 bond pdb=" N VAL A 207 " pdb=" CA VAL A 207 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.78e+00 bond pdb=" N TYR A 203 " pdb=" CA TYR A 203 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.42e-02 4.96e+03 6.03e+00 bond pdb=" N ASP A 204 " pdb=" CA ASP A 204 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.35e-02 5.49e+03 5.95e+00 ... (remaining 6501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 7893 0.90 - 1.81: 686 1.81 - 2.71: 163 2.71 - 3.61: 57 3.61 - 4.52: 20 Bond angle restraints: 8819 Sorted by residual: angle pdb=" CA GLY D 65 " pdb=" C GLY D 65 " pdb=" N ARG D 66 " ideal model delta sigma weight residual 118.55 122.45 -3.90 1.22e+00 6.72e-01 1.02e+01 angle pdb=" N ASP A 204 " pdb=" CA ASP A 204 " pdb=" C ASP A 204 " ideal model delta sigma weight residual 113.38 109.68 3.70 1.23e+00 6.61e-01 9.05e+00 angle pdb=" N ASN B 31 " pdb=" CA ASN B 31 " pdb=" C ASN B 31 " ideal model delta sigma weight residual 113.02 117.43 -4.41 1.49e+00 4.50e-01 8.75e+00 angle pdb=" O GLY D 65 " pdb=" C GLY D 65 " pdb=" N ARG D 66 " ideal model delta sigma weight residual 122.39 118.71 3.68 1.27e+00 6.20e-01 8.41e+00 angle pdb=" C GLY D 65 " pdb=" N ARG D 66 " pdb=" CA ARG D 66 " ideal model delta sigma weight residual 122.08 126.03 -3.95 1.53e+00 4.27e-01 6.65e+00 ... (remaining 8814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3379 17.67 - 35.35: 358 35.35 - 53.02: 70 53.02 - 70.69: 18 70.69 - 88.37: 4 Dihedral angle restraints: 3829 sinusoidal: 1501 harmonic: 2328 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual 93.00 49.47 43.53 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" CA ALA D 88 " pdb=" C ALA D 88 " pdb=" N VAL D 89 " pdb=" CA VAL D 89 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 61.21 31.79 1 1.00e+01 1.00e-02 1.44e+01 ... (remaining 3826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 600 0.036 - 0.072: 238 0.072 - 0.108: 69 0.108 - 0.143: 40 0.143 - 0.179: 3 Chirality restraints: 950 Sorted by residual: chirality pdb=" CA ILE A 202 " pdb=" N ILE A 202 " pdb=" C ILE A 202 " pdb=" CB ILE A 202 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA ILE A 313 " pdb=" N ILE A 313 " pdb=" C ILE A 313 " pdb=" CB ILE A 313 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA VAL A 207 " pdb=" N VAL A 207 " pdb=" C VAL A 207 " pdb=" CB VAL A 207 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 947 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 282 " 0.185 9.50e-02 1.11e+02 8.36e-02 5.68e+00 pdb=" NE ARG A 282 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 282 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 282 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 282 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 333 " -0.176 9.50e-02 1.11e+02 7.93e-02 4.98e+00 pdb=" NE ARG A 333 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 333 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 333 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 333 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 205 " -0.170 9.50e-02 1.11e+02 7.69e-02 4.69e+00 pdb=" NE ARG A 205 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 205 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 205 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 205 " -0.000 2.00e-02 2.50e+03 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 361 2.73 - 3.28: 6250 3.28 - 3.82: 10396 3.82 - 4.36: 13291 4.36 - 4.90: 22893 Nonbonded interactions: 53191 Sorted by model distance: nonbonded pdb=" O ASN A 287 " pdb=" OD1 ASN A 287 " model vdw 2.193 3.040 nonbonded pdb=" O SER B 82B" pdb=" OG SER B 82B" model vdw 2.345 3.040 nonbonded pdb=" O SER E 31 " pdb=" OG SER E 31 " model vdw 2.380 3.040 nonbonded pdb=" O SER C 77 " pdb=" OG SER C 77 " model vdw 2.453 3.040 nonbonded pdb=" OG SER B 98 " pdb=" N ARG B 99 " model vdw 2.483 3.120 ... (remaining 53186 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 'C' and (resid 1 through 10 or resid 12 through 27 or resid 29 or resid 3 \ 1 or resid 33 or resid 35 through 41 or resid 43 through 49 or resid 51 through \ 52 or resid 54 through 73 or resid 75 through 79 or resid 81 through 90 or resid \ 93 or resid 95 or resid 97 through 103 or resid 105 through 107)) selection = (chain 'E' and (resid 1 through 10 or resid 12 through 27 or resid 29 or resid 3 \ 1 or resid 33 or resid 35 through 41 or resid 43 through 49 or resid 51 through \ 52 or resid 54 through 73 or resid 75 through 79 or resid 81 through 90 or resid \ 93 or resid 95 or resid 97 through 103 or resid 105 through 107)) } 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 0.049 6511 Z= 0.161 Angle : 0.641 4.519 8829 Z= 0.362 Chirality : 0.046 0.179 950 Planarity : 0.007 0.084 1121 Dihedral : 15.038 88.368 2334 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.86 % Allowed : 22.84 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.09 (0.31), residues: 790 helix: 0.76 (0.44), residues: 130 sheet: 0.28 (0.33), residues: 243 loop : -0.20 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG D 71 TYR 0.034 0.003 TYR B 52 PHE 0.028 0.002 PHE D 67 TRP 0.012 0.002 TRP D 103 HIS 0.009 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6506) covalent geometry : angle 0.64103 ( 8819) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.69644 ( 10) hydrogen bonds : bond 0.16678 ( 263) hydrogen bonds : angle 7.68352 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7592 (tttm) cc_final: 0.7177 (tptp) REVERT: A 31 ASP cc_start: 0.7832 (m-30) cc_final: 0.7465 (m-30) REVERT: A 36 LYS cc_start: 0.7763 (tttt) cc_final: 0.7479 (tttp) REVERT: A 95 MET cc_start: 0.8052 (tpp) cc_final: 0.7741 (tpp) REVERT: A 304 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.6046 (mp0) REVERT: B 79 SER cc_start: 0.8569 (p) cc_final: 0.8330 (m) REVERT: C 37 GLN cc_start: 0.8723 (tt0) cc_final: 0.8487 (tt0) REVERT: C 38 GLN cc_start: 0.8654 (tt0) cc_final: 0.8398 (tt0) REVERT: D 82 MET cc_start: 0.7747 (mmm) cc_final: 0.7502 (mpp) outliers start: 6 outliers final: 4 residues processed: 166 average time/residue: 0.3961 time to fit residues: 69.8505 Evaluate side-chains 168 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 110 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0060 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.120742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108615 restraints weight = 8485.448| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.75 r_work: 0.3352 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6511 Z= 0.252 Angle : 0.612 6.166 8829 Z= 0.335 Chirality : 0.047 0.155 950 Planarity : 0.005 0.046 1121 Dihedral : 5.480 60.591 890 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.74 % Allowed : 19.68 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.13 (0.30), residues: 790 helix: 0.80 (0.44), residues: 131 sheet: 0.30 (0.34), residues: 235 loop : -0.18 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 24 TYR 0.023 0.003 TYR B 50 PHE 0.025 0.003 PHE D 29 TRP 0.022 0.002 TRP D 103 HIS 0.008 0.002 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 6506) covalent geometry : angle 0.61135 ( 8819) SS BOND : bond 0.00255 ( 5) SS BOND : angle 0.95523 ( 10) hydrogen bonds : bond 0.05327 ( 263) hydrogen bonds : angle 5.75015 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7720 (tttm) cc_final: 0.7232 (tptp) REVERT: A 31 ASP cc_start: 0.7942 (m-30) cc_final: 0.7503 (m-30) REVERT: A 36 LYS cc_start: 0.7781 (tttt) cc_final: 0.7519 (tttp) REVERT: A 71 LYS cc_start: 0.8025 (ttpp) cc_final: 0.7750 (ttpp) REVERT: A 131 SER cc_start: 0.8203 (p) cc_final: 0.7967 (p) REVERT: D 81 GLN cc_start: 0.7906 (tp40) cc_final: 0.7639 (tp40) REVERT: E 69 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7149 (p) outliers start: 26 outliers final: 7 residues processed: 182 average time/residue: 0.4105 time to fit residues: 79.1035 Evaluate side-chains 170 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 4 optimal weight: 0.2980 chunk 70 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 6 optimal weight: 0.0870 chunk 39 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 0.0870 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 83 GLN A 111 ASN A 194 ASN A 197 HIS A 287 ASN C 38 GLN E 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111038 restraints weight = 8412.544| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.66 r_work: 0.3394 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6511 Z= 0.126 Angle : 0.521 4.524 8829 Z= 0.288 Chirality : 0.042 0.142 950 Planarity : 0.004 0.049 1121 Dihedral : 4.335 20.467 881 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.16 % Allowed : 21.55 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.22 (0.30), residues: 790 helix: 0.85 (0.45), residues: 137 sheet: 0.37 (0.34), residues: 235 loop : -0.13 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.018 0.002 TYR B 52 PHE 0.023 0.002 PHE D 29 TRP 0.012 0.001 TRP D 103 HIS 0.009 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6506) covalent geometry : angle 0.52107 ( 8819) SS BOND : bond 0.00176 ( 5) SS BOND : angle 0.44623 ( 10) hydrogen bonds : bond 0.04291 ( 263) hydrogen bonds : angle 5.33265 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7698 (tttm) cc_final: 0.7151 (tptt) REVERT: A 31 ASP cc_start: 0.7898 (m-30) cc_final: 0.7387 (m-30) REVERT: A 36 LYS cc_start: 0.7708 (tttt) cc_final: 0.7471 (tttp) REVERT: A 71 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7658 (ttpp) REVERT: D 81 GLN cc_start: 0.7885 (tp40) cc_final: 0.7637 (tp40) REVERT: D 82 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.6641 (mmm) REVERT: E 69 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.7078 (p) outliers start: 22 outliers final: 9 residues processed: 178 average time/residue: 0.4467 time to fit residues: 84.4700 Evaluate side-chains 173 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.0010 chunk 10 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.0020 chunk 46 optimal weight: 2.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN C 38 GLN C 55 GLN E 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110399 restraints weight = 8475.922| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.76 r_work: 0.3376 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6511 Z= 0.160 Angle : 0.532 6.420 8829 Z= 0.290 Chirality : 0.043 0.145 950 Planarity : 0.004 0.049 1121 Dihedral : 4.390 22.023 881 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.59 % Allowed : 21.41 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.28 (0.30), residues: 790 helix: 0.88 (0.44), residues: 136 sheet: 0.45 (0.34), residues: 236 loop : -0.11 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.018 0.002 TYR B 50 PHE 0.015 0.002 PHE B 78 TRP 0.014 0.002 TRP D 103 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6506) covalent geometry : angle 0.53158 ( 8819) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.47709 ( 10) hydrogen bonds : bond 0.04292 ( 263) hydrogen bonds : angle 5.18682 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7739 (tttm) cc_final: 0.7353 (tttm) REVERT: A 31 ASP cc_start: 0.7944 (m-30) cc_final: 0.7611 (m-30) REVERT: A 36 LYS cc_start: 0.7720 (tttt) cc_final: 0.7468 (tttp) REVERT: A 71 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7680 (ttpp) REVERT: A 131 SER cc_start: 0.8165 (p) cc_final: 0.7939 (p) REVERT: D 81 GLN cc_start: 0.7910 (tp40) cc_final: 0.7653 (tp40) REVERT: D 82 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6591 (mmm) REVERT: E 69 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7081 (p) outliers start: 25 outliers final: 12 residues processed: 186 average time/residue: 0.4329 time to fit residues: 85.4431 Evaluate side-chains 184 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN C 38 GLN E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108303 restraints weight = 8529.447| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.73 r_work: 0.3348 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 6511 Z= 0.305 Angle : 0.618 6.270 8829 Z= 0.335 Chirality : 0.048 0.152 950 Planarity : 0.005 0.049 1121 Dihedral : 4.862 26.650 881 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.02 % Allowed : 21.55 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: -0.02 (0.30), residues: 790 helix: 0.47 (0.44), residues: 136 sheet: 0.36 (0.33), residues: 239 loop : -0.32 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 175 TYR 0.026 0.003 TYR B 50 PHE 0.028 0.003 PHE D 29 TRP 0.022 0.002 TRP D 103 HIS 0.007 0.002 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00722 ( 6506) covalent geometry : angle 0.61726 ( 8819) SS BOND : bond 0.00263 ( 5) SS BOND : angle 0.91821 ( 10) hydrogen bonds : bond 0.04996 ( 263) hydrogen bonds : angle 5.46837 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8007 (m-30) cc_final: 0.7651 (m-30) REVERT: A 95 MET cc_start: 0.8141 (tpp) cc_final: 0.7798 (ttp) REVERT: A 131 SER cc_start: 0.8237 (p) cc_final: 0.8004 (p) REVERT: A 245 GLU cc_start: 0.7815 (tp30) cc_final: 0.7453 (mp0) REVERT: D 81 GLN cc_start: 0.7912 (tp40) cc_final: 0.7617 (tp40) REVERT: D 82 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6616 (mmm) REVERT: E 69 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.7158 (p) outliers start: 28 outliers final: 17 residues processed: 188 average time/residue: 0.3924 time to fit residues: 78.3999 Evaluate side-chains 193 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 19 optimal weight: 0.0040 chunk 17 optimal weight: 0.1980 chunk 54 optimal weight: 0.0670 chunk 56 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.1530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN A 194 ASN A 287 ASN C 38 GLN E 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.123833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112189 restraints weight = 8479.287| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.68 r_work: 0.3405 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6511 Z= 0.108 Angle : 0.509 6.094 8829 Z= 0.279 Chirality : 0.042 0.138 950 Planarity : 0.004 0.049 1121 Dihedral : 4.337 21.889 881 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.59 % Allowed : 23.71 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.36 (0.30), residues: 790 helix: 1.19 (0.45), residues: 130 sheet: 0.45 (0.34), residues: 242 loop : -0.10 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.023 0.002 TYR A 121 PHE 0.029 0.002 PHE D 29 TRP 0.008 0.001 TRP D 103 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6506) covalent geometry : angle 0.50859 ( 8819) SS BOND : bond 0.00199 ( 5) SS BOND : angle 0.44989 ( 10) hydrogen bonds : bond 0.03953 ( 263) hydrogen bonds : angle 5.06192 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7379 (tttm) REVERT: A 31 ASP cc_start: 0.7939 (m-30) cc_final: 0.7653 (m-30) REVERT: A 36 LYS cc_start: 0.7704 (tttt) cc_final: 0.7468 (tttp) REVERT: A 95 MET cc_start: 0.8047 (tpp) cc_final: 0.7675 (ttp) REVERT: A 223 TYR cc_start: 0.7803 (t80) cc_final: 0.7592 (t80) REVERT: A 245 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: C 31 SER cc_start: 0.8385 (m) cc_final: 0.8025 (t) REVERT: D 81 GLN cc_start: 0.7890 (tp40) cc_final: 0.7638 (tp40) REVERT: E 69 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7091 (p) outliers start: 25 outliers final: 13 residues processed: 182 average time/residue: 0.4163 time to fit residues: 80.4825 Evaluate side-chains 186 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 27 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 320 ASN C 38 GLN E 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.122491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110611 restraints weight = 8407.172| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.73 r_work: 0.3377 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6511 Z= 0.172 Angle : 0.549 7.523 8829 Z= 0.296 Chirality : 0.044 0.151 950 Planarity : 0.004 0.048 1121 Dihedral : 4.431 23.715 881 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.88 % Allowed : 24.14 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 (0.30), residues: 790 helix: 1.12 (0.45), residues: 130 sheet: 0.47 (0.34), residues: 242 loop : -0.13 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.020 0.002 TYR B 33 PHE 0.014 0.002 PHE D 67 TRP 0.014 0.001 TRP D 103 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6506) covalent geometry : angle 0.54891 ( 8819) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.59656 ( 10) hydrogen bonds : bond 0.04237 ( 263) hydrogen bonds : angle 5.09598 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7388 (tttm) REVERT: A 31 ASP cc_start: 0.7947 (m-30) cc_final: 0.7640 (m-30) REVERT: A 36 LYS cc_start: 0.7751 (tttt) cc_final: 0.7479 (tttp) REVERT: A 95 MET cc_start: 0.8115 (tpp) cc_final: 0.7753 (ttp) REVERT: A 131 SER cc_start: 0.8170 (p) cc_final: 0.7935 (p) REVERT: A 245 GLU cc_start: 0.7827 (tp30) cc_final: 0.7396 (mp0) REVERT: C 31 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8067 (t) REVERT: D 81 GLN cc_start: 0.7899 (tp40) cc_final: 0.7612 (tp40) REVERT: E 69 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7089 (p) outliers start: 27 outliers final: 16 residues processed: 184 average time/residue: 0.3856 time to fit residues: 75.5008 Evaluate side-chains 187 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 0 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 10 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN C 38 GLN E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110596 restraints weight = 8415.123| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.74 r_work: 0.3374 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6511 Z= 0.171 Angle : 0.549 7.954 8829 Z= 0.299 Chirality : 0.044 0.166 950 Planarity : 0.004 0.048 1121 Dihedral : 4.454 23.632 881 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.88 % Allowed : 24.28 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.14 (0.30), residues: 790 helix: 0.65 (0.44), residues: 137 sheet: 0.46 (0.34), residues: 242 loop : -0.24 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.020 0.002 TYR B 33 PHE 0.034 0.002 PHE D 29 TRP 0.014 0.001 TRP D 103 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6506) covalent geometry : angle 0.54870 ( 8819) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.59566 ( 10) hydrogen bonds : bond 0.04223 ( 263) hydrogen bonds : angle 5.09457 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7394 (tttm) REVERT: A 31 ASP cc_start: 0.7953 (m-30) cc_final: 0.7644 (m-30) REVERT: A 36 LYS cc_start: 0.7751 (tttt) cc_final: 0.7479 (tttp) REVERT: A 95 MET cc_start: 0.8148 (tpp) cc_final: 0.7758 (ttp) REVERT: A 131 SER cc_start: 0.8172 (p) cc_final: 0.7959 (p) REVERT: A 245 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: A 330 PHE cc_start: 0.8252 (m-80) cc_final: 0.7873 (m-10) REVERT: C 31 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8074 (t) REVERT: E 69 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7090 (p) outliers start: 27 outliers final: 18 residues processed: 179 average time/residue: 0.4408 time to fit residues: 83.8916 Evaluate side-chains 192 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN E 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111468 restraints weight = 8491.777| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.68 r_work: 0.3396 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6511 Z= 0.150 Angle : 0.552 8.167 8829 Z= 0.299 Chirality : 0.044 0.172 950 Planarity : 0.004 0.048 1121 Dihedral : 4.413 22.999 881 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 25.00 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.15 (0.30), residues: 790 helix: 0.71 (0.45), residues: 137 sheet: 0.42 (0.33), residues: 248 loop : -0.22 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.019 0.002 TYR A 121 PHE 0.013 0.002 PHE B 78 TRP 0.012 0.001 TRP D 103 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6506) covalent geometry : angle 0.55216 ( 8819) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.53306 ( 10) hydrogen bonds : bond 0.04139 ( 263) hydrogen bonds : angle 5.10020 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7375 (tttm) REVERT: A 31 ASP cc_start: 0.7970 (m-30) cc_final: 0.7678 (m-30) REVERT: A 36 LYS cc_start: 0.7718 (tttt) cc_final: 0.7488 (tttp) REVERT: A 95 MET cc_start: 0.8115 (tpp) cc_final: 0.7743 (ttp) REVERT: A 245 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 330 PHE cc_start: 0.8227 (m-80) cc_final: 0.7814 (m-10) REVERT: C 31 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8071 (t) outliers start: 24 outliers final: 16 residues processed: 181 average time/residue: 0.4202 time to fit residues: 81.0388 Evaluate side-chains 189 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 17 optimal weight: 0.3980 chunk 42 optimal weight: 0.0270 chunk 75 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 73 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN C 38 GLN E 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111825 restraints weight = 8330.487| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.65 r_work: 0.3401 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6511 Z= 0.147 Angle : 0.546 8.284 8829 Z= 0.297 Chirality : 0.044 0.174 950 Planarity : 0.004 0.048 1121 Dihedral : 4.379 22.628 881 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.16 % Allowed : 25.72 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.22 (0.30), residues: 790 helix: 0.76 (0.45), residues: 137 sheet: 0.49 (0.33), residues: 247 loop : -0.20 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.019 0.002 TYR B 33 PHE 0.032 0.002 PHE D 29 TRP 0.012 0.001 TRP D 103 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6506) covalent geometry : angle 0.54594 ( 8819) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.52150 ( 10) hydrogen bonds : bond 0.04088 ( 263) hydrogen bonds : angle 5.06720 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7368 (tttm) REVERT: A 31 ASP cc_start: 0.7962 (m-30) cc_final: 0.7657 (m-30) REVERT: A 36 LYS cc_start: 0.7724 (tttt) cc_final: 0.7493 (tttp) REVERT: A 95 MET cc_start: 0.8081 (tpp) cc_final: 0.7700 (ttp) REVERT: A 223 TYR cc_start: 0.7773 (t80) cc_final: 0.7549 (t80) REVERT: A 245 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: A 330 PHE cc_start: 0.8221 (m-80) cc_final: 0.7794 (m-10) REVERT: C 31 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8047 (t) outliers start: 22 outliers final: 19 residues processed: 179 average time/residue: 0.4182 time to fit residues: 79.7907 Evaluate side-chains 190 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 0.0020 chunk 29 optimal weight: 0.2980 chunk 71 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 45 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 overall best weight: 0.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN E 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113405 restraints weight = 8495.834| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.74 r_work: 0.3420 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6511 Z= 0.108 Angle : 0.528 7.993 8829 Z= 0.287 Chirality : 0.043 0.176 950 Planarity : 0.004 0.047 1121 Dihedral : 4.214 20.527 881 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.02 % Allowed : 25.72 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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: 0.41 (0.31), residues: 790 helix: 1.23 (0.46), residues: 130 sheet: 0.54 (0.33), residues: 247 loop : -0.12 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.018 0.002 TYR A 121 PHE 0.012 0.001 PHE B 78 TRP 0.008 0.001 TRP D 103 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6506) covalent geometry : angle 0.52854 ( 8819) SS BOND : bond 0.00173 ( 5) SS BOND : angle 0.40897 ( 10) hydrogen bonds : bond 0.03751 ( 263) hydrogen bonds : angle 4.94454 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.18 seconds wall clock time: 44 minutes 23.58 seconds (2663.58 seconds total)