Starting phenix.real_space_refine on Tue Aug 4 16:52:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9swq_55324/08_2026/9swq_55324.cif Found real_map, /net/cci-nas-00/data/ceres_data/9swq_55324/08_2026/9swq_55324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9swq_55324/08_2026/9swq_55324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9swq_55324/08_2026/9swq_55324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9swq_55324/08_2026/9swq_55324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9swq_55324/08_2026/9swq_55324.map" } resolution = 3.31 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= 0.021 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 24 5.16 5 C 3204 2.51 5 N 874 2.21 5 O 904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 5006 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2502 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2504 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 1.55, per 1000 atoms: 0.31 Number of scatterers: 5006 At special positions: 0 Unit cell: (59.532, 94.38, 108.9, 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 24 16.00 O 904 8.00 N 874 7.00 C 3204 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: 0.39 Conformation dependent library (CDL) restraints added in 204.7 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 60.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 removed outlier: 3.507A pdb=" N VAL A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 67 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.418A pdb=" N THR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.749A pdb=" N TYR A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 134 removed outlier: 4.047A pdb=" N LEU A 121 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 174 through 187 removed outlier: 4.180A pdb=" N GLN A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 211 through 216 removed outlier: 4.433A pdb=" N ALA A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.832A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.596A pdb=" N HIS A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 35 removed outlier: 3.507A pdb=" N GLY B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 70 removed outlier: 4.379A pdb=" N TYR B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 80 through 89 removed outlier: 3.906A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 116 through 134 removed outlier: 3.683A pdb=" N MET B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 155 through 167 removed outlier: 4.938A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS B 165 " --> pdb=" O TRP B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 Proline residue: B 173 - end of helix removed outlier: 3.581A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 262 through 275 removed outlier: 4.192A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 Processing helix chain 'B' and resid 324 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 225 removed outlier: 5.839A pdb=" N PHE A 221 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU A 246 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 223 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN A 242 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER A 243 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL A 258 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR A 245 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR A 256 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU A 247 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 219 through 225 removed outlier: 6.522A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU B 248 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE B 221 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU B 246 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP B 223 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN B 242 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER B 243 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 259 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 777 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: 0.73 Time building geometry restraints manager: 0.53 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: 1459 1.34 - 1.45: 816 1.45 - 1.57: 2818 1.57 - 1.69: 2 1.69 - 1.81: 28 Bond restraints: 5123 Sorted by residual: bond pdb=" C PRO B 39 " pdb=" N PRO B 40 " ideal model delta sigma weight residual 1.336 1.387 -0.051 1.20e-02 6.94e+03 1.79e+01 bond pdb=" C PRO A 39 " pdb=" N PRO A 40 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.09e+00 bond pdb=" CB GLU B 38 " pdb=" CG GLU B 38 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.95e+00 bond pdb=" CB GLU A 68 " pdb=" CG GLU A 68 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB ASP B 205 " pdb=" CG ASP B 205 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.75e+00 ... (remaining 5118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 6831 3.17 - 6.34: 113 6.34 - 9.51: 23 9.51 - 12.68: 9 12.68 - 15.85: 1 Bond angle restraints: 6977 Sorted by residual: angle pdb=" N PRO A 115 " pdb=" CA PRO A 115 " pdb=" CB PRO A 115 " ideal model delta sigma weight residual 103.08 109.35 -6.27 9.70e-01 1.06e+00 4.18e+01 angle pdb=" CA GLU B 38 " pdb=" CB GLU B 38 " pdb=" CG GLU B 38 " ideal model delta sigma weight residual 114.10 123.83 -9.73 2.00e+00 2.50e-01 2.37e+01 angle pdb=" CA ARG B 45 " pdb=" C ARG B 45 " pdb=" N TYR B 46 " ideal model delta sigma weight residual 117.07 122.37 -5.30 1.14e+00 7.69e-01 2.16e+01 angle pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" C LEU A 172 " ideal model delta sigma weight residual 109.81 119.85 -10.04 2.21e+00 2.05e-01 2.06e+01 angle pdb=" CA LEU A 172 " pdb=" CB LEU A 172 " pdb=" CG LEU A 172 " ideal model delta sigma weight residual 116.30 132.15 -15.85 3.50e+00 8.16e-02 2.05e+01 ... (remaining 6972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2583 17.94 - 35.88: 338 35.88 - 53.82: 110 53.82 - 71.76: 19 71.76 - 89.70: 9 Dihedral angle restraints: 3059 sinusoidal: 1187 harmonic: 1872 Sorted by residual: dihedral pdb=" CA GLU A 69 " pdb=" C GLU A 69 " pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA SER B 162 " pdb=" C SER B 162 " pdb=" N TYR B 163 " pdb=" CA TYR B 163 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA GLY B 138 " pdb=" C GLY B 138 " pdb=" N LEU B 139 " pdb=" CA LEU B 139 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 3056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 697 0.079 - 0.159: 84 0.159 - 0.238: 4 0.238 - 0.318: 2 0.318 - 0.397: 1 Chirality restraints: 788 Sorted by residual: chirality pdb=" CG LEU A 70 " pdb=" CB LEU A 70 " pdb=" CD1 LEU A 70 " pdb=" CD2 LEU A 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU A 330 " pdb=" CB LEU A 330 " pdb=" CD1 LEU A 330 " pdb=" CD2 LEU A 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 785 not shown) Planarity restraints: 899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 274 " -0.015 2.00e-02 2.50e+03 1.98e-02 7.81e+00 pdb=" CG TYR A 274 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 274 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 274 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 274 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 274 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 274 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 274 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 208 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C VAL B 208 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL B 208 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 209 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 216 " -0.040 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 217 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.033 5.00e-02 4.00e+02 ... (remaining 896 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1417 2.82 - 3.34: 4361 3.34 - 3.86: 8155 3.86 - 4.38: 8731 4.38 - 4.90: 15474 Nonbonded interactions: 38138 Sorted by model distance: nonbonded pdb=" OE1 GLU B 69 " pdb=" OH TYR B 77 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 167 " pdb=" OE1 GLU A 260 " model vdw 2.322 3.040 nonbonded pdb=" OG SER A 324 " pdb=" OG SER A 326 " model vdw 2.342 3.040 nonbonded pdb=" OG SER B 280 " pdb=" OD2 ASP B 283 " model vdw 2.356 3.040 nonbonded pdb=" OE1 GLN B 55 " pdb=" NH1 ARG B 95 " model vdw 2.378 3.120 ... (remaining 38133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 4 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 336)) } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 0.081 5123 Z= 0.222 Angle : 1.057 15.850 6977 Z= 0.523 Chirality : 0.052 0.397 788 Planarity : 0.007 0.059 899 Dihedral : 18.519 89.699 1859 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.88 % Allowed : 30.89 % Favored : 67.23 % 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: -1.85 (0.30), residues: 634 helix: -1.06 (0.24), residues: 343 sheet: 0.05 (0.83), residues: 40 loop : -1.49 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 197 TYR 0.048 0.001 TYR A 274 PHE 0.014 0.001 PHE A 117 TRP 0.011 0.001 TRP A 34 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 ( 5123) covalent geometry : angle 1.05678 / 0.52 ( 6977) hydrogen bonds : bond 0.15429 / 10.11 ( 261) hydrogen bonds : angle 6.89986 / 4.98 ( 777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8980 (mt) cc_final: 0.8720 (tt) REVERT: A 24 VAL cc_start: 0.9094 (t) cc_final: 0.8837 (p) REVERT: A 27 SER cc_start: 0.8323 (t) cc_final: 0.8023 (p) REVERT: A 30 LEU cc_start: 0.8733 (tp) cc_final: 0.8467 (tp) REVERT: B 20 LYS cc_start: 0.8161 (mttt) cc_final: 0.7773 (mttp) REVERT: B 27 SER cc_start: 0.8673 (m) cc_final: 0.8390 (t) REVERT: B 305 SER cc_start: 0.8215 (m) cc_final: 0.7738 (p) outliers start: 10 outliers final: 3 residues processed: 166 average time/residue: 0.0652 time to fit residues: 14.3698 Evaluate side-chains 116 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.083878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.063724 restraints weight = 14802.319| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.98 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5123 Z= 0.124 Angle : 0.667 8.947 6977 Z= 0.317 Chirality : 0.040 0.169 788 Planarity : 0.005 0.040 899 Dihedral : 5.248 53.518 717 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 7.16 % Allowed : 30.32 % Favored : 62.52 % 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: -0.36 (0.32), residues: 634 helix: 0.55 (0.27), residues: 356 sheet: 0.25 (0.93), residues: 30 loop : -1.41 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.020 0.001 TYR B 77 PHE 0.017 0.001 PHE A 221 TRP 0.007 0.001 TRP B 161 HIS 0.003 0.001 HIS B 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 5123) covalent geometry : angle 0.66737 / 0.32 ( 6977) hydrogen bonds : bond 0.03429 / 2.30 ( 261) hydrogen bonds : angle 4.78105 / 3.48 ( 777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.115 Fit side-chains REVERT: A 23 LEU cc_start: 0.9177 (mt) cc_final: 0.8879 (tt) REVERT: A 27 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8415 (p) REVERT: A 49 LEU cc_start: 0.9431 (mm) cc_final: 0.9222 (mp) REVERT: A 69 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: A 176 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8952 (mm-40) REVERT: A 240 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.5060 (t80) REVERT: A 286 GLU cc_start: 0.9028 (pt0) cc_final: 0.8801 (pt0) REVERT: B 20 LYS cc_start: 0.7886 (mttt) cc_final: 0.7674 (mttp) REVERT: B 95 ARG cc_start: 0.8500 (mpt180) cc_final: 0.8297 (mpt180) REVERT: B 100 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8972 (mm) REVERT: B 286 GLU cc_start: 0.9135 (tp30) cc_final: 0.8608 (tp30) REVERT: B 289 LYS cc_start: 0.9363 (mttm) cc_final: 0.9063 (mttm) outliers start: 38 outliers final: 21 residues processed: 138 average time/residue: 0.0510 time to fit residues: 9.5017 Evaluate side-chains 131 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 5.9990 chunk 61 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 HIS A 55 GLN A 185 HIS B 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.082649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062398 restraints weight = 15082.500| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.87 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5123 Z= 0.128 Angle : 0.637 8.029 6977 Z= 0.304 Chirality : 0.039 0.142 788 Planarity : 0.005 0.040 899 Dihedral : 4.982 56.522 716 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 7.16 % Allowed : 29.76 % Favored : 63.09 % 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: 0.41 (0.34), residues: 634 helix: 1.39 (0.29), residues: 347 sheet: 0.36 (0.95), residues: 30 loop : -1.33 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 281 TYR 0.016 0.001 TYR B 77 PHE 0.006 0.001 PHE A 269 TRP 0.006 0.001 TRP A 161 HIS 0.010 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 5123) covalent geometry : angle 0.63672 / 0.30 ( 6977) hydrogen bonds : bond 0.03188 / 2.15 ( 261) hydrogen bonds : angle 4.61728 / 3.35 ( 777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.9197 (mt) cc_final: 0.8872 (tt) REVERT: A 27 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8450 (p) REVERT: A 54 LEU cc_start: 0.9714 (tp) cc_final: 0.9281 (tt) REVERT: A 69 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 120 MET cc_start: 0.8600 (mmm) cc_final: 0.8171 (mmm) REVERT: A 240 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5158 (t80) REVERT: A 261 TYR cc_start: 0.8923 (m-80) cc_final: 0.8648 (m-80) REVERT: A 286 GLU cc_start: 0.8977 (pt0) cc_final: 0.8728 (pt0) REVERT: B 100 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9007 (mm) REVERT: B 120 MET cc_start: 0.8423 (mtt) cc_final: 0.8175 (mpp) REVERT: B 286 GLU cc_start: 0.9125 (tp30) cc_final: 0.8625 (tp30) REVERT: B 289 LYS cc_start: 0.9376 (mttm) cc_final: 0.9129 (mttm) REVERT: B 293 ARG cc_start: 0.8423 (tmm-80) cc_final: 0.8141 (ttt180) REVERT: B 296 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8839 (tm-30) outliers start: 38 outliers final: 28 residues processed: 129 average time/residue: 0.0636 time to fit residues: 10.9997 Evaluate side-chains 130 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS B 61 ASN B 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.083637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062981 restraints weight = 14867.007| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 4.94 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5123 Z= 0.113 Angle : 0.623 8.381 6977 Z= 0.292 Chirality : 0.039 0.148 788 Planarity : 0.005 0.042 899 Dihedral : 4.558 59.417 714 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 7.16 % Allowed : 29.76 % Favored : 63.09 % 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: 0.69 (0.34), residues: 634 helix: 1.64 (0.29), residues: 348 sheet: 0.13 (0.93), residues: 30 loop : -1.19 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.015 0.001 TYR B 77 PHE 0.010 0.001 PHE A 221 TRP 0.005 0.001 TRP A 161 HIS 0.012 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 5123) covalent geometry : angle 0.62325 / 0.29 ( 6977) hydrogen bonds : bond 0.02988 / 2.02 ( 261) hydrogen bonds : angle 4.41839 / 3.20 ( 777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9453 (mm) cc_final: 0.9221 (mp) REVERT: A 54 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9302 (tt) REVERT: A 120 MET cc_start: 0.8518 (mmm) cc_final: 0.8193 (mmm) REVERT: A 240 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5207 (t80) REVERT: A 261 TYR cc_start: 0.8950 (m-80) cc_final: 0.8744 (m-80) REVERT: A 286 GLU cc_start: 0.9003 (pt0) cc_final: 0.8727 (pt0) REVERT: B 100 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9044 (mm) REVERT: B 120 MET cc_start: 0.8438 (mtt) cc_final: 0.8202 (mpp) REVERT: B 286 GLU cc_start: 0.9187 (tp30) cc_final: 0.8653 (tp30) REVERT: B 289 LYS cc_start: 0.9364 (mttm) cc_final: 0.9087 (mttm) REVERT: B 293 ARG cc_start: 0.8491 (tmm-80) cc_final: 0.8232 (ttt180) outliers start: 38 outliers final: 29 residues processed: 127 average time/residue: 0.0508 time to fit residues: 8.9079 Evaluate side-chains 131 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.0010 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063080 restraints weight = 15100.185| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.93 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5123 Z= 0.121 Angle : 0.639 9.831 6977 Z= 0.299 Chirality : 0.039 0.148 788 Planarity : 0.005 0.040 899 Dihedral : 4.449 58.059 714 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 7.72 % Allowed : 28.63 % Favored : 63.65 % 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: 0.79 (0.35), residues: 634 helix: 1.68 (0.29), residues: 352 sheet: -0.17 (1.33), residues: 16 loop : -1.04 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.015 0.001 TYR B 77 PHE 0.024 0.001 PHE B 117 TRP 0.008 0.001 TRP B 161 HIS 0.007 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 5123) covalent geometry : angle 0.63897 / 0.30 ( 6977) hydrogen bonds : bond 0.02965 / 2.01 ( 261) hydrogen bonds : angle 4.36143 / 3.16 ( 777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.185 Fit side-chains REVERT: A 49 LEU cc_start: 0.9432 (mm) cc_final: 0.9196 (mp) REVERT: A 54 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9321 (tt) REVERT: A 120 MET cc_start: 0.8582 (mmm) cc_final: 0.8292 (mmm) REVERT: A 240 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5227 (t80) REVERT: A 261 TYR cc_start: 0.9054 (m-80) cc_final: 0.8568 (m-80) REVERT: A 286 GLU cc_start: 0.9003 (pt0) cc_final: 0.8710 (pt0) REVERT: B 100 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9077 (mm) REVERT: B 120 MET cc_start: 0.8454 (mtt) cc_final: 0.8190 (mpp) REVERT: B 286 GLU cc_start: 0.9158 (tp30) cc_final: 0.8640 (tp30) REVERT: B 289 LYS cc_start: 0.9360 (mttm) cc_final: 0.9074 (mttm) outliers start: 41 outliers final: 30 residues processed: 124 average time/residue: 0.0538 time to fit residues: 9.1234 Evaluate side-chains 127 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.058539 restraints weight = 15392.619| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 4.65 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5123 Z= 0.251 Angle : 0.710 8.870 6977 Z= 0.354 Chirality : 0.043 0.146 788 Planarity : 0.006 0.078 899 Dihedral : 4.773 54.814 714 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 9.04 % Allowed : 27.12 % Favored : 63.84 % 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: 0.73 (0.35), residues: 634 helix: 1.62 (0.29), residues: 351 sheet: -0.70 (0.71), residues: 43 loop : -1.00 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.022 0.001 TYR B 77 PHE 0.025 0.002 PHE B 117 TRP 0.007 0.001 TRP A 82 HIS 0.005 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.25 ( 5123) covalent geometry : angle 0.70975 / 0.35 ( 6977) hydrogen bonds : bond 0.03631 / 2.54 ( 261) hydrogen bonds : angle 4.65103 / 3.36 ( 777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8568 (mmm) cc_final: 0.8291 (mmm) REVERT: A 240 TYR cc_start: 0.6215 (OUTLIER) cc_final: 0.5533 (t80) REVERT: A 261 TYR cc_start: 0.8978 (m-80) cc_final: 0.8662 (m-80) REVERT: A 286 GLU cc_start: 0.9028 (pt0) cc_final: 0.8735 (pt0) REVERT: B 61 ASN cc_start: 0.9455 (OUTLIER) cc_final: 0.9133 (t0) REVERT: B 100 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9013 (tp) REVERT: B 120 MET cc_start: 0.8397 (mtt) cc_final: 0.7941 (mpp) REVERT: B 210 ASP cc_start: 0.8892 (m-30) cc_final: 0.8509 (t0) REVERT: B 286 GLU cc_start: 0.9212 (tp30) cc_final: 0.8779 (tp30) REVERT: B 296 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.8774 (tm-30) REVERT: B 332 HIS cc_start: 0.9650 (OUTLIER) cc_final: 0.9316 (t-90) outliers start: 48 outliers final: 30 residues processed: 117 average time/residue: 0.0552 time to fit residues: 8.8748 Evaluate side-chains 120 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 0.0370 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 HIS B 287 GLN B 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.081537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.061537 restraints weight = 14837.124| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.80 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5123 Z= 0.120 Angle : 0.669 9.830 6977 Z= 0.316 Chirality : 0.040 0.157 788 Planarity : 0.005 0.043 899 Dihedral : 4.417 48.704 714 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.84 % Allowed : 31.07 % Favored : 63.09 % 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: 0.96 (0.35), residues: 634 helix: 1.78 (0.29), residues: 353 sheet: -0.51 (1.26), residues: 16 loop : -0.87 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.015 0.001 TYR B 77 PHE 0.024 0.001 PHE B 117 TRP 0.008 0.001 TRP A 161 HIS 0.002 0.001 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 5123) covalent geometry : angle 0.66875 / 0.32 ( 6977) hydrogen bonds : bond 0.02957 / 2.01 ( 261) hydrogen bonds : angle 4.34317 / 3.17 ( 777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9495 (mm) cc_final: 0.9259 (mp) REVERT: A 120 MET cc_start: 0.8591 (mmm) cc_final: 0.8258 (mmm) REVERT: A 240 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5531 (t80) REVERT: A 286 GLU cc_start: 0.9004 (pt0) cc_final: 0.8735 (pt0) REVERT: B 100 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9030 (tp) REVERT: B 105 PHE cc_start: 0.9127 (m-80) cc_final: 0.8797 (m-80) REVERT: B 286 GLU cc_start: 0.9175 (tp30) cc_final: 0.8698 (tp30) REVERT: B 289 LYS cc_start: 0.9301 (mttm) cc_final: 0.8945 (mttm) outliers start: 31 outliers final: 22 residues processed: 118 average time/residue: 0.0573 time to fit residues: 9.2528 Evaluate side-chains 115 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 332 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 43 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.061495 restraints weight = 15048.436| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.83 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5123 Z= 0.122 Angle : 0.683 9.395 6977 Z= 0.321 Chirality : 0.040 0.189 788 Planarity : 0.005 0.042 899 Dihedral : 4.320 47.764 714 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.08 % Allowed : 31.83 % Favored : 63.09 % 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: 0.97 (0.35), residues: 634 helix: 1.78 (0.29), residues: 353 sheet: -0.57 (1.24), residues: 16 loop : -0.86 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.015 0.001 TYR B 77 PHE 0.022 0.001 PHE B 117 TRP 0.006 0.001 TRP A 161 HIS 0.002 0.000 HIS B 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 5123) covalent geometry : angle 0.68332 / 0.32 ( 6977) hydrogen bonds : bond 0.02981 / 2.04 ( 261) hydrogen bonds : angle 4.28412 / 3.12 ( 777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9494 (mm) cc_final: 0.9263 (mp) REVERT: A 120 MET cc_start: 0.8605 (mmm) cc_final: 0.8247 (mmm) REVERT: A 143 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8431 (pt0) REVERT: A 240 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.5633 (t80) REVERT: A 286 GLU cc_start: 0.8963 (pt0) cc_final: 0.8671 (pt0) REVERT: B 100 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9023 (tp) REVERT: B 105 PHE cc_start: 0.9161 (m-80) cc_final: 0.8838 (m-80) REVERT: B 210 ASP cc_start: 0.8882 (m-30) cc_final: 0.8504 (t0) REVERT: B 286 GLU cc_start: 0.9166 (tp30) cc_final: 0.8638 (tp30) REVERT: B 289 LYS cc_start: 0.9337 (mttm) cc_final: 0.8981 (mttm) outliers start: 27 outliers final: 21 residues processed: 113 average time/residue: 0.0551 time to fit residues: 8.5974 Evaluate side-chains 117 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 30 optimal weight: 0.0040 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.0030 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.082499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.062468 restraints weight = 15041.289| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.90 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5123 Z= 0.116 Angle : 0.689 9.892 6977 Z= 0.317 Chirality : 0.040 0.162 788 Planarity : 0.005 0.041 899 Dihedral : 4.236 46.390 714 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.65 % Allowed : 31.07 % Favored : 63.28 % 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: 1.00 (0.35), residues: 634 helix: 1.83 (0.29), residues: 353 sheet: -0.87 (1.18), residues: 16 loop : -0.86 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.015 0.001 TYR B 77 PHE 0.021 0.001 PHE B 117 TRP 0.006 0.001 TRP A 161 HIS 0.004 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5123) covalent geometry : angle 0.68937 / 0.32 ( 6977) hydrogen bonds : bond 0.02893 / 1.96 ( 261) hydrogen bonds : angle 4.25144 / 3.07 ( 777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8635 (mmm) cc_final: 0.8271 (mmm) REVERT: A 240 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.5868 (t80) REVERT: A 286 GLU cc_start: 0.8981 (pt0) cc_final: 0.8682 (pt0) REVERT: B 100 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9021 (tp) REVERT: B 105 PHE cc_start: 0.9142 (m-80) cc_final: 0.8811 (m-80) REVERT: B 106 TYR cc_start: 0.8458 (t80) cc_final: 0.8250 (t80) REVERT: B 204 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9023 (mt) REVERT: B 210 ASP cc_start: 0.8884 (m-30) cc_final: 0.8497 (t0) REVERT: B 286 GLU cc_start: 0.9147 (tp30) cc_final: 0.8628 (tp30) REVERT: B 289 LYS cc_start: 0.9351 (mttm) cc_final: 0.9111 (mttm) outliers start: 30 outliers final: 23 residues processed: 114 average time/residue: 0.0610 time to fit residues: 9.5758 Evaluate side-chains 123 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.079556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.059372 restraints weight = 15243.556| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.76 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5123 Z= 0.177 Angle : 0.712 9.444 6977 Z= 0.339 Chirality : 0.042 0.166 788 Planarity : 0.005 0.044 899 Dihedral : 4.354 45.330 714 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.46 % Allowed : 31.83 % Favored : 62.71 % 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: 0.97 (0.35), residues: 634 helix: 1.80 (0.29), residues: 354 sheet: -1.24 (0.80), residues: 29 loop : -0.79 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 293 TYR 0.017 0.001 TYR B 77 PHE 0.021 0.002 PHE B 117 TRP 0.005 0.001 TRP A 161 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 5123) covalent geometry : angle 0.71170 / 0.34 ( 6977) hydrogen bonds : bond 0.03215 / 2.18 ( 261) hydrogen bonds : angle 4.39589 / 3.18 ( 777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.199 Fit side-chains REVERT: A 120 MET cc_start: 0.8649 (mmm) cc_final: 0.8278 (mmm) REVERT: A 240 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5944 (t80) REVERT: A 286 GLU cc_start: 0.8989 (pt0) cc_final: 0.8698 (pt0) REVERT: B 100 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9088 (tp) REVERT: B 105 PHE cc_start: 0.9165 (m-80) cc_final: 0.8847 (m-80) REVERT: B 106 TYR cc_start: 0.8533 (t80) cc_final: 0.8302 (t80) REVERT: B 210 ASP cc_start: 0.8910 (m-30) cc_final: 0.8531 (t0) REVERT: B 286 GLU cc_start: 0.9166 (tp30) cc_final: 0.8651 (tp30) REVERT: B 289 LYS cc_start: 0.9328 (mttm) cc_final: 0.8965 (mttm) outliers start: 29 outliers final: 19 residues processed: 106 average time/residue: 0.0618 time to fit residues: 9.1273 Evaluate side-chains 112 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.060359 restraints weight = 15311.885| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.82 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5123 Z= 0.137 Angle : 0.698 10.106 6977 Z= 0.327 Chirality : 0.041 0.174 788 Planarity : 0.005 0.043 899 Dihedral : 4.294 44.017 714 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.27 % Allowed : 31.64 % Favored : 63.09 % 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: 1.02 (0.35), residues: 634 helix: 1.82 (0.29), residues: 354 sheet: -1.18 (1.20), residues: 16 loop : -0.79 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.017 0.001 TYR B 77 PHE 0.021 0.001 PHE B 117 TRP 0.006 0.001 TRP A 161 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5123) covalent geometry : angle 0.69838 / 0.33 ( 6977) hydrogen bonds : bond 0.02985 / 2.03 ( 261) hydrogen bonds : angle 4.30349 / 3.13 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 984.57 seconds wall clock time: 17 minutes 41.37 seconds (1061.37 seconds total)