Starting phenix.real_space_refine on Sun Apr 5 06:37:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x9a_33069/04_2026/7x9a_33069.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x9a_33069/04_2026/7x9a_33069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x9a_33069/04_2026/7x9a_33069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x9a_33069/04_2026/7x9a_33069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x9a_33069/04_2026/7x9a_33069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x9a_33069/04_2026/7x9a_33069.map" } resolution = 3.2 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2000 atoms to isotropic. 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 54 5.16 5 C 4591 2.51 5 N 1210 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7156 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2427 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1623 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2443 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 384 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 279 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 31} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 1.47, per 1000 atoms: 0.21 Number of scatterers: 7156 At special positions: 0 Unit cell: (114.95, 124.355, 85.69, 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 54 16.00 O 1301 8.00 N 1210 7.00 C 4591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 33 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 198 " 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: 0.68 Conformation dependent library (CDL) restraints added in 171.4 milliseconds 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 43.4% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 37 through 67 removed outlier: 3.686A pdb=" N PHE R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 104 removed outlier: 3.978A pdb=" N ILE R 77 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix removed outlier: 3.675A pdb=" N LEU R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 143 Proline residue: R 117 - end of helix Processing helix chain 'R' and resid 151 through 171 Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 204 through 220 Processing helix chain 'R' and resid 221 through 245 removed outlier: 3.694A pdb=" N ILE R 234 " --> pdb=" O CYS R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 287 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 320 removed outlier: 4.141A pdb=" N LEU R 303 " --> pdb=" O ASN R 299 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA R 309 " --> pdb=" O CYS R 305 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS R 314 " --> pdb=" O MET R 310 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN R 316 " --> pdb=" O SER R 312 " (cutoff:3.500A) Proline residue: R 317 - end of helix Processing helix chain 'R' and resid 324 through 329 removed outlier: 3.608A pdb=" N ARG R 329 " --> pdb=" O LYS R 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 33 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.640A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.699A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.798A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.599A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 22 removed outlier: 4.033A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'P' and resid 13 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.081A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.450A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.301A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.673A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.507A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.452A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.418A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 358 hydrogen bonds defined for protein. 1035 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: 1.14 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2312 1.34 - 1.46: 1772 1.46 - 1.58: 3151 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7310 Sorted by residual: bond pdb=" CB TYC P 36 " pdb=" CG TYC P 36 " ideal model delta sigma weight residual 1.501 1.391 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N TRP R 288 " pdb=" CA TRP R 288 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.25e+00 bond pdb=" C LEU R 277 " pdb=" N PRO R 278 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 bond pdb=" C ASP R 287 " pdb=" N TRP R 288 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.29e-02 6.01e+03 8.44e-01 bond pdb=" C LEU R 218 " pdb=" N GLN R 219 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.52e-02 4.33e+03 7.38e-01 ... (remaining 7305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9866 1.87 - 3.74: 77 3.74 - 5.61: 18 5.61 - 7.48: 4 7.48 - 9.35: 1 Bond angle restraints: 9966 Sorted by residual: angle pdb=" CA LEU R 94 " pdb=" CB LEU R 94 " pdb=" CG LEU R 94 " ideal model delta sigma weight residual 116.30 125.65 -9.35 3.50e+00 8.16e-02 7.14e+00 angle pdb=" C TRP R 288 " pdb=" N ASN R 289 " pdb=" CA ASN R 289 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.89e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.83e+00 angle pdb=" CA TRP R 288 " pdb=" C TRP R 288 " pdb=" O TRP R 288 " ideal model delta sigma weight residual 119.59 116.74 2.85 1.18e+00 7.18e-01 5.82e+00 angle pdb=" CA TRP R 288 " pdb=" CB TRP R 288 " pdb=" CG TRP R 288 " ideal model delta sigma weight residual 113.60 109.22 4.38 1.90e+00 2.77e-01 5.32e+00 ... (remaining 9961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 3997 15.37 - 30.74: 230 30.74 - 46.11: 57 46.11 - 61.48: 5 61.48 - 76.85: 2 Dihedral angle restraints: 4291 sinusoidal: 1507 harmonic: 2784 Sorted by residual: dihedral pdb=" CB CYS R 33 " pdb=" SG CYS R 33 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -116.46 30.46 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA ASP R 86 " pdb=" CB ASP R 86 " pdb=" CG ASP R 86 " pdb=" OD1 ASP R 86 " ideal model delta sinusoidal sigma weight residual -30.00 -85.72 55.72 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP R 31 " pdb=" CB ASP R 31 " pdb=" CG ASP R 31 " pdb=" OD1 ASP R 31 " ideal model delta sinusoidal sigma weight residual -30.00 -80.64 50.64 1 2.00e+01 2.50e-03 8.78e+00 ... (remaining 4288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 764 0.033 - 0.066: 309 0.066 - 0.099: 79 0.099 - 0.131: 24 0.131 - 0.164: 2 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CA TRP R 288 " pdb=" N TRP R 288 " pdb=" C TRP R 288 " pdb=" CB TRP R 288 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA LEU R 94 " pdb=" N LEU R 94 " pdb=" C LEU R 94 " pdb=" CB LEU R 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1175 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 288 " -0.012 2.00e-02 2.50e+03 8.43e-03 1.77e+00 pdb=" CG TRP R 288 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP R 288 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP R 288 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 288 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP R 288 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 288 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 288 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 288 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 288 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO R 172 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 222 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO R 223 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO R 223 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 223 " -0.017 5.00e-02 4.00e+02 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1639 2.78 - 3.31: 7039 3.31 - 3.84: 12063 3.84 - 4.37: 13598 4.37 - 4.90: 23507 Nonbonded interactions: 57846 Sorted by model distance: nonbonded pdb=" O TRP R 276 " pdb=" OG1 THR R 280 " model vdw 2.251 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.257 3.040 nonbonded pdb=" O LEU B 210 " pdb=" N ARG B 219 " model vdw 2.284 3.120 nonbonded pdb=" ND2 ASN B 119 " pdb=" O GLY B 144 " model vdw 2.293 3.120 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.339 3.040 ... (remaining 57841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.290 Find NCS groups from input model: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.002 0.110 7312 Z= 0.116 Angle : 0.489 9.352 9970 Z= 0.262 Chirality : 0.039 0.164 1178 Planarity : 0.003 0.031 1262 Dihedral : 10.375 76.846 2475 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: -2.79 (0.25), residues: 935 helix: -0.73 (0.24), residues: 392 sheet: -1.88 (0.36), residues: 172 loop : -3.01 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 150 TYR 0.013 0.001 TYR R 100 PHE 0.006 0.001 PHE B 241 TRP 0.023 0.001 TRP R 288 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7310) covalent geometry : angle 0.48853 ( 9966) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.92084 ( 4) hydrogen bonds : bond 0.14959 ( 358) hydrogen bonds : angle 5.64668 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 TYR cc_start: 0.8313 (m-10) cc_final: 0.7954 (m-80) REVERT: B 138 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 264 TYR cc_start: 0.7707 (m-10) cc_final: 0.7114 (m-10) REVERT: B 297 TRP cc_start: 0.7084 (m100) cc_final: 0.6548 (m100) REVERT: C 47 GLU cc_start: 0.7950 (mp0) cc_final: 0.7697 (mp0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.0874 time to fit residues: 25.5666 Evaluate side-chains 149 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 76 ASN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 326 ASN A 204 GLN A 244 HIS A 347 ASN B 17 GLN B 220 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.108756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.090042 restraints weight = 19732.479| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.04 r_work: 0.3405 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7312 Z= 0.110 Angle : 0.580 9.871 9970 Z= 0.287 Chirality : 0.041 0.162 1178 Planarity : 0.003 0.037 1262 Dihedral : 3.433 29.638 1017 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.61 % Allowed : 13.76 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.27), residues: 935 helix: 0.26 (0.27), residues: 402 sheet: -1.67 (0.35), residues: 175 loop : -2.61 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 260 TYR 0.012 0.001 TYR C 40 PHE 0.025 0.001 PHE B 199 TRP 0.017 0.001 TRP B 211 HIS 0.007 0.001 HIS P 26 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7310) covalent geometry : angle 0.57987 ( 9966) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.90567 ( 4) hydrogen bonds : bond 0.03459 ( 358) hydrogen bonds : angle 4.28372 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 MET cc_start: 0.6499 (ptp) cc_final: 0.6218 (ptp) REVERT: A 18 MET cc_start: 0.8887 (ppp) cc_final: 0.8222 (ppp) REVERT: A 216 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 258 TRP cc_start: 0.8592 (m100) cc_final: 0.7811 (m100) REVERT: B 138 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8299 (mt-10) REVERT: B 156 GLN cc_start: 0.7844 (mt0) cc_final: 0.7446 (mt0) REVERT: B 211 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.6658 (m100) REVERT: B 297 TRP cc_start: 0.8150 (m100) cc_final: 0.7423 (m100) outliers start: 19 outliers final: 12 residues processed: 179 average time/residue: 0.0695 time to fit residues: 16.9383 Evaluate side-chains 173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 ASN R 326 ASN A 213 HIS A 269 ASN A 322 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.101740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082601 restraints weight = 19423.457| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.93 r_work: 0.3253 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7312 Z= 0.166 Angle : 0.609 9.629 9970 Z= 0.304 Chirality : 0.042 0.178 1178 Planarity : 0.003 0.040 1262 Dihedral : 3.859 30.096 1017 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.71 % Allowed : 16.51 % Favored : 79.78 % 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: -1.32 (0.28), residues: 935 helix: 0.59 (0.27), residues: 404 sheet: -1.56 (0.35), residues: 189 loop : -2.20 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 260 TYR 0.015 0.001 TYR A 287 PHE 0.020 0.002 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7310) covalent geometry : angle 0.60842 ( 9966) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.10530 ( 4) hydrogen bonds : bond 0.03477 ( 358) hydrogen bonds : angle 4.14624 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 92 MET cc_start: 0.7786 (tpt) cc_final: 0.7494 (tpt) REVERT: R 153 ARG cc_start: 0.7590 (mmt180) cc_final: 0.7385 (mmp-170) REVERT: R 248 MET cc_start: 0.6827 (ptp) cc_final: 0.6497 (ptp) REVERT: B 156 GLN cc_start: 0.7945 (mt0) cc_final: 0.7670 (mt0) REVERT: B 211 TRP cc_start: 0.7886 (OUTLIER) cc_final: 0.6935 (m100) REVERT: B 292 PHE cc_start: 0.8063 (m-10) cc_final: 0.7699 (m-10) outliers start: 27 outliers final: 21 residues processed: 171 average time/residue: 0.0679 time to fit residues: 16.1951 Evaluate side-chains 165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 59 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 17 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.102916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083852 restraints weight = 19893.361| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.96 r_work: 0.3270 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7312 Z= 0.121 Angle : 0.581 9.703 9970 Z= 0.285 Chirality : 0.041 0.190 1178 Planarity : 0.003 0.041 1262 Dihedral : 3.974 30.498 1017 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.44 % Allowed : 17.33 % Favored : 79.23 % 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: -1.04 (0.28), residues: 935 helix: 0.78 (0.27), residues: 407 sheet: -1.45 (0.37), residues: 163 loop : -1.99 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 260 TYR 0.023 0.001 TYR A 287 PHE 0.018 0.001 PHE A 250 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7310) covalent geometry : angle 0.58131 ( 9966) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.72700 ( 4) hydrogen bonds : bond 0.03215 ( 358) hydrogen bonds : angle 4.06624 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 200 ASP cc_start: 0.7707 (p0) cc_final: 0.7454 (p0) REVERT: R 248 MET cc_start: 0.6917 (ptp) cc_final: 0.6644 (ptp) REVERT: A 18 MET cc_start: 0.8821 (ppp) cc_final: 0.8164 (ppp) REVERT: A 286 CYS cc_start: 0.8543 (t) cc_final: 0.8209 (t) REVERT: A 287 TYR cc_start: 0.7019 (m-80) cc_final: 0.6773 (m-10) REVERT: B 264 TYR cc_start: 0.8136 (m-10) cc_final: 0.7852 (m-10) REVERT: B 292 PHE cc_start: 0.8037 (m-10) cc_final: 0.7481 (m-10) REVERT: B 297 TRP cc_start: 0.8321 (m100) cc_final: 0.7677 (m100) outliers start: 25 outliers final: 22 residues processed: 169 average time/residue: 0.0748 time to fit residues: 17.3401 Evaluate side-chains 168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain P residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 54 optimal weight: 0.0000 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 76 ASN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN A 294 ASN B 17 GLN B 32 GLN B 142 HIS B 175 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.097938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078988 restraints weight = 19570.549| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.79 r_work: 0.3180 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7312 Z= 0.188 Angle : 0.619 9.307 9970 Z= 0.310 Chirality : 0.042 0.199 1178 Planarity : 0.003 0.041 1262 Dihedral : 4.361 35.638 1017 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.13 % Allowed : 18.57 % Favored : 77.30 % 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: -0.82 (0.28), residues: 935 helix: 0.92 (0.27), residues: 400 sheet: -1.53 (0.36), residues: 167 loop : -1.65 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 260 TYR 0.015 0.001 TYR A 287 PHE 0.020 0.002 PHE A 274 TRP 0.019 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7310) covalent geometry : angle 0.61829 ( 9966) SS BOND : bond 0.00192 ( 2) SS BOND : angle 1.04065 ( 4) hydrogen bonds : bond 0.03449 ( 358) hydrogen bonds : angle 4.16886 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 MET cc_start: 0.7009 (ptp) cc_final: 0.6654 (ptp) REVERT: B 57 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8585 (ptpp) REVERT: B 292 PHE cc_start: 0.8533 (m-10) cc_final: 0.7829 (m-10) REVERT: B 339 TRP cc_start: 0.8751 (m100) cc_final: 0.8006 (m100) outliers start: 30 outliers final: 25 residues processed: 168 average time/residue: 0.0652 time to fit residues: 15.5530 Evaluate side-chains 167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 90 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.099325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.080279 restraints weight = 19520.770| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.84 r_work: 0.3205 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7312 Z= 0.136 Angle : 0.598 9.620 9970 Z= 0.298 Chirality : 0.042 0.210 1178 Planarity : 0.003 0.041 1262 Dihedral : 4.275 34.366 1017 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.26 % Allowed : 19.12 % Favored : 76.62 % 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: -0.82 (0.28), residues: 935 helix: 0.88 (0.28), residues: 407 sheet: -1.49 (0.36), residues: 164 loop : -1.68 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 260 TYR 0.014 0.001 TYR B 124 PHE 0.016 0.001 PHE A 250 TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7310) covalent geometry : angle 0.59737 ( 9966) SS BOND : bond 0.00279 ( 2) SS BOND : angle 1.02835 ( 4) hydrogen bonds : bond 0.03243 ( 358) hydrogen bonds : angle 4.11493 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 31 ASP cc_start: 0.7647 (m-30) cc_final: 0.7333 (t70) REVERT: R 248 MET cc_start: 0.6995 (ptp) cc_final: 0.6643 (ptp) REVERT: A 287 TYR cc_start: 0.7048 (m-80) cc_final: 0.6699 (m-10) REVERT: B 57 LYS cc_start: 0.8957 (ptpp) cc_final: 0.8647 (ptpp) REVERT: B 264 TYR cc_start: 0.8177 (m-10) cc_final: 0.7174 (m-10) REVERT: B 292 PHE cc_start: 0.8623 (m-10) cc_final: 0.7861 (m-10) REVERT: B 339 TRP cc_start: 0.8698 (m100) cc_final: 0.7946 (m100) outliers start: 31 outliers final: 27 residues processed: 167 average time/residue: 0.0688 time to fit residues: 16.0862 Evaluate side-chains 167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain P residue 31 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081326 restraints weight = 19533.481| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.89 r_work: 0.3228 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7312 Z= 0.127 Angle : 0.598 9.262 9970 Z= 0.298 Chirality : 0.041 0.189 1178 Planarity : 0.003 0.042 1262 Dihedral : 4.139 30.173 1017 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.40 % Allowed : 19.53 % Favored : 76.07 % 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: -0.78 (0.28), residues: 935 helix: 0.91 (0.27), residues: 408 sheet: -1.46 (0.37), residues: 157 loop : -1.66 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.011 0.001 TYR B 124 PHE 0.023 0.001 PHE A 274 TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7310) covalent geometry : angle 0.59826 ( 9966) SS BOND : bond 0.00330 ( 2) SS BOND : angle 0.92744 ( 4) hydrogen bonds : bond 0.03177 ( 358) hydrogen bonds : angle 4.07036 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 31 ASP cc_start: 0.7678 (m-30) cc_final: 0.7305 (t70) REVERT: R 39 MET cc_start: 0.8350 (ptp) cc_final: 0.7968 (ptp) REVERT: R 248 MET cc_start: 0.6943 (ptp) cc_final: 0.6589 (ptp) REVERT: A 18 MET cc_start: 0.8800 (ppp) cc_final: 0.8117 (ppp) REVERT: B 264 TYR cc_start: 0.8102 (m-10) cc_final: 0.7011 (m-10) REVERT: B 292 PHE cc_start: 0.8690 (m-10) cc_final: 0.7904 (m-10) REVERT: B 297 TRP cc_start: 0.8343 (m100) cc_final: 0.7627 (m100) outliers start: 32 outliers final: 25 residues processed: 166 average time/residue: 0.0670 time to fit residues: 15.7068 Evaluate side-chains 157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain P residue 31 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.099831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080946 restraints weight = 19520.549| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.83 r_work: 0.3228 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7312 Z= 0.133 Angle : 0.619 9.465 9970 Z= 0.307 Chirality : 0.042 0.217 1178 Planarity : 0.003 0.041 1262 Dihedral : 4.135 30.726 1017 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.58 % Allowed : 20.91 % Favored : 75.52 % 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: -0.69 (0.28), residues: 935 helix: 0.96 (0.28), residues: 407 sheet: -1.49 (0.36), residues: 163 loop : -1.53 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 237 TYR 0.023 0.001 TYR A 287 PHE 0.015 0.001 PHE A 250 TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7310) covalent geometry : angle 0.61926 ( 9966) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.99675 ( 4) hydrogen bonds : bond 0.03210 ( 358) hydrogen bonds : angle 4.07203 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 31 ASP cc_start: 0.7637 (m-30) cc_final: 0.7311 (t70) REVERT: R 39 MET cc_start: 0.8388 (ptp) cc_final: 0.8135 (ptm) REVERT: R 248 MET cc_start: 0.6856 (ptp) cc_final: 0.6509 (ptp) REVERT: A 18 MET cc_start: 0.8816 (ppp) cc_final: 0.8137 (ppp) REVERT: B 45 MET cc_start: 0.8623 (mmm) cc_final: 0.8365 (tpp) REVERT: B 264 TYR cc_start: 0.7885 (m-10) cc_final: 0.6956 (m-10) REVERT: B 297 TRP cc_start: 0.8334 (m100) cc_final: 0.7601 (m100) outliers start: 26 outliers final: 20 residues processed: 156 average time/residue: 0.0661 time to fit residues: 14.4947 Evaluate side-chains 153 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.098112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078942 restraints weight = 19478.986| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.88 r_work: 0.3175 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7312 Z= 0.166 Angle : 0.660 17.517 9970 Z= 0.324 Chirality : 0.043 0.209 1178 Planarity : 0.003 0.041 1262 Dihedral : 4.167 28.899 1017 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.85 % Allowed : 20.91 % Favored : 75.24 % 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 (0.29), residues: 935 helix: 0.95 (0.27), residues: 408 sheet: -1.43 (0.37), residues: 161 loop : -1.56 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 237 TYR 0.008 0.001 TYR R 220 PHE 0.027 0.001 PHE A 274 TRP 0.021 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7310) covalent geometry : angle 0.66009 ( 9966) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.85905 ( 4) hydrogen bonds : bond 0.03373 ( 358) hydrogen bonds : angle 4.16386 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 31 ASP cc_start: 0.7706 (m-30) cc_final: 0.7406 (t70) REVERT: R 84 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: R 245 MET cc_start: 0.7571 (ppp) cc_final: 0.7330 (ppp) REVERT: R 248 MET cc_start: 0.6776 (ptp) cc_final: 0.6334 (ptp) REVERT: A 298 GLU cc_start: 0.9309 (tt0) cc_final: 0.8942 (tt0) REVERT: B 45 MET cc_start: 0.8675 (mmm) cc_final: 0.8403 (tpp) REVERT: B 57 LYS cc_start: 0.8932 (ptpp) cc_final: 0.8488 (ptpt) REVERT: B 264 TYR cc_start: 0.8079 (m-10) cc_final: 0.7286 (m-10) REVERT: B 292 PHE cc_start: 0.8876 (m-10) cc_final: 0.7952 (m-10) REVERT: B 339 TRP cc_start: 0.8700 (m100) cc_final: 0.8004 (m100) REVERT: C 47 GLU cc_start: 0.8361 (mp0) cc_final: 0.8086 (mp0) outliers start: 28 outliers final: 22 residues processed: 154 average time/residue: 0.0632 time to fit residues: 13.8086 Evaluate side-chains 154 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 72 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080444 restraints weight = 19449.909| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.82 r_work: 0.3212 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7312 Z= 0.131 Angle : 0.660 17.142 9970 Z= 0.320 Chirality : 0.042 0.209 1178 Planarity : 0.003 0.041 1262 Dihedral : 4.085 30.552 1017 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.16 % Allowed : 21.73 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.29), residues: 935 helix: 0.95 (0.28), residues: 409 sheet: -1.28 (0.39), residues: 148 loop : -1.62 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 237 TYR 0.008 0.001 TYR B 124 PHE 0.016 0.001 PHE R 98 TRP 0.021 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7310) covalent geometry : angle 0.65951 ( 9966) SS BOND : bond 0.00282 ( 2) SS BOND : angle 0.85738 ( 4) hydrogen bonds : bond 0.03316 ( 358) hydrogen bonds : angle 4.14108 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 31 ASP cc_start: 0.7701 (m-30) cc_final: 0.7402 (t70) REVERT: R 245 MET cc_start: 0.7578 (ppp) cc_final: 0.7334 (ppp) REVERT: R 248 MET cc_start: 0.6939 (ptp) cc_final: 0.6525 (ptp) REVERT: A 18 MET cc_start: 0.8886 (ppp) cc_final: 0.8177 (ppp) REVERT: A 298 GLU cc_start: 0.9342 (tt0) cc_final: 0.8984 (tt0) REVERT: B 264 TYR cc_start: 0.7960 (m-10) cc_final: 0.7099 (m-10) REVERT: B 292 PHE cc_start: 0.8843 (m-10) cc_final: 0.7974 (m-10) REVERT: B 297 TRP cc_start: 0.8333 (m100) cc_final: 0.7586 (m100) REVERT: C 47 GLU cc_start: 0.8348 (mp0) cc_final: 0.8054 (mp0) outliers start: 23 outliers final: 19 residues processed: 150 average time/residue: 0.0653 time to fit residues: 13.7115 Evaluate side-chains 153 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 33 CYS Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 298 HIS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.096013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077249 restraints weight = 19763.058| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.76 r_work: 0.3128 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 7312 Z= 0.212 Angle : 0.709 16.749 9970 Z= 0.348 Chirality : 0.044 0.210 1178 Planarity : 0.003 0.040 1262 Dihedral : 4.337 28.042 1017 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.58 % Allowed : 21.87 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.28), residues: 935 helix: 0.88 (0.27), residues: 408 sheet: -1.49 (0.37), residues: 163 loop : -1.60 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 237 TYR 0.008 0.001 TYR B 59 PHE 0.032 0.002 PHE A 274 TRP 0.022 0.002 TRP B 169 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 7310) covalent geometry : angle 0.70850 ( 9966) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.88520 ( 4) hydrogen bonds : bond 0.03593 ( 358) hydrogen bonds : angle 4.33826 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.72 seconds wall clock time: 28 minutes 43.66 seconds (1723.66 seconds total)