Starting phenix.real_space_refine on Thu Mar 13 09:59:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x9a_33069/03_2025/7x9a_33069.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x9a_33069/03_2025/7x9a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x9a_33069/03_2025/7x9a_33069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x9a_33069/03_2025/7x9a_33069.map" model { file = "/net/cci-nas-00/data/ceres_data/7x9a_33069/03_2025/7x9a_33069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x9a_33069/03_2025/7x9a_33069.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 8} 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: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 5.16, per 1000 atoms: 0.72 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: 1.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.81 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: 1.99 Time building geometry restraints manager: 2.31 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- 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 7310 Z= 0.121 Angle : 0.489 9.352 9966 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 : 7.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.001 TRP R 288 HIS 0.002 0.000 HIS B 142 PHE 0.006 0.001 PHE B 241 TYR 0.013 0.001 TYR R 100 ARG 0.001 0.000 ARG B 150 *********************** 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 : 0.744 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: 0.2122 time to fit residues: 61.4062 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 : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 219 GLN R 326 ASN A 244 HIS A 347 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.105412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086564 restraints weight = 19438.996| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.96 r_work: 0.3335 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7310 Z= 0.191 Angle : 0.591 9.944 9966 Z= 0.295 Chirality : 0.042 0.167 1178 Planarity : 0.003 0.038 1262 Dihedral : 3.560 29.001 1017 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.03 % Allowed : 14.72 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.27), residues: 935 helix: 0.22 (0.27), residues: 403 sheet: -1.74 (0.35), residues: 178 loop : -2.50 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.007 0.001 HIS P 26 PHE 0.024 0.001 PHE B 199 TYR 0.012 0.001 TYR C 40 ARG 0.004 0.000 ARG R 260 *********************** 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 192 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 120 GLN cc_start: 0.8682 (mt0) cc_final: 0.8422 (mt0) REVERT: R 153 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7227 (mmt180) REVERT: R 248 MET cc_start: 0.6620 (ptp) cc_final: 0.6341 (ptp) REVERT: A 18 MET cc_start: 0.8912 (ppp) cc_final: 0.8250 (ppp) REVERT: A 216 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 258 TRP cc_start: 0.8685 (m100) cc_final: 0.7863 (m100) REVERT: B 138 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8469 (mt-10) REVERT: B 156 GLN cc_start: 0.7907 (mt0) cc_final: 0.7571 (mt0) REVERT: B 211 TRP cc_start: 0.7722 (OUTLIER) cc_final: 0.6725 (m100) REVERT: B 297 TRP cc_start: 0.8325 (m100) cc_final: 0.7596 (m100) outliers start: 22 outliers final: 15 residues processed: 181 average time/residue: 0.1753 time to fit residues: 43.2583 Evaluate side-chains 169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 153 ARG Chi-restraints excluded: chain R residue 171 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 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 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 83 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 326 ASN A 213 HIS A 269 ASN A 306 GLN A 322 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** 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 = 0.3751 r_free = 0.3751 target = 0.101975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082930 restraints weight = 19544.201| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.94 r_work: 0.3262 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 0.064 7310 Z= 0.213 Angle : 0.593 9.708 9966 Z= 0.294 Chirality : 0.041 0.176 1178 Planarity : 0.003 0.040 1262 Dihedral : 3.656 29.984 1017 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.16 % Allowed : 17.47 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.28), residues: 935 helix: 0.59 (0.27), residues: 404 sheet: -1.69 (0.35), residues: 177 loop : -2.16 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.020 0.001 PHE B 292 TYR 0.018 0.001 TYR A 287 ARG 0.004 0.000 ARG R 260 *********************** 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 183 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 MET cc_start: 0.6809 (ptp) cc_final: 0.6477 (ptp) REVERT: A 287 TYR cc_start: 0.7596 (m-80) cc_final: 0.7378 (m-80) REVERT: B 211 TRP cc_start: 0.7826 (OUTLIER) cc_final: 0.6880 (m100) REVERT: B 264 TYR cc_start: 0.8246 (m-10) cc_final: 0.7880 (m-10) REVERT: B 292 PHE cc_start: 0.8001 (m-10) cc_final: 0.7684 (m-10) REVERT: B 297 TRP cc_start: 0.8294 (m100) cc_final: 0.7670 (m100) outliers start: 23 outliers final: 20 residues processed: 173 average time/residue: 0.1762 time to fit residues: 41.8404 Evaluate side-chains 168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 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 298 HIS 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 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 65 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 76 ASN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 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 = 0.3760 r_free = 0.3760 target = 0.102448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083355 restraints weight = 19851.711| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 4.01 r_work: 0.3270 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7310 Z= 0.173 Angle : 0.578 9.848 9966 Z= 0.285 Chirality : 0.041 0.195 1178 Planarity : 0.003 0.040 1262 Dihedral : 3.619 29.347 1017 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.30 % Allowed : 18.43 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.28), residues: 935 helix: 0.71 (0.28), residues: 407 sheet: -1.50 (0.36), residues: 167 loop : -1.96 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.022 0.001 PHE A 274 TYR 0.008 0.001 TYR R 47 ARG 0.004 0.000 ARG R 260 *********************** 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 185 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 76 ASN cc_start: 0.9278 (m110) cc_final: 0.8952 (m110) REVERT: R 93 CYS cc_start: 0.8907 (m) cc_final: 0.8290 (m) REVERT: R 153 ARG cc_start: 0.7700 (mmt180) cc_final: 0.7401 (mmp-170) REVERT: R 200 ASP cc_start: 0.7696 (p0) cc_final: 0.7442 (p0) REVERT: R 248 MET cc_start: 0.6908 (ptp) cc_final: 0.6634 (ptp) REVERT: A 18 MET cc_start: 0.8821 (ppp) cc_final: 0.8163 (ppp) REVERT: A 258 TRP cc_start: 0.8791 (m100) cc_final: 0.8575 (m100) REVERT: B 45 MET cc_start: 0.8532 (ttp) cc_final: 0.8265 (mtp) REVERT: B 211 TRP cc_start: 0.7829 (OUTLIER) cc_final: 0.6842 (m100) REVERT: B 264 TYR cc_start: 0.8188 (m-10) cc_final: 0.7754 (m-10) REVERT: B 292 PHE cc_start: 0.8036 (m-10) cc_final: 0.7446 (m-10) REVERT: B 297 TRP cc_start: 0.8307 (m100) cc_final: 0.7671 (m100) outliers start: 24 outliers final: 20 residues processed: 175 average time/residue: 0.1722 time to fit residues: 41.3440 Evaluate side-chains 167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 298 HIS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain A residue 187 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 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 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 35 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** A 306 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.101884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082637 restraints weight = 19572.998| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.95 r_work: 0.3251 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7310 Z= 0.183 Angle : 0.579 9.866 9966 Z= 0.285 Chirality : 0.041 0.196 1178 Planarity : 0.003 0.042 1262 Dihedral : 3.651 29.707 1017 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.54 % Allowed : 17.74 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 935 helix: 0.82 (0.28), residues: 406 sheet: -1.35 (0.37), residues: 158 loop : -1.91 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE A 250 TYR 0.024 0.001 TYR A 287 ARG 0.005 0.000 ARG R 260 *********************** 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 193 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 ILE cc_start: 0.9316 (pt) cc_final: 0.9066 (tp) REVERT: R 93 CYS cc_start: 0.8909 (m) cc_final: 0.8283 (m) REVERT: R 153 ARG cc_start: 0.7720 (mmt180) cc_final: 0.7472 (mmp-170) REVERT: R 248 MET cc_start: 0.6926 (ptp) cc_final: 0.6636 (ptp) REVERT: A 216 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8136 (mm-30) REVERT: A 286 CYS cc_start: 0.8607 (t) cc_final: 0.8282 (t) REVERT: A 287 TYR cc_start: 0.7314 (m-80) cc_final: 0.6346 (m-10) REVERT: B 57 LYS cc_start: 0.8884 (ptpp) cc_final: 0.8553 (ptpt) REVERT: B 264 TYR cc_start: 0.8139 (m-10) cc_final: 0.7714 (m-10) REVERT: B 292 PHE cc_start: 0.8171 (m-10) cc_final: 0.7545 (m-10) REVERT: B 297 TRP cc_start: 0.8278 (m100) cc_final: 0.7618 (m100) outliers start: 33 outliers final: 29 residues processed: 178 average time/residue: 0.1636 time to fit residues: 40.1458 Evaluate side-chains 173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 225 CYS Chi-restraints excluded: chain R residue 293 ILE 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 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 285 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 85 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** B 32 GLN B 142 HIS ** B 175 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 = 0.3731 r_free = 0.3731 target = 0.100545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081508 restraints weight = 19356.611| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.92 r_work: 0.3232 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7310 Z= 0.190 Angle : 0.593 9.831 9966 Z= 0.293 Chirality : 0.041 0.214 1178 Planarity : 0.003 0.042 1262 Dihedral : 3.687 29.368 1017 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.81 % Allowed : 18.43 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 935 helix: 1.01 (0.28), residues: 400 sheet: -1.31 (0.37), residues: 156 loop : -1.64 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.024 0.001 PHE A 274 TYR 0.010 0.001 TYR A 287 ARG 0.006 0.000 ARG R 260 *********************** 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 188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 ILE cc_start: 0.9353 (pt) cc_final: 0.9102 (tp) REVERT: R 129 PHE cc_start: 0.9216 (m-10) cc_final: 0.9016 (m-10) REVERT: R 153 ARG cc_start: 0.7736 (mmt180) cc_final: 0.7520 (mmp-170) REVERT: R 248 MET cc_start: 0.6910 (ptp) cc_final: 0.6478 (ptp) REVERT: A 18 MET cc_start: 0.8798 (ppp) cc_final: 0.8149 (ppp) REVERT: B 292 PHE cc_start: 0.8282 (m-10) cc_final: 0.7609 (m-10) REVERT: B 297 TRP cc_start: 0.8285 (m100) cc_final: 0.7627 (m100) outliers start: 35 outliers final: 27 residues processed: 172 average time/residue: 0.1669 time to fit residues: 39.8544 Evaluate side-chains 170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 225 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 293 ILE 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 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 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.083174 restraints weight = 19500.005| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.83 r_work: 0.3252 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7310 Z= 0.176 Angle : 0.608 10.479 9966 Z= 0.296 Chirality : 0.041 0.212 1178 Planarity : 0.003 0.042 1262 Dihedral : 3.710 29.199 1017 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.81 % Allowed : 18.98 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.29), residues: 935 helix: 1.02 (0.28), residues: 401 sheet: -1.36 (0.36), residues: 166 loop : -1.52 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE A 250 TYR 0.012 0.001 TYR A 287 ARG 0.004 0.000 ARG R 260 *********************** 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 188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 39 MET cc_start: 0.8325 (ptp) cc_final: 0.7886 (ptp) REVERT: R 43 LEU cc_start: 0.8907 (mp) cc_final: 0.8698 (mp) REVERT: R 52 ILE cc_start: 0.9356 (pt) cc_final: 0.9104 (tp) REVERT: R 76 ASN cc_start: 0.9277 (m110) cc_final: 0.8953 (m-40) REVERT: R 153 ARG cc_start: 0.7731 (mmt180) cc_final: 0.7519 (mmp-170) REVERT: R 248 MET cc_start: 0.6965 (ptp) cc_final: 0.6609 (ptp) REVERT: A 18 MET cc_start: 0.8843 (ppp) cc_final: 0.8203 (ppp) REVERT: B 57 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8555 (ptpt) REVERT: B 262 MET cc_start: 0.6917 (ttt) cc_final: 0.6717 (ttt) REVERT: B 264 TYR cc_start: 0.8092 (m-10) cc_final: 0.6842 (m-10) REVERT: B 292 PHE cc_start: 0.8349 (m-10) cc_final: 0.7641 (m-10) REVERT: B 297 TRP cc_start: 0.8270 (m100) cc_final: 0.7573 (m100) outliers start: 35 outliers final: 28 residues processed: 172 average time/residue: 0.1733 time to fit residues: 40.8279 Evaluate side-chains 175 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 132 VAL Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 225 CYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 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 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 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 13 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 0.0040 chunk 88 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.082196 restraints weight = 19357.376| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.88 r_work: 0.3248 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7310 Z= 0.188 Angle : 0.610 9.924 9966 Z= 0.299 Chirality : 0.041 0.211 1178 Planarity : 0.003 0.041 1262 Dihedral : 3.742 29.217 1017 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.13 % Allowed : 20.22 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 935 helix: 1.09 (0.28), residues: 400 sheet: -1.32 (0.37), residues: 166 loop : -1.47 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.025 0.001 PHE A 274 TYR 0.008 0.001 TYR A 287 ARG 0.008 0.000 ARG R 260 *********************** 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 179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 39 MET cc_start: 0.8310 (ptp) cc_final: 0.8013 (ptp) REVERT: R 45 LEU cc_start: 0.9069 (mt) cc_final: 0.8809 (pp) REVERT: R 52 ILE cc_start: 0.9374 (pt) cc_final: 0.9119 (tp) REVERT: R 76 ASN cc_start: 0.9242 (m110) cc_final: 0.8896 (m-40) REVERT: R 153 ARG cc_start: 0.7783 (mmt180) cc_final: 0.7576 (mmp-170) REVERT: R 248 MET cc_start: 0.6978 (ptp) cc_final: 0.6629 (ptp) REVERT: A 18 MET cc_start: 0.8856 (ppp) cc_final: 0.8220 (ppp) REVERT: B 57 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8507 (ptpt) REVERT: B 262 MET cc_start: 0.6979 (ttt) cc_final: 0.6776 (ttt) REVERT: B 264 TYR cc_start: 0.8110 (m-10) cc_final: 0.6902 (m-10) REVERT: B 292 PHE cc_start: 0.8443 (m-10) cc_final: 0.7718 (m-10) REVERT: B 297 TRP cc_start: 0.8282 (m100) cc_final: 0.7554 (m100) outliers start: 30 outliers final: 26 residues processed: 170 average time/residue: 0.1652 time to fit residues: 38.5060 Evaluate side-chains 179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 293 ILE 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 189 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 0.0170 overall best weight: 0.7824 ------------------------------------------------------------------------------- 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 ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.082041 restraints weight = 19557.918| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.84 r_work: 0.3231 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7310 Z= 0.205 Angle : 0.639 9.658 9966 Z= 0.312 Chirality : 0.042 0.286 1178 Planarity : 0.003 0.043 1262 Dihedral : 3.807 28.492 1017 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.13 % Allowed : 21.05 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.28), residues: 935 helix: 0.97 (0.28), residues: 407 sheet: -1.44 (0.36), residues: 169 loop : -1.53 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE R 98 TYR 0.009 0.001 TYR B 59 ARG 0.008 0.000 ARG R 260 *********************** 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 173 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 52 ILE cc_start: 0.9379 (pt) cc_final: 0.9089 (tp) REVERT: R 92 MET cc_start: 0.8114 (tpt) cc_final: 0.7786 (tpt) REVERT: R 153 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7615 (mmp-170) REVERT: R 248 MET cc_start: 0.6873 (ptp) cc_final: 0.6521 (ptp) REVERT: A 258 TRP cc_start: 0.8723 (m100) cc_final: 0.8509 (m100) REVERT: B 45 MET cc_start: 0.8763 (mmm) cc_final: 0.8523 (tpt) REVERT: B 57 LYS cc_start: 0.8932 (ptpp) cc_final: 0.8611 (ptpt) REVERT: B 264 TYR cc_start: 0.8132 (m-10) cc_final: 0.6982 (m-10) REVERT: B 292 PHE cc_start: 0.8544 (m-10) cc_final: 0.7773 (m-10) REVERT: B 297 TRP cc_start: 0.8295 (m100) cc_final: 0.7572 (m100) outliers start: 30 outliers final: 26 residues processed: 162 average time/residue: 0.1680 time to fit residues: 37.3226 Evaluate side-chains 162 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 293 ILE 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 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 189 SER 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 67 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.100310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.081080 restraints weight = 19830.192| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.95 r_work: 0.3221 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7310 Z= 0.204 Angle : 0.646 9.895 9966 Z= 0.315 Chirality : 0.043 0.282 1178 Planarity : 0.003 0.041 1262 Dihedral : 3.836 28.680 1017 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.58 % Allowed : 22.15 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 935 helix: 0.97 (0.28), residues: 406 sheet: -1.40 (0.36), residues: 164 loop : -1.57 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.030 0.001 PHE A 274 TYR 0.009 0.001 TYR R 47 ARG 0.009 0.001 ARG R 260 ********************** 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 176 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 MET cc_start: 0.8205 (tpt) cc_final: 0.7847 (tpt) REVERT: R 153 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7529 (mmp-170) REVERT: R 245 MET cc_start: 0.7508 (ppp) cc_final: 0.7307 (ppp) REVERT: R 248 MET cc_start: 0.6885 (ptp) cc_final: 0.6443 (ptp) REVERT: R 260 ARG cc_start: 0.9278 (mtp-110) cc_final: 0.8986 (ttm-80) REVERT: A 18 MET cc_start: 0.8876 (ppp) cc_final: 0.8161 (ppp) REVERT: B 45 MET cc_start: 0.8771 (mmm) cc_final: 0.8283 (tpt) REVERT: B 264 TYR cc_start: 0.8309 (m-10) cc_final: 0.6900 (m-10) REVERT: B 292 PHE cc_start: 0.8697 (m-10) cc_final: 0.7884 (m-10) REVERT: B 297 TRP cc_start: 0.8245 (m100) cc_final: 0.7517 (m100) outliers start: 26 outliers final: 25 residues processed: 169 average time/residue: 0.1639 time to fit residues: 38.3210 Evaluate side-chains 169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL 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 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 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 189 SER 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 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.0010 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.101451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.082661 restraints weight = 19188.752| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.88 r_work: 0.3259 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7310 Z= 0.179 Angle : 0.665 17.004 9966 Z= 0.319 Chirality : 0.043 0.265 1178 Planarity : 0.003 0.042 1262 Dihedral : 3.792 29.241 1017 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.85 % Allowed : 22.15 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.28), residues: 935 helix: 0.92 (0.27), residues: 408 sheet: -1.17 (0.38), residues: 154 loop : -1.64 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.001 PHE R 98 TYR 0.010 0.001 TYR R 47 ARG 0.009 0.000 ARG R 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.74 seconds wall clock time: 67 minutes 3.55 seconds (4023.55 seconds total)