Starting phenix.real_space_refine on Fri Oct 10 16:34:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3x_38906/10_2025/8y3x_38906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3x_38906/10_2025/8y3x_38906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3x_38906/10_2025/8y3x_38906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3x_38906/10_2025/8y3x_38906.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3x_38906/10_2025/8y3x_38906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3x_38906/10_2025/8y3x_38906.cif" } resolution = 3.11 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 4907 2.51 5 N 1409 2.21 5 O 1405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7757 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 210} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 210} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1918 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 11, 'ARG:plan': 8, 'ASP:plan': 14, 'GLN:plan1': 10, 'TYR:plan': 4, 'PHE:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 248 Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1888 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 11, 'GLN:plan1': 13, 'ARG:plan': 9, 'TYR:plan': 3, 'ASP:plan': 12, 'PHE:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 264 Chain: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 550 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 14, 'GLN:plan1': 20, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 233 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.11, per 1000 atoms: 0.27 Number of scatterers: 7757 At special positions: 0 Unit cell: (68.04, 78.96, 197.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 6 15.00 O 1405 8.00 N 1409 7.00 C 4907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 473.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 61.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.608A pdb=" N LEU A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.857A pdb=" N VAL A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 196 through 201 removed outlier: 4.217A pdb=" N ILE A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 95 through 108 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 110 through 124 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.505A pdb=" N ALA B 131 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.604A pdb=" N LEU B 138 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.586A pdb=" N ARG B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 79 Processing helix chain 'C' and resid 80 through 107 removed outlier: 3.635A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Proline residue: C 98 - end of helix removed outlier: 4.186A pdb=" N MET C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.887A pdb=" N ALA C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 165 removed outlier: 3.856A pdb=" N GLY C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 3.609A pdb=" N GLY C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 207 removed outlier: 3.632A pdb=" N THR C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 229 through 261 removed outlier: 3.680A pdb=" N SER C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.668A pdb=" N ILE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 300 removed outlier: 3.511A pdb=" N GLY C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 320 removed outlier: 3.925A pdb=" N SER C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 355 removed outlier: 4.134A pdb=" N LEU C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 79 Processing helix chain 'D' and resid 80 through 116 removed outlier: 4.159A pdb=" N LEU D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Proline residue: D 98 - end of helix removed outlier: 3.641A pdb=" N TYR D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 141 Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.573A pdb=" N GLY D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 3.912A pdb=" N GLY D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 removed outlier: 5.036A pdb=" N THR D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 261 removed outlier: 4.306A pdb=" N SER D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 removed outlier: 4.333A pdb=" N GLN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 319 removed outlier: 3.512A pdb=" N ARG D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) Proline residue: D 281 - end of helix removed outlier: 3.789A pdb=" N LEU D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 359 removed outlier: 3.548A pdb=" N ARG D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS D 358 " --> pdb=" O GLN D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 123 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 152 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 25 removed outlier: 5.436A pdb=" N GLN A 19 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS A 9 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE A 23 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU A 5 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N MET A 25 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG A 3 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL A 7 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 56 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 6.465A pdb=" N LEU A 159 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA A 193 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 161 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 31 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 32 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU A 210 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR A 34 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 25 removed outlier: 6.492A pdb=" N ALA B 17 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA B 10 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN B 19 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER B 8 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 21 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL B 7 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 56 " --> pdb=" O VAL B 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.401A pdb=" N GLY B 82 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP B 162 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 84 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 159 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA B 193 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 161 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 31 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'D' and resid 151 through 152 504 hydrogen bonds defined for protein. 1467 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: 1.17 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2396 1.33 - 1.45: 1039 1.45 - 1.57: 4383 1.57 - 1.69: 10 1.69 - 1.81: 52 Bond restraints: 7880 Sorted by residual: bond pdb=" N VAL C 185 " pdb=" CA VAL C 185 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.19e-02 7.06e+03 9.58e+00 bond pdb=" N VAL C 186 " pdb=" CA VAL C 186 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 9.06e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.72e+00 bond pdb=" N ILE C 121 " pdb=" CA ILE C 121 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.02e+00 bond pdb=" N ILE C 211 " pdb=" CA ILE C 211 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.96e+00 ... (remaining 7875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 10530 2.48 - 4.95: 208 4.95 - 7.43: 23 7.43 - 9.90: 3 9.90 - 12.38: 2 Bond angle restraints: 10766 Sorted by residual: angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 129.08 10.79 1.00e+00 1.00e+00 1.16e+02 angle pdb=" PB ATP A 301 " pdb=" O3B ATP A 301 " pdb=" PG ATP A 301 " ideal model delta sigma weight residual 139.87 130.49 9.38 1.00e+00 1.00e+00 8.80e+01 angle pdb=" N ALA C 225 " pdb=" CA ALA C 225 " pdb=" C ALA C 225 " ideal model delta sigma weight residual 114.62 108.03 6.59 1.14e+00 7.69e-01 3.34e+01 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 131.79 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N VAL C 100 " pdb=" CA VAL C 100 " pdb=" C VAL C 100 " ideal model delta sigma weight residual 112.96 108.55 4.41 1.00e+00 1.00e+00 1.95e+01 ... (remaining 10761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4087 16.99 - 33.98: 378 33.98 - 50.97: 158 50.97 - 67.95: 37 67.95 - 84.94: 8 Dihedral angle restraints: 4668 sinusoidal: 1413 harmonic: 3255 Sorted by residual: dihedral pdb=" CA GLU E 114 " pdb=" C GLU E 114 " pdb=" N ARG E 115 " pdb=" CA ARG E 115 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA HIS A 195 " pdb=" C HIS A 195 " pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA SER D 264 " pdb=" C SER D 264 " pdb=" N ILE D 265 " pdb=" CA ILE D 265 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1129 0.066 - 0.131: 153 0.131 - 0.197: 28 0.197 - 0.262: 4 0.262 - 0.328: 2 Chirality restraints: 1316 Sorted by residual: chirality pdb=" CB THR C 360 " pdb=" CA THR C 360 " pdb=" OG1 THR C 360 " pdb=" CG2 THR C 360 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB VAL B 96 " pdb=" CA VAL B 96 " pdb=" CG1 VAL B 96 " pdb=" CG2 VAL B 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LEU C 198 " pdb=" N LEU C 198 " pdb=" C LEU C 198 " pdb=" CB LEU C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1313 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 110 " 0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C LYS E 110 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS E 110 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA E 111 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 280 " 0.060 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO D 281 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 104 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ALA E 104 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA E 104 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS E 105 " -0.017 2.00e-02 2.50e+03 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 98 2.64 - 3.21: 7270 3.21 - 3.77: 11761 3.77 - 4.34: 15138 4.34 - 4.90: 25522 Nonbonded interactions: 59789 Sorted by model distance: nonbonded pdb=" OG SER A 139 " pdb=" OE1 GLU A 142 " model vdw 2.075 3.040 nonbonded pdb=" O ASP A 169 " pdb=" OG SER A 173 " model vdw 2.117 3.040 nonbonded pdb=" NH2 ARG A 79 " pdb=" O GLY D 272 " model vdw 2.215 3.120 nonbonded pdb=" O ASP C 76 " pdb=" OG SER C 79 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 11 " pdb=" OG1 THR B 43 " model vdw 2.244 3.040 ... (remaining 59784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 196 or (resid 197 through 198 and ( \ name N or name CA or name C or name O or name CB )) or resid 199 through 301)) selection = (chain 'B' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 301)) } ncs_group { reference = (chain 'C' and ((resid 63 through 65 and (name N or name CA or name C or name O \ or name CB )) or resid 66 through 74 or (resid 75 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 220 or (resid 221 thro \ ugh 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ rough 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) \ or resid 228 through 229 or (resid 230 through 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 232 or (resid 233 through 234 and (name N \ or name CA or name C or name O or name CB )) or resid 235 through 307 or (resid \ 308 through 319 and (name N or name CA or name C or name O or name CB )) or (res \ id 320 through 326 and (name N or name CA or name C or name O or name CB )) or r \ esid 327 through 331 or (resid 332 and (name N or name CA or name C or name O or \ name CB )) or resid 333 through 353 or (resid 354 and (name N or name CA or nam \ e C or name O or name CB )) or resid 355 through 359 or (resid 360 through 361 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 63 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 105 or (resid 106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 107 through 108 or (resid 109 \ through 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 218 or (resid 219 through 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 233 or (resid 234 and (name N or name CA o \ r name C or name O or name CB )) or resid 235 through 256 or (resid 257 and (nam \ e N or name CA or name C or name O or name CB )) or resid 258 through 262 or (re \ sid 263 and (name N or name CA or name C or name O or name CB )) or resid 264 th \ rough 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) \ or resid 303 through 333 or (resid 334 and (name N or name CA or name C or name \ O or name CB )) or resid 335 through 361)) } 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: 13.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.100 Find NCS groups from input model: 0.080 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.007 0.063 7880 Z= 0.359 Angle : 0.839 12.378 10766 Z= 0.508 Chirality : 0.052 0.328 1316 Planarity : 0.005 0.090 1396 Dihedral : 16.972 84.942 2568 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.31 % Favored : 88.63 % Rotamer: Outliers : 1.47 % Allowed : 27.36 % Favored : 71.17 % 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 aren not related in a simple way. whole: -1.11 (0.25), residues: 1135 helix: 0.58 (0.21), residues: 637 sheet: -2.27 (0.51), residues: 68 loop : -2.53 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 233 TYR 0.008 0.002 TYR C 68 PHE 0.018 0.002 PHE B 23 TRP 0.012 0.002 TRP D 345 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 7880) covalent geometry : angle 0.83877 (10766) hydrogen bonds : bond 0.17702 ( 504) hydrogen bonds : angle 6.68365 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.255 Fit side-chains REVERT: A 71 ASN cc_start: 0.8114 (m-40) cc_final: 0.7825 (t0) REVERT: C 224 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5921 (mt) REVERT: C 306 LEU cc_start: 0.6683 (mt) cc_final: 0.6349 (pp) outliers start: 9 outliers final: 2 residues processed: 138 average time/residue: 0.1449 time to fit residues: 24.5871 Evaluate side-chains 104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.205959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141192 restraints weight = 8799.160| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.13 r_work: 0.3350 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7880 Z= 0.234 Angle : 0.724 12.049 10766 Z= 0.369 Chirality : 0.044 0.216 1316 Planarity : 0.005 0.059 1396 Dihedral : 9.662 88.927 1273 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.90 % Favored : 90.57 % Rotamer: Outliers : 6.68 % Allowed : 21.99 % Favored : 71.34 % 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 aren not related in a simple way. whole: -0.63 (0.25), residues: 1135 helix: 1.04 (0.21), residues: 638 sheet: -1.63 (0.59), residues: 50 loop : -2.54 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 53 TYR 0.021 0.002 TYR C 105 PHE 0.013 0.002 PHE A 23 TRP 0.015 0.002 TRP D 345 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 7880) covalent geometry : angle 0.72433 (10766) hydrogen bonds : bond 0.06004 ( 504) hydrogen bonds : angle 5.10260 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.310 Fit side-chains REVERT: A 71 ASN cc_start: 0.8446 (m-40) cc_final: 0.7676 (t0) REVERT: A 84 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7829 (pt) REVERT: B 53 ARG cc_start: 0.8884 (ttm170) cc_final: 0.8474 (mtm180) REVERT: C 224 LEU cc_start: 0.5375 (OUTLIER) cc_final: 0.5141 (mt) REVERT: C 319 PHE cc_start: 0.6174 (t80) cc_final: 0.5900 (t80) REVERT: D 79 SER cc_start: 0.8426 (p) cc_final: 0.8214 (p) REVERT: D 241 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7397 (mp) REVERT: D 268 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: D 302 GLU cc_start: 0.6318 (tm-30) cc_final: 0.6048 (tp30) outliers start: 41 outliers final: 21 residues processed: 146 average time/residue: 0.1110 time to fit residues: 21.0767 Evaluate side-chains 129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 0.5980 chunk 105 optimal weight: 30.0000 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 9 optimal weight: 0.0970 chunk 85 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.208132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.166436 restraints weight = 8751.487| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.70 r_work: 0.3522 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7880 Z= 0.149 Angle : 0.608 12.361 10766 Z= 0.309 Chirality : 0.040 0.148 1316 Planarity : 0.004 0.052 1396 Dihedral : 8.989 88.786 1271 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.84 % Favored : 91.63 % Rotamer: Outliers : 6.51 % Allowed : 21.50 % Favored : 71.99 % 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 aren not related in a simple way. whole: -0.12 (0.26), residues: 1135 helix: 1.39 (0.21), residues: 649 sheet: -1.70 (0.54), residues: 68 loop : -2.25 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 262 TYR 0.015 0.001 TYR C 105 PHE 0.019 0.001 PHE C 247 TRP 0.011 0.001 TRP D 345 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7880) covalent geometry : angle 0.60836 (10766) hydrogen bonds : bond 0.04550 ( 504) hydrogen bonds : angle 4.70981 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.293 Fit side-chains REVERT: A 71 ASN cc_start: 0.8451 (m-40) cc_final: 0.7665 (t0) REVERT: A 208 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 53 ARG cc_start: 0.8897 (ttm170) cc_final: 0.8492 (mtm180) REVERT: C 68 TYR cc_start: 0.7880 (t80) cc_final: 0.7595 (t80) REVERT: C 224 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.4991 (mt) REVERT: C 319 PHE cc_start: 0.5767 (t80) cc_final: 0.5408 (t80) REVERT: D 79 SER cc_start: 0.8317 (p) cc_final: 0.8083 (p) REVERT: D 268 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7879 (tt0) outliers start: 40 outliers final: 20 residues processed: 134 average time/residue: 0.1090 time to fit residues: 18.9478 Evaluate side-chains 122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 40.0000 chunk 25 optimal weight: 0.2980 chunk 102 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.206842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.165987 restraints weight = 8776.618| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.71 r_work: 0.3497 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7880 Z= 0.187 Angle : 0.655 11.749 10766 Z= 0.328 Chirality : 0.042 0.175 1316 Planarity : 0.004 0.054 1396 Dihedral : 9.211 89.848 1271 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.02 % Favored : 91.45 % Rotamer: Outliers : 7.17 % Allowed : 21.34 % Favored : 71.50 % 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 aren not related in a simple way. whole: 0.05 (0.26), residues: 1135 helix: 1.57 (0.21), residues: 642 sheet: -0.86 (0.63), residues: 60 loop : -2.33 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.009 0.001 TYR C 105 PHE 0.014 0.002 PHE C 247 TRP 0.014 0.002 TRP D 345 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 7880) covalent geometry : angle 0.65461 (10766) hydrogen bonds : bond 0.04976 ( 504) hydrogen bonds : angle 4.65081 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.302 Fit side-chains REVERT: A 83 MET cc_start: 0.8585 (ptt) cc_final: 0.7880 (ttt) REVERT: A 87 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: A 183 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7621 (t80) REVERT: A 208 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8276 (mt) REVERT: C 68 TYR cc_start: 0.7927 (t80) cc_final: 0.7629 (t80) REVERT: C 224 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4805 (mt) REVERT: C 342 MET cc_start: 0.8731 (mmm) cc_final: 0.8477 (mmt) REVERT: D 241 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7115 (mp) REVERT: D 268 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7935 (tt0) outliers start: 44 outliers final: 24 residues processed: 132 average time/residue: 0.1091 time to fit residues: 18.7107 Evaluate side-chains 128 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.208560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.165883 restraints weight = 8730.730| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.50 r_work: 0.3548 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7880 Z= 0.153 Angle : 0.602 11.981 10766 Z= 0.303 Chirality : 0.040 0.147 1316 Planarity : 0.004 0.051 1396 Dihedral : 8.749 86.053 1271 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.84 % Favored : 91.63 % Rotamer: Outliers : 5.70 % Allowed : 22.15 % Favored : 72.15 % 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 aren not related in a simple way. whole: 0.20 (0.26), residues: 1135 helix: 1.70 (0.21), residues: 650 sheet: -1.78 (0.53), residues: 80 loop : -2.17 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.007 0.001 TYR C 105 PHE 0.034 0.002 PHE C 247 TRP 0.014 0.001 TRP D 345 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7880) covalent geometry : angle 0.60242 (10766) hydrogen bonds : bond 0.04296 ( 504) hydrogen bonds : angle 4.47498 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.281 Fit side-chains REVERT: A 83 MET cc_start: 0.8472 (ptt) cc_final: 0.7845 (ttt) REVERT: A 183 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7599 (t80) REVERT: C 68 TYR cc_start: 0.7926 (t80) cc_final: 0.7547 (t80) REVERT: C 224 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.4789 (mt) REVERT: C 306 LEU cc_start: 0.6390 (mt) cc_final: 0.5547 (pp) REVERT: D 268 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7853 (tt0) outliers start: 35 outliers final: 25 residues processed: 126 average time/residue: 0.1153 time to fit residues: 18.5377 Evaluate side-chains 128 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.212830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.174065 restraints weight = 8562.675| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.40 r_work: 0.3645 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7880 Z= 0.181 Angle : 0.640 11.941 10766 Z= 0.319 Chirality : 0.042 0.175 1316 Planarity : 0.004 0.053 1396 Dihedral : 8.866 80.700 1271 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.11 % Favored : 91.37 % Rotamer: Outliers : 6.19 % Allowed : 21.17 % Favored : 72.64 % 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 aren not related in a simple way. whole: 0.28 (0.26), residues: 1135 helix: 1.77 (0.21), residues: 648 sheet: -1.37 (0.59), residues: 73 loop : -2.21 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.006 0.001 TYR C 105 PHE 0.021 0.002 PHE C 247 TRP 0.014 0.002 TRP D 345 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 7880) covalent geometry : angle 0.63956 (10766) hydrogen bonds : bond 0.04724 ( 504) hydrogen bonds : angle 4.42762 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.287 Fit side-chains REVERT: A 83 MET cc_start: 0.8424 (ptt) cc_final: 0.7776 (ttt) REVERT: A 87 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: A 183 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 208 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8324 (mt) REVERT: C 68 TYR cc_start: 0.7842 (t80) cc_final: 0.7468 (t80) REVERT: C 95 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8489 (tt) REVERT: C 224 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4795 (mt) REVERT: C 342 MET cc_start: 0.8746 (mmm) cc_final: 0.8526 (mmt) REVERT: D 241 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.6935 (mp) REVERT: D 268 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: D 330 PHE cc_start: 0.4138 (OUTLIER) cc_final: 0.3845 (m-80) outliers start: 38 outliers final: 25 residues processed: 125 average time/residue: 0.1048 time to fit residues: 17.0571 Evaluate side-chains 129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 82 optimal weight: 0.0570 chunk 25 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS C 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.215360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.176216 restraints weight = 8633.781| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.31 r_work: 0.3687 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7880 Z= 0.134 Angle : 0.582 12.193 10766 Z= 0.292 Chirality : 0.040 0.190 1316 Planarity : 0.003 0.051 1396 Dihedral : 8.509 86.779 1271 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.05 % Favored : 92.42 % Rotamer: Outliers : 5.70 % Allowed : 22.64 % Favored : 71.66 % 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 aren not related in a simple way. whole: 0.52 (0.26), residues: 1135 helix: 1.97 (0.21), residues: 650 sheet: -1.58 (0.56), residues: 80 loop : -2.08 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.005 0.001 TYR C 105 PHE 0.021 0.001 PHE C 247 TRP 0.012 0.001 TRP D 345 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7880) covalent geometry : angle 0.58244 (10766) hydrogen bonds : bond 0.03958 ( 504) hydrogen bonds : angle 4.28192 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.298 Fit side-chains REVERT: A 83 MET cc_start: 0.8337 (ptt) cc_final: 0.7833 (ttt) REVERT: A 183 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7610 (t80) REVERT: B 80 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7820 (mt0) REVERT: C 68 TYR cc_start: 0.7883 (t80) cc_final: 0.7542 (t80) REVERT: C 95 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8454 (tt) REVERT: C 224 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.4834 (mt) REVERT: C 306 LEU cc_start: 0.6442 (mt) cc_final: 0.5493 (pp) REVERT: C 342 MET cc_start: 0.8611 (mmm) cc_final: 0.8385 (mmt) REVERT: D 241 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7105 (mp) REVERT: D 268 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7950 (tt0) outliers start: 35 outliers final: 25 residues processed: 127 average time/residue: 0.1015 time to fit residues: 17.0846 Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.209986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.170835 restraints weight = 8606.800| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.38 r_work: 0.3615 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 7880 Z= 0.296 Angle : 0.746 11.957 10766 Z= 0.370 Chirality : 0.046 0.236 1316 Planarity : 0.005 0.055 1396 Dihedral : 9.334 89.661 1271 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.02 % Favored : 91.45 % Rotamer: Outliers : 6.84 % Allowed : 22.96 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 1135 helix: 1.71 (0.21), residues: 649 sheet: -1.31 (0.61), residues: 73 loop : -2.26 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 53 TYR 0.010 0.002 TYR B 205 PHE 0.019 0.002 PHE C 247 TRP 0.018 0.003 TRP D 345 HIS 0.006 0.002 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00747 ( 7880) covalent geometry : angle 0.74597 (10766) hydrogen bonds : bond 0.05785 ( 504) hydrogen bonds : angle 4.50151 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.290 Fit side-chains REVERT: A 87 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: A 208 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 207 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7555 (tmm) REVERT: C 68 TYR cc_start: 0.7873 (t80) cc_final: 0.7573 (t80) REVERT: C 95 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8588 (tt) REVERT: C 224 LEU cc_start: 0.5227 (OUTLIER) cc_final: 0.4894 (mt) REVERT: D 268 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: D 330 PHE cc_start: 0.4497 (OUTLIER) cc_final: 0.4217 (m-80) outliers start: 42 outliers final: 29 residues processed: 135 average time/residue: 0.1128 time to fit residues: 19.7547 Evaluate side-chains 135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 7.9990 chunk 49 optimal weight: 30.0000 chunk 14 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 0 optimal weight: 0.0870 chunk 73 optimal weight: 0.3980 chunk 22 optimal weight: 0.4980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS B 216 HIS D 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.215432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.174969 restraints weight = 8594.974| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.31 r_work: 0.3708 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7880 Z= 0.124 Angle : 0.584 12.093 10766 Z= 0.294 Chirality : 0.040 0.224 1316 Planarity : 0.004 0.053 1396 Dihedral : 8.564 86.180 1271 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.22 % Favored : 92.25 % Rotamer: Outliers : 5.21 % Allowed : 24.27 % Favored : 70.52 % 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 aren not related in a simple way. whole: 0.53 (0.26), residues: 1135 helix: 1.97 (0.21), residues: 653 sheet: -1.49 (0.58), residues: 80 loop : -2.10 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 261 TYR 0.004 0.001 TYR C 105 PHE 0.019 0.001 PHE C 247 TRP 0.013 0.001 TRP D 345 HIS 0.004 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7880) covalent geometry : angle 0.58450 (10766) hydrogen bonds : bond 0.03897 ( 504) hydrogen bonds : angle 4.22679 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.305 Fit side-chains REVERT: A 83 MET cc_start: 0.8320 (ptt) cc_final: 0.7852 (ttt) REVERT: A 183 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7586 (t80) REVERT: B 80 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7785 (mt0) REVERT: C 68 TYR cc_start: 0.7834 (t80) cc_final: 0.7542 (t80) REVERT: C 95 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8452 (tt) REVERT: C 224 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4784 (mt) REVERT: C 258 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 342 MET cc_start: 0.8645 (mmm) cc_final: 0.8410 (mmt) outliers start: 32 outliers final: 26 residues processed: 122 average time/residue: 0.1049 time to fit residues: 16.8152 Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.0270 chunk 100 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 84 optimal weight: 20.0000 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.213638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.173173 restraints weight = 8533.071| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.28 r_work: 0.3666 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7880 Z= 0.164 Angle : 0.621 11.976 10766 Z= 0.310 Chirality : 0.041 0.218 1316 Planarity : 0.004 0.052 1396 Dihedral : 8.683 82.310 1271 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.49 % Favored : 92.07 % Rotamer: Outliers : 5.37 % Allowed : 24.27 % Favored : 70.36 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1135 helix: 1.98 (0.21), residues: 654 sheet: -1.46 (0.58), residues: 80 loop : -2.07 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 53 TYR 0.006 0.001 TYR C 105 PHE 0.019 0.002 PHE C 247 TRP 0.012 0.002 TRP D 345 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7880) covalent geometry : angle 0.62120 (10766) hydrogen bonds : bond 0.04405 ( 504) hydrogen bonds : angle 4.24339 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.291 Fit side-chains REVERT: A 83 MET cc_start: 0.8283 (ptt) cc_final: 0.7789 (ttt) REVERT: A 87 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: B 80 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7770 (mt0) REVERT: C 68 TYR cc_start: 0.7894 (t80) cc_final: 0.7623 (t80) REVERT: C 95 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 224 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4780 (mt) REVERT: C 342 MET cc_start: 0.8631 (mmm) cc_final: 0.8396 (mmt) REVERT: C 354 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7837 (tm-30) outliers start: 33 outliers final: 25 residues processed: 128 average time/residue: 0.1077 time to fit residues: 18.0053 Evaluate side-chains 128 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 54 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 30.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.213087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.173385 restraints weight = 8612.911| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.18 r_work: 0.3676 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7880 Z= 0.187 Angle : 0.640 11.881 10766 Z= 0.320 Chirality : 0.042 0.215 1316 Planarity : 0.004 0.053 1396 Dihedral : 8.761 80.933 1271 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.40 % Favored : 92.16 % Rotamer: Outliers : 5.70 % Allowed : 24.10 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.26), residues: 1135 helix: 1.97 (0.21), residues: 652 sheet: -1.48 (0.56), residues: 90 loop : -2.08 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 261 TYR 0.006 0.001 TYR B 205 PHE 0.019 0.002 PHE C 247 TRP 0.013 0.002 TRP D 345 HIS 0.004 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 7880) covalent geometry : angle 0.63975 (10766) hydrogen bonds : bond 0.04613 ( 504) hydrogen bonds : angle 4.25106 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2774.29 seconds wall clock time: 48 minutes 4.34 seconds (2884.34 seconds total)