Starting phenix.real_space_refine on Sun May 11 07:47:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3x_38906/05_2025/8y3x_38906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3x_38906/05_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_38906/05_2025/8y3x_38906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3x_38906/05_2025/8y3x_38906.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3x_38906/05_2025/8y3x_38906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3x_38906/05_2025/8y3x_38906.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 10, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 8} 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: {'GLN:plan1': 13, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 9} 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: {'GLN:plan1': 20, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 9} 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: 8.78, per 1000 atoms: 1.13 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.78 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: 2.08 Time building geometry restraints manager: 2.56 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 218 or \ resid 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 218 or resid 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: 17.120 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.800 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (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 TRP 0.012 0.002 TRP D 345 HIS 0.006 0.001 HIS A 195 PHE 0.018 0.002 PHE B 23 TYR 0.008 0.002 TYR C 68 ARG 0.004 0.001 ARG C 233 Details of bonding type rmsd hydrogen bonds : bond 0.17702 ( 504) hydrogen bonds : angle 6.68365 ( 1467) covalent geometry : bond 0.00716 ( 7880) covalent geometry : angle 0.83877 (10766) *********************** 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 : 0.917 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: 0.2952 time to fit residues: 50.3257 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 : 0.838 ------------------------------------------------------------------------------- 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 93 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.206366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165880 restraints weight = 8650.025| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.85 r_work: 0.3466 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7880 Z= 0.250 Angle : 0.751 13.369 10766 Z= 0.380 Chirality : 0.045 0.216 1316 Planarity : 0.005 0.062 1396 Dihedral : 9.732 89.827 1273 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.55 % Favored : 90.93 % Rotamer: Outliers : 7.33 % Allowed : 21.66 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1135 helix: 1.01 (0.21), residues: 635 sheet: -2.50 (0.52), residues: 77 loop : -2.51 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 60 HIS 0.005 0.001 HIS B 214 PHE 0.015 0.002 PHE A 23 TYR 0.021 0.002 TYR C 105 ARG 0.005 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.06107 ( 504) hydrogen bonds : angle 5.09710 ( 1467) covalent geometry : bond 0.00605 ( 7880) covalent geometry : angle 0.75057 (10766) *********************** 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 161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.777 Fit side-chains REVERT: A 71 ASN cc_start: 0.8450 (m-40) cc_final: 0.7746 (t0) REVERT: A 84 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7876 (pt) REVERT: B 53 ARG cc_start: 0.8941 (ttm170) cc_final: 0.8544 (mtm180) REVERT: B 74 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7722 (t) REVERT: B 207 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7721 (tmm) REVERT: C 68 TYR cc_start: 0.7912 (t80) cc_final: 0.7658 (t80) REVERT: C 224 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.5215 (mt) REVERT: C 319 PHE cc_start: 0.6251 (t80) cc_final: 0.5927 (t80) REVERT: D 79 SER cc_start: 0.8433 (p) cc_final: 0.8193 (p) REVERT: D 241 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7432 (mp) REVERT: D 268 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: D 302 GLU cc_start: 0.6423 (tm-30) cc_final: 0.6115 (tp30) outliers start: 45 outliers final: 20 residues processed: 153 average time/residue: 0.2299 time to fit residues: 45.9126 Evaluate side-chains 131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 74 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL 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 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 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 36 optimal weight: 0.3980 chunk 89 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 86 optimal weight: 30.0000 chunk 73 optimal weight: 0.9980 chunk 44 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** ** D 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 = 0.4387 r_free = 0.4387 target = 0.206831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165535 restraints weight = 8822.960| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.59 r_work: 0.3514 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7880 Z= 0.189 Angle : 0.654 11.792 10766 Z= 0.331 Chirality : 0.042 0.162 1316 Planarity : 0.004 0.053 1396 Dihedral : 9.203 89.010 1271 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.11 % Favored : 91.37 % Rotamer: Outliers : 6.84 % Allowed : 21.34 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1135 helix: 1.32 (0.21), residues: 645 sheet: -1.76 (0.54), residues: 68 loop : -2.34 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 345 HIS 0.004 0.001 HIS B 214 PHE 0.021 0.002 PHE C 247 TYR 0.015 0.001 TYR C 105 ARG 0.004 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 504) hydrogen bonds : angle 4.79033 ( 1467) covalent geometry : bond 0.00449 ( 7880) covalent geometry : angle 0.65426 (10766) *********************** 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: 42 poor density : 102 time to evaluate : 0.771 Fit side-chains REVERT: A 84 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 87 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: A 195 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7785 (p-80) REVERT: A 208 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8292 (mt) REVERT: B 74 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7579 (t) REVERT: C 68 TYR cc_start: 0.7921 (t80) cc_final: 0.7512 (t80) REVERT: C 224 LEU cc_start: 0.5248 (OUTLIER) cc_final: 0.4957 (mt) REVERT: C 319 PHE cc_start: 0.5885 (t80) cc_final: 0.5491 (t80) REVERT: D 79 SER cc_start: 0.8344 (p) cc_final: 0.8103 (p) REVERT: D 241 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7454 (mp) REVERT: D 268 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7819 (tt0) outliers start: 42 outliers final: 24 residues processed: 137 average time/residue: 0.2409 time to fit residues: 43.0346 Evaluate side-chains 127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 84 ILE 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 195 HIS 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 74 VAL 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ** 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 = 0.4384 r_free = 0.4384 target = 0.206683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166003 restraints weight = 8689.718| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.67 r_work: 0.3502 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7880 Z= 0.187 Angle : 0.650 11.720 10766 Z= 0.328 Chirality : 0.042 0.170 1316 Planarity : 0.004 0.053 1396 Dihedral : 8.962 83.445 1271 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.11 % Favored : 91.37 % Rotamer: Outliers : 7.00 % Allowed : 21.99 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1135 helix: 1.50 (0.21), residues: 644 sheet: -1.51 (0.56), residues: 68 loop : -2.31 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 345 HIS 0.004 0.001 HIS B 214 PHE 0.031 0.002 PHE C 247 TYR 0.006 0.001 TYR B 205 ARG 0.004 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 504) hydrogen bonds : angle 4.66750 ( 1467) covalent geometry : bond 0.00447 ( 7880) covalent geometry : angle 0.65039 (10766) *********************** 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 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.829 Fit side-chains REVERT: A 83 MET cc_start: 0.8577 (ptt) cc_final: 0.7819 (ttt) REVERT: A 84 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7791 (pt) REVERT: A 87 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: A 183 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7671 (t80) REVERT: C 224 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4754 (mt) REVERT: C 307 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7914 (ttp-170) REVERT: D 241 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7431 (mp) REVERT: D 268 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: D 302 GLU cc_start: 0.6473 (tp30) cc_final: 0.6204 (tp30) outliers start: 43 outliers final: 27 residues processed: 131 average time/residue: 0.2408 time to fit residues: 41.0241 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 84 ILE 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 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 74 VAL 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 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 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 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 29 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 11 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 40.0000 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 12 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.207154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165553 restraints weight = 8717.917| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.47 r_work: 0.3536 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7880 Z= 0.176 Angle : 0.630 11.519 10766 Z= 0.317 Chirality : 0.041 0.157 1316 Planarity : 0.004 0.053 1396 Dihedral : 8.796 79.437 1271 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.75 % Favored : 91.72 % Rotamer: Outliers : 7.00 % Allowed : 21.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1135 helix: 1.65 (0.21), residues: 650 sheet: -1.84 (0.54), residues: 80 loop : -2.22 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 345 HIS 0.004 0.001 HIS A 195 PHE 0.023 0.002 PHE C 247 TYR 0.005 0.001 TYR B 205 ARG 0.005 0.001 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 504) hydrogen bonds : angle 4.51337 ( 1467) covalent geometry : bond 0.00421 ( 7880) covalent geometry : angle 0.63012 (10766) *********************** 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: 43 poor density : 91 time to evaluate : 0.765 Fit side-chains REVERT: A 83 MET cc_start: 0.8528 (ptt) cc_final: 0.7780 (ttt) REVERT: A 84 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7695 (mp) REVERT: A 87 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: A 183 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7604 (t80) REVERT: A 208 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8229 (mt) REVERT: C 224 LEU cc_start: 0.5130 (OUTLIER) cc_final: 0.4819 (mt) REVERT: C 306 LEU cc_start: 0.6519 (mt) cc_final: 0.5590 (pp) REVERT: C 342 MET cc_start: 0.8619 (mmm) cc_final: 0.8379 (mmt) REVERT: D 241 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7395 (mp) REVERT: D 268 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7863 (tt0) outliers start: 43 outliers final: 26 residues processed: 126 average time/residue: 0.2172 time to fit residues: 36.3038 Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 84 ILE 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 74 VAL 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 B residue 210 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 334 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 2 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 40.0000 chunk 16 optimal weight: 0.0870 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.210922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171608 restraints weight = 8490.866| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.38 r_work: 0.3603 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7880 Z= 0.228 Angle : 0.688 11.712 10766 Z= 0.343 Chirality : 0.044 0.208 1316 Planarity : 0.004 0.055 1396 Dihedral : 9.145 84.482 1271 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.11 % Favored : 91.37 % Rotamer: Outliers : 7.82 % Allowed : 20.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1135 helix: 1.63 (0.21), residues: 648 sheet: -1.46 (0.59), residues: 73 loop : -2.31 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 345 HIS 0.005 0.002 HIS B 214 PHE 0.020 0.002 PHE C 247 TYR 0.008 0.001 TYR B 205 ARG 0.004 0.001 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.05261 ( 504) hydrogen bonds : angle 4.54083 ( 1467) covalent geometry : bond 0.00561 ( 7880) covalent geometry : angle 0.68800 (10766) *********************** 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 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 99 time to evaluate : 0.778 Fit side-chains REVERT: A 83 MET cc_start: 0.8430 (ptt) cc_final: 0.7770 (ttt) REVERT: A 84 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7849 (mp) REVERT: A 87 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8275 (m-30) REVERT: A 92 MET cc_start: 0.8866 (mmm) cc_final: 0.8502 (mmt) REVERT: A 155 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7972 (pttt) REVERT: A 183 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7575 (t80) REVERT: A 208 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8328 (mt) REVERT: B 51 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8622 (mm) REVERT: C 95 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8582 (tt) REVERT: C 224 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4857 (mt) REVERT: D 241 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7398 (mp) REVERT: D 268 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7938 (tt0) outliers start: 48 outliers final: 30 residues processed: 139 average time/residue: 0.2120 time to fit residues: 39.0964 Evaluate side-chains 137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 84 ILE 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 155 LYS 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 51 ILE Chi-restraints excluded: chain B residue 74 VAL 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 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR 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 297 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 20.0000 chunk 36 optimal weight: 0.0030 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 78 optimal weight: 40.0000 chunk 100 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.2188 ------------------------------------------------------------------------------- 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 C 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.215668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.176812 restraints weight = 8577.322| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.36 r_work: 0.3691 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7880 Z= 0.117 Angle : 0.569 12.027 10766 Z= 0.287 Chirality : 0.039 0.205 1316 Planarity : 0.004 0.053 1396 Dihedral : 8.459 89.756 1271 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.31 % Favored : 92.16 % Rotamer: Outliers : 5.86 % Allowed : 23.29 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1135 helix: 1.92 (0.21), residues: 651 sheet: -1.53 (0.57), residues: 80 loop : -2.05 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 345 HIS 0.004 0.001 HIS C 358 PHE 0.018 0.001 PHE C 247 TYR 0.003 0.000 TYR C 102 ARG 0.005 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 504) hydrogen bonds : angle 4.27931 ( 1467) covalent geometry : bond 0.00248 ( 7880) covalent geometry : angle 0.56909 (10766) *********************** 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 133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.819 Fit side-chains REVERT: A 83 MET cc_start: 0.8354 (ptt) cc_final: 0.7792 (ttt) REVERT: A 90 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 92 MET cc_start: 0.8695 (mmm) cc_final: 0.8423 (mmt) REVERT: A 183 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7667 (t80) REVERT: B 53 ARG cc_start: 0.8892 (ttm170) cc_final: 0.8539 (mtm180) REVERT: B 80 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7797 (mt0) REVERT: C 95 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8534 (tt) REVERT: C 224 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4766 (mt) REVERT: C 306 LEU cc_start: 0.6581 (mt) cc_final: 0.5624 (pp) REVERT: C 342 MET cc_start: 0.8606 (mmm) cc_final: 0.8384 (mmt) REVERT: D 241 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7487 (mp) REVERT: D 268 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7848 (tt0) outliers start: 36 outliers final: 27 residues processed: 126 average time/residue: 0.2178 time to fit residues: 36.0431 Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain A residue 136 ILE 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 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL 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 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 109 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 20.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN B 24 HIS ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.212425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.172606 restraints weight = 8585.428| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.35 r_work: 0.3644 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7880 Z= 0.193 Angle : 0.644 11.918 10766 Z= 0.321 Chirality : 0.042 0.187 1316 Planarity : 0.004 0.054 1396 Dihedral : 8.843 81.693 1271 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.93 % Favored : 91.54 % Rotamer: Outliers : 6.68 % Allowed : 23.45 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1135 helix: 1.91 (0.21), residues: 651 sheet: -1.54 (0.58), residues: 80 loop : -2.12 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 345 HIS 0.004 0.001 HIS B 214 PHE 0.016 0.001 PHE C 247 TYR 0.006 0.001 TYR B 205 ARG 0.005 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 504) hydrogen bonds : angle 4.33051 ( 1467) covalent geometry : bond 0.00474 ( 7880) covalent geometry : angle 0.64369 (10766) *********************** 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 140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.772 Fit side-chains REVERT: A 83 MET cc_start: 0.8359 (ptt) cc_final: 0.7795 (ttt) REVERT: A 87 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: A 90 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8580 (pp) REVERT: A 92 MET cc_start: 0.8791 (mmm) cc_final: 0.8464 (mmt) REVERT: A 183 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7591 (t80) REVERT: C 224 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4840 (mt) REVERT: C 342 MET cc_start: 0.8689 (mmm) cc_final: 0.8451 (mmt) REVERT: D 241 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7363 (mp) REVERT: D 268 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7890 (tt0) outliers start: 41 outliers final: 28 residues processed: 132 average time/residue: 0.2270 time to fit residues: 39.4739 Evaluate side-chains 131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain A residue 110 SER 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 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 297 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 93 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.0570 chunk 48 optimal weight: 30.0000 chunk 76 optimal weight: 0.0010 chunk 22 optimal weight: 0.8980 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 HIS ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.215293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175443 restraints weight = 8716.787| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.39 r_work: 0.3696 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4222 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= 0.130 Angle : 0.577 12.040 10766 Z= 0.290 Chirality : 0.040 0.170 1316 Planarity : 0.003 0.053 1396 Dihedral : 8.455 87.278 1271 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.96 % Favored : 92.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1135 helix: 2.06 (0.21), residues: 652 sheet: -1.37 (0.59), residues: 80 loop : -2.09 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 345 HIS 0.004 0.001 HIS C 358 PHE 0.016 0.001 PHE C 247 TYR 0.004 0.001 TYR C 102 ARG 0.004 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 504) hydrogen bonds : angle 4.19429 ( 1467) covalent geometry : bond 0.00291 ( 7880) covalent geometry : angle 0.57741 (10766) *********************** 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 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.764 Fit side-chains REVERT: A 90 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8366 (pp) REVERT: A 174 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8263 (mm-30) REVERT: A 183 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7602 (t80) REVERT: B 80 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7766 (mt0) REVERT: C 224 LEU cc_start: 0.5020 (OUTLIER) cc_final: 0.4743 (mt) REVERT: C 306 LEU cc_start: 0.6517 (mt) cc_final: 0.5540 (pp) REVERT: C 342 MET cc_start: 0.8698 (mmm) cc_final: 0.8480 (mmt) REVERT: D 241 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7465 (mp) REVERT: D 268 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7895 (tt0) outliers start: 35 outliers final: 27 residues processed: 123 average time/residue: 0.2311 time to fit residues: 37.1392 Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 90 LEU 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 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 315 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 HIS B 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.211335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171541 restraints weight = 8609.786| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 1.24 r_work: 0.3662 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7880 Z= 0.230 Angle : 0.680 11.776 10766 Z= 0.338 Chirality : 0.044 0.205 1316 Planarity : 0.004 0.055 1396 Dihedral : 8.992 83.745 1271 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.67 % Favored : 91.89 % Rotamer: Outliers : 5.37 % Allowed : 24.59 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1135 helix: 1.92 (0.21), residues: 652 sheet: -1.57 (0.55), residues: 90 loop : -2.15 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 345 HIS 0.005 0.001 HIS A 195 PHE 0.015 0.002 PHE C 247 TYR 0.007 0.001 TYR B 205 ARG 0.005 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 504) hydrogen bonds : angle 4.30889 ( 1467) covalent geometry : bond 0.00570 ( 7880) covalent geometry : angle 0.68013 (10766) ********************** 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 133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.821 Fit side-chains REVERT: A 83 MET cc_start: 0.8361 (ptt) cc_final: 0.7800 (ttt) REVERT: A 87 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: C 224 LEU cc_start: 0.4987 (OUTLIER) cc_final: 0.4716 (mt) REVERT: C 306 LEU cc_start: 0.6555 (mt) cc_final: 0.5545 (pp) REVERT: C 342 MET cc_start: 0.8708 (mmm) cc_final: 0.8462 (mmt) REVERT: D 241 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7284 (mp) REVERT: D 268 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7901 (tt0) outliers start: 33 outliers final: 26 residues processed: 126 average time/residue: 0.2306 time to fit residues: 38.0395 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 : 0.855 ------------------------------------------------------------------------------- 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 110 SER 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 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 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 315 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 18 optimal weight: 0.1980 chunk 13 optimal weight: 0.1980 chunk 82 optimal weight: 20.0000 chunk 31 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 11 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.214684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.174601 restraints weight = 8545.351| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.20 r_work: 0.3717 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7880 Z= 0.133 Angle : 0.597 11.871 10766 Z= 0.297 Chirality : 0.040 0.164 1316 Planarity : 0.004 0.053 1396 Dihedral : 8.504 85.801 1271 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.96 % Favored : 92.60 % Rotamer: Outliers : 5.37 % Allowed : 25.08 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1135 helix: 2.08 (0.21), residues: 654 sheet: -1.38 (0.58), residues: 80 loop : -2.06 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 345 HIS 0.004 0.001 HIS C 358 PHE 0.015 0.001 PHE C 247 TYR 0.004 0.001 TYR C 102 ARG 0.004 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 504) hydrogen bonds : angle 4.14340 ( 1467) covalent geometry : bond 0.00298 ( 7880) covalent geometry : angle 0.59712 (10766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5262.51 seconds wall clock time: 92 minutes 5.32 seconds (5525.32 seconds total)