Starting phenix.real_space_refine on Sun May 18 16:25:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6c_49056/05_2025/9n6c_49056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6c_49056/05_2025/9n6c_49056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n6c_49056/05_2025/9n6c_49056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6c_49056/05_2025/9n6c_49056.map" model { file = "/net/cci-nas-00/data/ceres_data/9n6c_49056/05_2025/9n6c_49056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6c_49056/05_2025/9n6c_49056.cif" } resolution = 2.99 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= 0.004 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 123 5.49 5 S 17 5.16 5 C 10685 2.51 5 N 3015 2.21 5 O 3456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17296 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3082 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 8, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 211 Chain: "B" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3046 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 8, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 508 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 21, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 231 Chain: "C" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3336 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 10, 'TRANS': 436} Chain breaks: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 13, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "D" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 2977 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 625 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 23, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 278 Chain: "E" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2394 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 295} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 71 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1496 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain breaks: 1 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 872 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 17, 'rna3p': 23} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" 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: 11.93, per 1000 atoms: 0.69 Number of scatterers: 17296 At special positions: 0 Unit cell: (140.445, 122.323, 148.6, 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 17 16.00 P 123 15.00 O 3456 8.00 N 3015 7.00 C 10685 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: 4.24 Conformation dependent library (CDL) restraints added in 2.1 seconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 16 sheets defined 52.4% alpha, 15.4% beta 16 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 5.90 Creating SS restraints... Processing helix chain 'A' and resid 6 through 21 removed outlier: 3.632A pdb=" N ASP A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 14 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 30 Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.552A pdb=" N GLN A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 100 removed outlier: 4.369A pdb=" N ILE A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.670A pdb=" N VAL A 113 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.895A pdb=" N ILE A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.632A pdb=" N ILE A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 218 through 242 removed outlier: 4.051A pdb=" N PHE A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 267 Processing helix chain 'A' and resid 273 through 298 removed outlier: 3.748A pdb=" N HIS A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.636A pdb=" N ILE A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 350 through 371 removed outlier: 3.536A pdb=" N THR A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.544A pdb=" N GLN A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.888A pdb=" N THR A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 Processing helix chain 'B' and resid 23 through 30 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.717A pdb=" N GLN B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 100 removed outlier: 3.528A pdb=" N ILE B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 154 through 171 removed outlier: 3.854A pdb=" N LYS B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.758A pdb=" N PHE B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.877A pdb=" N LEU B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 260 removed outlier: 4.032A pdb=" N THR B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 Processing helix chain 'B' and resid 302 through 318 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 369 removed outlier: 3.617A pdb=" N THR B 355 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.510A pdb=" N LEU B 379 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 380 " --> pdb=" O PRO B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 380' Processing helix chain 'B' and resid 394 through 409 removed outlier: 4.043A pdb=" N THR B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 4.103A pdb=" N LEU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 425 " --> pdb=" O PRO B 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 420 through 425' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.512A pdb=" N LEU C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 28 removed outlier: 3.755A pdb=" N LEU C 27 " --> pdb=" O ASN C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.554A pdb=" N GLN C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 100 removed outlier: 3.743A pdb=" N ILE C 83 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 171 removed outlier: 3.623A pdb=" N ILE C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.714A pdb=" N ARG C 186 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 187 " --> pdb=" O ILE C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.519A pdb=" N ASP C 213 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 241 Processing helix chain 'C' and resid 242 through 267 removed outlier: 3.884A pdb=" N THR C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 294 removed outlier: 3.631A pdb=" N LEU C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.984A pdb=" N PHE C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 350 through 371 removed outlier: 3.627A pdb=" N ILE C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 380 removed outlier: 3.546A pdb=" N LEU C 379 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 380 " --> pdb=" O PRO C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 376 through 380' Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.628A pdb=" N GLN C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 removed outlier: 3.532A pdb=" N ARG C 404 " --> pdb=" O THR C 400 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 removed outlier: 3.578A pdb=" N SER C 425 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL C 427 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 23 through 30 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.882A pdb=" N GLN D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 100 removed outlier: 3.588A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP D 93 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.809A pdb=" N VAL D 113 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 171 removed outlier: 3.690A pdb=" N LYS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 207 through 212 removed outlier: 4.482A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 207 through 212' Processing helix chain 'D' and resid 222 through 240 removed outlier: 3.507A pdb=" N PHE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 264 Processing helix chain 'D' and resid 276 through 291 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 302 through 318 removed outlier: 3.570A pdb=" N LYS D 316 " --> pdb=" O ASN D 312 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 371 removed outlier: 3.637A pdb=" N ILE D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.563A pdb=" N LEU D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 14 through 23 removed outlier: 3.513A pdb=" N GLN E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN E 23 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 27 removed outlier: 3.540A pdb=" N LYS E 27 " --> pdb=" O GLU E 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 27' Processing helix chain 'E' and resid 48 through 63 removed outlier: 3.506A pdb=" N ASN E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER E 60 " --> pdb=" O ARG E 56 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E 61 " --> pdb=" O PHE E 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 80 through 86 removed outlier: 3.509A pdb=" N ASN E 84 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.774A pdb=" N SER E 113 " --> pdb=" O ASP E 109 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 115 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.777A pdb=" N ASN E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 176 removed outlier: 3.501A pdb=" N ASP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP E 173 " --> pdb=" O SER E 169 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 213 removed outlier: 3.596A pdb=" N VAL E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 264 removed outlier: 3.653A pdb=" N LEU E 264 " --> pdb=" O HIS E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 287 removed outlier: 3.741A pdb=" N ASN E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.628A pdb=" N ARG E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.651A pdb=" N ILE E 302 " --> pdb=" O GLY E 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 64 removed outlier: 6.960A pdb=" N GLU A 60 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N HIS A 53 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN A 62 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLY A 51 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER A 64 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS A 49 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU A 47 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS A 129 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS A 49 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 55 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N TYR A 121 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 182 removed outlier: 6.550A pdb=" N GLY A 382 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL A 415 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 384 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR A 70 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ARG A 433 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 71 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 64 removed outlier: 6.616A pdb=" N GLU B 60 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS B 53 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLN B 62 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY B 51 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER B 64 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS B 49 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU B 47 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYS B 129 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 49 " --> pdb=" O ASN B 127 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE B 55 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N TYR B 121 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 128 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 216 through 217 removed outlier: 8.093A pdb=" N PHE B 217 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR B 181 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY B 382 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL B 415 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 384 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR B 417 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 386 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR B 70 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B 418 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE B 72 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 435 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 Processing sheet with id=AA7, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 64 removed outlier: 6.585A pdb=" N ARG C 59 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU C 47 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS C 129 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS C 49 " --> pdb=" O ASN C 127 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE C 55 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N TYR C 121 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 137 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.317A pdb=" N LEU C 178 " --> pdb=" O ILE C 383 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU C 385 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 180 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N ASP C 387 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR C 182 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ARG C 433 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL C 71 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU C 435 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL C 73 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N GLU C 437 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.700A pdb=" N LEU C 337 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 342 " --> pdb=" O LYS C 339 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 64 removed outlier: 6.439A pdb=" N ARG D 59 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS D 49 " --> pdb=" O ASN D 127 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE D 55 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 11.243A pdb=" N TYR D 121 " --> pdb=" O PHE D 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 178 through 182 removed outlier: 3.545A pdb=" N THR D 417 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR D 70 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR D 418 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE D 72 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ARG D 433 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL D 71 " --> pdb=" O ARG D 433 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU D 435 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL D 73 " --> pdb=" O LEU D 435 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N GLU D 437 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 321 through 329 removed outlier: 4.323A pdb=" N TRP D 323 " --> pdb=" O LYS D 338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 35 Processing sheet with id=AB6, first strand: chain 'E' and resid 180 through 184 removed outlier: 3.510A pdb=" N SER E 191 " --> pdb=" O THR E 180 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 182 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 188 " --> pdb=" O MET E 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 233 through 234 782 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 4.87 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: 4365 1.33 - 1.45: 3729 1.45 - 1.57: 9490 1.57 - 1.69: 240 1.69 - 1.81: 29 Bond restraints: 17853 Sorted by residual: bond pdb=" C GLN E 63 " pdb=" N PRO E 64 " ideal model delta sigma weight residual 1.334 1.348 -0.014 8.40e-03 1.42e+04 2.98e+00 bond pdb=" N SER B 242 " pdb=" CA SER B 242 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" C3' DC H 32 " pdb=" O3' DC H 32 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" O5' A I 150 " pdb=" C5' A I 150 " ideal model delta sigma weight residual 1.424 1.441 -0.017 1.50e-02 4.44e+03 1.22e+00 bond pdb=" C3' DG H 21 " pdb=" O3' DG H 21 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.13e+00 ... (remaining 17848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 24522 1.93 - 3.85: 285 3.85 - 5.78: 22 5.78 - 7.71: 4 7.71 - 9.63: 2 Bond angle restraints: 24835 Sorted by residual: angle pdb=" N ILE A 22 " pdb=" CA ILE A 22 " pdb=" C ILE A 22 " ideal model delta sigma weight residual 113.53 109.65 3.88 9.80e-01 1.04e+00 1.57e+01 angle pdb=" CA GLU A 42 " pdb=" CB GLU A 42 " pdb=" CG GLU A 42 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.37e+00 angle pdb=" C SER B 242 " pdb=" CA SER B 242 " pdb=" CB SER B 242 " ideal model delta sigma weight residual 110.42 116.08 -5.66 1.99e+00 2.53e-01 8.10e+00 angle pdb=" CA LEU E 16 " pdb=" CB LEU E 16 " pdb=" CG LEU E 16 " ideal model delta sigma weight residual 116.30 125.93 -9.63 3.50e+00 8.16e-02 7.58e+00 angle pdb=" C4' U I 151 " pdb=" C3' U I 151 " pdb=" C2' U I 151 " ideal model delta sigma weight residual 102.60 105.32 -2.72 1.00e+00 1.00e+00 7.39e+00 ... (remaining 24830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 9893 35.37 - 70.75: 598 70.75 - 106.12: 25 106.12 - 141.50: 1 141.50 - 176.87: 6 Dihedral angle restraints: 10523 sinusoidal: 4543 harmonic: 5980 Sorted by residual: dihedral pdb=" O4' U I 152 " pdb=" C1' U I 152 " pdb=" N1 U I 152 " pdb=" C2 U I 152 " ideal model delta sinusoidal sigma weight residual 232.00 60.48 171.52 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" C5' U I 151 " pdb=" C4' U I 151 " pdb=" C3' U I 151 " pdb=" O3' U I 151 " ideal model delta sinusoidal sigma weight residual 147.00 108.98 38.02 1 8.00e+00 1.56e-02 3.18e+01 dihedral pdb=" O4' U I 151 " pdb=" C4' U I 151 " pdb=" C3' U I 151 " pdb=" C2' U I 151 " ideal model delta sinusoidal sigma weight residual 24.00 -10.49 34.49 1 8.00e+00 1.56e-02 2.64e+01 ... (remaining 10520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2335 0.041 - 0.082: 486 0.082 - 0.123: 171 0.123 - 0.165: 9 0.165 - 0.206: 2 Chirality restraints: 3003 Sorted by residual: chirality pdb=" C3' C I 124 " pdb=" C4' C I 124 " pdb=" O3' C I 124 " pdb=" C2' C I 124 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' C I 125 " pdb=" C4' C I 125 " pdb=" O3' C I 125 " pdb=" C2' C I 125 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CA ILE D 139 " pdb=" N ILE D 139 " pdb=" C ILE D 139 " pdb=" CB ILE D 139 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 3000 not shown) Planarity restraints: 2726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 42 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C GLU A 42 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU A 42 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 43 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 78 " 0.008 2.00e-02 2.50e+03 1.23e-02 2.63e+00 pdb=" CG PHE A 78 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 78 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 78 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 78 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 78 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 240 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO E 241 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 241 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 241 " -0.022 5.00e-02 4.00e+02 ... (remaining 2723 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 9034 3.01 - 3.48: 16432 3.48 - 3.96: 25774 3.96 - 4.43: 29412 4.43 - 4.90: 46290 Nonbonded interactions: 126942 Sorted by model distance: nonbonded pdb=" O2' U I 152 " pdb=" N2 G I 153 " model vdw 2.540 3.120 nonbonded pdb=" O3' U I 151 " pdb=" O2 U I 152 " model vdw 2.556 3.040 nonbonded pdb=" O4' DC H 79 " pdb=" O2 DC H 79 " model vdw 2.567 3.040 nonbonded pdb=" O5' DG H 80 " pdb=" O4' DG H 80 " model vdw 2.570 2.432 nonbonded pdb=" O2' ATP C 601 " pdb=" O3' ATP C 601 " model vdw 2.584 2.432 ... (remaining 126937 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 6 through 40 and (name N or name CA or name C or name O o \ r name CB )) or resid 41 or (resid 42 through 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 53 or (resid 54 and ( \ name N or name CA or name C or name O or name CB )) or resid 55 through 59 or (r \ esid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 thr \ ough 84 or (resid 85 through 86 and (name N or name CA or name C or name O or na \ me CB )) or resid 87 through 98 or (resid 99 and (name N or name CA or name C or \ name O or name CB )) or resid 100 through 108 or (resid 109 through 110 and (na \ me N or name CA or name C or name O or name CB )) or resid 111 through 116 or (r \ esid 117 through 118 and (name N or name CA or name C or name O or name CB )) or \ resid 119 through 124 or (resid 125 through 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 130 or (resid 131 through 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 through 142 o \ r (resid 143 through 144 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 145 through 151 and (name N or name CA or name C or name O or name C \ B )) or resid 152 or (resid 153 and (name N or name CA or name C or name O or na \ me CB )) or resid 154 or (resid 155 and (name N or name CA or name C or name O o \ r name CB )) or resid 156 through 158 or (resid 159 and (name N or name CA or na \ me C or name O or name CB )) or resid 160 through 165 or (resid 166 through 172 \ and (name N or name CA or name C or name O or name CB )) or resid 173 through 18 \ 5 or (resid 186 and (name N or name CA or name C or name O or name CB )) or resi \ d 187 or (resid 204 through 208 and (name N or name CA or name C or name O or na \ me CB )) or resid 209 or (resid 210 through 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 through 214 or (resid 215 through 216 and \ (name N or name CA or name C or name O or name CB )) or resid 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 or (resid \ 220 through 221 and (name N or name CA or name C or name O or name CB )) or resi \ d 222 through 234 or (resid 235 through 236 and (name N or name CA or name C or \ name O or name CB )) or resid 237 through 264 or resid 275 through 307 or (resid \ 308 and (name N or name CA or name C or name O or name CB )) or resid 309 throu \ gh 311 or (resid 312 and (name N or name CA or name C or name O or name CB )) or \ resid 313 through 319 or (resid 320 and (name N or name CA or name C or name O \ or name CB )) or resid 321 through 344 or (resid 345 and (name N or name CA or n \ ame C or name O or name CB )) or resid 346 through 369 or (resid 370 and (name N \ or name CA or name C or name O or name CB )) or resid 371 through 374 or (resid \ 375 through 376 and (name N or name CA or name C or name O or name CB )) or res \ id 377 through 425 or (resid 426 and (name N or name CA or name C or name O or n \ ame CB )) or resid 427 or (resid 428 through 429 and (name N or name CA or name \ C or name O or name CB )) or resid 430 through 437)) selection = (chain 'B' and ((resid 6 through 40 and (name N or name CA or name C or name O o \ r name CB )) or resid 41 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 through 59 or (res \ id 60 and (name N or name CA or name C or name O or name CB )) or resid 61 throu \ gh 100 or (resid 101 and (name N or name CA or name C or name O or name CB )) or \ resid 102 through 116 or (resid 117 through 118 and (name N or name CA or name \ C or name O or name CB )) or resid 119 through 124 or (resid 125 through 126 and \ (name N or name CA or name C or name O or name CB )) or resid 127 through 154 o \ r (resid 155 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 56 through 158 or (resid 159 and (name N or name CA or name C or name O or name \ CB )) or resid 160 through 165 or (resid 166 through 172 and (name N or name CA \ or name C or name O or name CB )) or resid 173 through 187 or (resid 204 through \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throu \ gh 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 or (resid 213 through 216 and (name N or name CA or name C or name O \ or name CB )) or resid 217 or (resid 218 and (name N or name CA or name C or nam \ e O or name CB )) or resid 219 or (resid 220 through 221 and (name N or name CA \ or name C or name O or name CB )) or resid 222 through 234 or (resid 235 through \ 236 and (name N or name CA or name C or name O or name CB )) or resid 237 throu \ gh 238 or (resid 239 through 264 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 275 through 303 and (name N or name CA or name C or name O o \ r name CB )) or resid 304 through 307 or (resid 308 and (name N or name CA or na \ me C or name O or name CB )) or resid 309 through 311 or (resid 312 and (name N \ or name CA or name C or name O or name CB )) or resid 313 through 319 or (resid \ 320 and (name N or name CA or name C or name O or name CB )) or resid 321 throug \ h 326 or (resid 327 through 328 and (name N or name CA or name C or name O or na \ me CB )) or (resid 329 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 337 or (resid 338 and (name N or name CA or nam \ e C or name O or name CB )) or resid 339 through 344 or (resid 345 and (name N o \ r name CA or name C or name O or name CB )) or resid 346 or (resid 347 and (name \ N or name CA or name C or name O or name CB )) or resid 348 through 369 or (res \ id 370 and (name N or name CA or name C or name O or name CB )) or resid 371 thr \ ough 374 or (resid 375 through 376 and (name N or name CA or name C or name O or \ name CB )) or resid 377 through 387 or (resid 388 and (name N or name CA or nam \ e C or name O or name CB )) or resid 389 through 395 or (resid 396 and (name N o \ r name CA or name C or name O or name CB )) or resid 397 through 425 or (resid 4 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 427 or (res \ id 428 through 429 and (name N or name CA or name C or name O or name CB )) or r \ esid 430 through 437)) selection = (chain 'C' and ((resid 6 through 40 and (name N or name CA or name C or name O o \ r name CB )) or resid 41 or (resid 42 through 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 53 or (resid 54 and ( \ name N or name CA or name C or name O or name CB )) or resid 55 through 84 or (r \ esid 85 through 86 and (name N or name CA or name C or name O or name CB )) or r \ esid 87 through 98 or (resid 99 and (name N or name CA or name C or name O or na \ me CB )) or resid 100 or (resid 101 and (name N or name CA or name C or name O o \ r name CB )) or resid 102 through 108 or (resid 109 through 110 and (name N or n \ ame CA or name C or name O or name CB )) or resid 111 through 116 or (resid 117 \ through 118 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 9 through 130 or (resid 131 through 132 and (name N or name CA or name C or name \ O or name CB )) or resid 133 through 142 or (resid 143 through 144 and (name N \ or name CA or name C or name O or name CB )) or (resid 145 through 151 and (name \ N or name CA or name C or name O or name CB )) or resid 152 or (resid 153 and ( \ name N or name CA or name C or name O or name CB )) or resid 154 or (resid 155 a \ nd (name N or name CA or name C or name O or name CB )) or resid 156 through 158 \ or (resid 159 and (name N or name CA or name C or name O or name CB )) or resid \ 160 through 165 or (resid 166 through 172 and (name N or name CA or name C or n \ ame O or name CB )) or resid 173 through 185 or (resid 186 and (name N or name C \ A or name C or name O or name CB )) or resid 187 or (resid 204 through 208 and ( \ name N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 t \ hrough 211 and (name N or name CA or name C or name O or name CB )) or resid 212 \ through 213 or (resid 214 through 216 and (name N or name CA or name C or name \ O or name CB )) or resid 217 through 219 or (resid 220 through 221 and (name N o \ r name CA or name C or name O or name CB )) or resid 222 through 234 or (resid 2 \ 35 through 236 and (name N or name CA or name C or name O or name CB )) or resid \ 237 through 239 or (resid 240 through 264 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 275 through 303 and (name N or name CA or name C o \ r name O or name CB )) or resid 304 through 307 or (resid 308 and (name N or nam \ e CA or name C or name O or name CB )) or resid 309 through 311 or (resid 312 an \ d (name N or name CA or name C or name O or name CB )) or resid 313 through 319 \ or (resid 320 and (name N or name CA or name C or name O or name CB )) or resid \ 321 through 326 or (resid 327 through 328 and (name N or name CA or name C or na \ me O or name CB )) or (resid 329 through 334 and (name N or name CA or name C or \ name O or name CB )) or resid 335 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB )) or resid 339 through 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB )) or resid 344 or (resid 345 \ and (name N or name CA or name C or name O or name CB )) or resid 346 or (resid \ 347 and (name N or name CA or name C or name O or name CB )) or resid 348 throu \ gh 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or \ resid 371 through 374 or (resid 375 through 376 and (name N or name CA or name \ C or name O or name CB )) or resid 377 through 387 or (resid 388 and (name N or \ name CA or name C or name O or name CB )) or resid 389 through 395 or (resid 396 \ and (name N or name CA or name C or name O or name CB )) or resid 397 through 4 \ 02 or (resid 403 and (name N or name CA or name C or name O or name CB )) or res \ id 404 through 436 or (resid 437 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'D' and ((resid 6 through 40 and (name N or name CA or name C or name O o \ r name CB )) or resid 41 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 84 or (resid 85 throu \ gh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 100 or (resid 101 and (name N or name CA or name C or name O or name CB )) or \ resid 102 through 109 or (resid 110 and (name N or name CA or name C or name O \ or name CB )) or resid 111 through 117 or (resid 118 and (name N or name CA or n \ ame C or name O or name CB )) or resid 119 through 148 or (resid 149 through 151 \ and (name N or name CA or name C or name O or name CB )) or resid 152 or (resid \ 153 and (name N or name CA or name C or name O or name CB )) or resid 154 throu \ gh 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) or \ resid 187 or resid 204 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 220 or (resid 221 and (name N or \ name CA or name C or name O or name CB )) or resid 222 through 241 or (resid 24 \ 2 through 277 and (name N or name CA or name C or name O or name CB )) or resid \ 278 through 326 or (resid 327 through 328 and (name N or name CA or name C or na \ me O or name CB )) or (resid 329 through 334 and (name N or name CA or name C or \ name O or name CB )) or resid 335 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB )) or resid 339 through 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB )) or resid 344 through 346 o \ r (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 48 through 395 or (resid 396 and (name N or name CA or name C or name O or name \ CB )) or resid 397 through 425 or (resid 426 and (name N or name CA or name C or \ name O or name CB )) or resid 427 or (resid 428 through 429 and (name N or name \ CA or name C or name O or name CB )) or resid 430 through 437)) } 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: 7.670 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: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.580 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17853 Z= 0.116 Angle : 0.514 9.634 24835 Z= 0.305 Chirality : 0.038 0.206 3003 Planarity : 0.003 0.039 2726 Dihedral : 20.199 176.869 6629 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.13 % Favored : 94.77 % Rotamer: Outliers : 1.81 % Allowed : 24.17 % Favored : 74.02 % 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: 0.20 (0.18), residues: 2008 helix: 1.46 (0.17), residues: 879 sheet: 0.74 (0.28), residues: 330 loop : -1.71 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 323 HIS 0.003 0.001 HIS C 394 PHE 0.028 0.001 PHE A 78 TYR 0.014 0.001 TYR C 26 ARG 0.004 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.29801 ( 818) hydrogen bonds : angle 7.13184 ( 2312) covalent geometry : bond 0.00219 (17853) covalent geometry : angle 0.51435 (24835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 1.847 Fit side-chains REVERT: C 85 ASP cc_start: 0.7845 (m-30) cc_final: 0.7642 (m-30) outliers start: 25 outliers final: 13 residues processed: 99 average time/residue: 1.1058 time to fit residues: 125.9255 Evaluate side-chains 80 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 HIS E 88 HIS E 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.095210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.063347 restraints weight = 47303.844| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.43 r_work: 0.2824 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17853 Z= 0.132 Angle : 0.517 7.809 24835 Z= 0.291 Chirality : 0.040 0.209 3003 Planarity : 0.003 0.041 2726 Dihedral : 20.040 178.714 3724 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.53 % Favored : 94.32 % Rotamer: Outliers : 3.55 % Allowed : 23.23 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.19), residues: 2008 helix: 2.19 (0.17), residues: 926 sheet: 0.96 (0.28), residues: 330 loop : -1.81 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 323 HIS 0.004 0.001 HIS C 394 PHE 0.015 0.001 PHE A 14 TYR 0.010 0.001 TYR A 182 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.05401 ( 818) hydrogen bonds : angle 4.40951 ( 2312) covalent geometry : bond 0.00273 (17853) covalent geometry : angle 0.51749 (24835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 79 time to evaluate : 1.695 Fit side-chains revert: symmetry clash REVERT: A 216 GLU cc_start: 0.8831 (tt0) cc_final: 0.8387 (mm-30) REVERT: B 112 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8404 (mt-10) REVERT: C 147 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7846 (p90) REVERT: C 333 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8890 (p90) REVERT: D 343 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8822 (tp30) REVERT: E 73 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8083 (mmt) outliers start: 49 outliers final: 13 residues processed: 117 average time/residue: 1.0075 time to fit residues: 135.6180 Evaluate side-chains 87 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue -7 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 73 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 60 optimal weight: 0.1980 chunk 173 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 176 optimal weight: 0.0070 chunk 149 optimal weight: 0.6980 chunk 190 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 129 optimal weight: 20.0000 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 41 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.096766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065719 restraints weight = 46345.783| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.96 r_work: 0.2884 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17853 Z= 0.108 Angle : 0.477 6.588 24835 Z= 0.265 Chirality : 0.039 0.228 3003 Planarity : 0.003 0.041 2726 Dihedral : 19.913 179.515 3712 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.28 % Favored : 94.57 % Rotamer: Outliers : 2.82 % Allowed : 23.52 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.19), residues: 2008 helix: 2.55 (0.17), residues: 929 sheet: 1.11 (0.28), residues: 329 loop : -1.80 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 323 HIS 0.004 0.001 HIS C 394 PHE 0.012 0.001 PHE A 14 TYR 0.007 0.001 TYR E 284 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 818) hydrogen bonds : angle 3.92366 ( 2312) covalent geometry : bond 0.00220 (17853) covalent geometry : angle 0.47663 (24835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 1.758 Fit side-chains REVERT: A 216 GLU cc_start: 0.8810 (tt0) cc_final: 0.8515 (mm-30) REVERT: A 224 ASP cc_start: 0.7999 (t70) cc_final: 0.7537 (t0) REVERT: B 66 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 112 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 119 VAL cc_start: 0.6364 (OUTLIER) cc_final: 0.6161 (m) REVERT: B 124 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8626 (pp) REVERT: C 147 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7814 (p90) REVERT: C 333 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8839 (p90) REVERT: D 60 GLU cc_start: 0.7749 (tp30) cc_final: 0.7250 (tp30) REVERT: D 115 ASN cc_start: 0.9447 (OUTLIER) cc_final: 0.9178 (m110) REVERT: D 343 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8817 (tp30) REVERT: E 73 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8078 (mmt) outliers start: 39 outliers final: 15 residues processed: 106 average time/residue: 1.1394 time to fit residues: 138.2673 Evaluate side-chains 91 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue -7 MET Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 73 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 60 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 161 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN E 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.096241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064801 restraints weight = 46318.451| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.92 r_work: 0.2862 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17853 Z= 0.117 Angle : 0.482 7.996 24835 Z= 0.268 Chirality : 0.039 0.221 3003 Planarity : 0.003 0.040 2726 Dihedral : 19.914 178.121 3712 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.88 % Favored : 93.97 % Rotamer: Outliers : 3.11 % Allowed : 23.44 % Favored : 73.44 % 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: 1.27 (0.19), residues: 2008 helix: 2.62 (0.17), residues: 937 sheet: 1.25 (0.28), residues: 332 loop : -1.88 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 323 HIS 0.004 0.001 HIS B 419 PHE 0.021 0.001 PHE B 217 TYR 0.008 0.001 TYR C 26 ARG 0.006 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 818) hydrogen bonds : angle 3.72815 ( 2312) covalent geometry : bond 0.00251 (17853) covalent geometry : angle 0.48175 (24835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 1.905 Fit side-chains REVERT: A 216 GLU cc_start: 0.8766 (tt0) cc_final: 0.8380 (mm-30) REVERT: A 224 ASP cc_start: 0.8025 (t70) cc_final: 0.7598 (t0) REVERT: B 66 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8362 (mm-30) REVERT: B 112 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8459 (mt-10) REVERT: B 124 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8691 (pp) REVERT: C 147 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7820 (p90) REVERT: C 333 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8876 (p90) REVERT: D 60 GLU cc_start: 0.7815 (tp30) cc_final: 0.7452 (tp30) REVERT: D 101 GLU cc_start: 0.7836 (mp0) cc_final: 0.7421 (tp30) REVERT: D 112 GLU cc_start: 0.8767 (mm-30) cc_final: 0.7879 (mp0) REVERT: D 115 ASN cc_start: 0.9447 (OUTLIER) cc_final: 0.9193 (m110) outliers start: 43 outliers final: 18 residues processed: 113 average time/residue: 1.0649 time to fit residues: 138.1543 Evaluate side-chains 94 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue -7 MET Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 45 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 184 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** 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 = 0.3659 r_free = 0.3659 target = 0.096134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065234 restraints weight = 47020.843| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.96 r_work: 0.2876 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17853 Z= 0.117 Angle : 0.483 9.900 24835 Z= 0.267 Chirality : 0.039 0.222 3003 Planarity : 0.003 0.041 2726 Dihedral : 19.870 178.100 3712 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % Rotamer: Outliers : 2.82 % Allowed : 24.38 % Favored : 72.79 % 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: 1.30 (0.19), residues: 2008 helix: 2.65 (0.17), residues: 939 sheet: 1.25 (0.28), residues: 335 loop : -1.89 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 228 HIS 0.005 0.001 HIS A 394 PHE 0.008 0.001 PHE B 226 TYR 0.006 0.001 TYR A 182 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 818) hydrogen bonds : angle 3.61045 ( 2312) covalent geometry : bond 0.00254 (17853) covalent geometry : angle 0.48303 (24835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 1.647 Fit side-chains REVERT: A 53 HIS cc_start: 0.8399 (t-90) cc_final: 0.7671 (m-70) REVERT: A 60 GLU cc_start: 0.7875 (tp30) cc_final: 0.7292 (mm-30) REVERT: A 216 GLU cc_start: 0.8573 (tt0) cc_final: 0.8256 (mm-30) REVERT: A 224 ASP cc_start: 0.8138 (t70) cc_final: 0.7715 (t0) REVERT: B 66 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7677 (tm-30) REVERT: B 112 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8524 (mt-10) REVERT: B 124 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 216 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8544 (mm-30) REVERT: C 147 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7707 (p90) REVERT: C 333 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8867 (p90) REVERT: D 60 GLU cc_start: 0.7996 (tp30) cc_final: 0.7681 (tp30) REVERT: D 112 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8035 (mp0) REVERT: D 115 ASN cc_start: 0.9456 (OUTLIER) cc_final: 0.9223 (m110) REVERT: E 73 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8085 (mmt) outliers start: 39 outliers final: 18 residues processed: 106 average time/residue: 1.0598 time to fit residues: 128.9621 Evaluate side-chains 98 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue -7 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 73 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 134 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** 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 = 0.3656 r_free = 0.3656 target = 0.095574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.063339 restraints weight = 46428.978| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.22 r_work: 0.2854 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17853 Z= 0.126 Angle : 0.491 8.152 24835 Z= 0.271 Chirality : 0.040 0.221 3003 Planarity : 0.003 0.042 2726 Dihedral : 19.877 178.781 3711 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.73 % Rotamer: Outliers : 3.18 % Allowed : 23.88 % Favored : 72.94 % 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: 1.31 (0.19), residues: 2008 helix: 2.72 (0.17), residues: 935 sheet: 1.28 (0.27), residues: 332 loop : -1.95 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 323 HIS 0.004 0.001 HIS C 394 PHE 0.009 0.001 PHE B 226 TYR 0.008 0.001 TYR C 26 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 818) hydrogen bonds : angle 3.58309 ( 2312) covalent geometry : bond 0.00278 (17853) covalent geometry : angle 0.49082 (24835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 74 time to evaluate : 2.147 Fit side-chains REVERT: A 53 HIS cc_start: 0.8392 (t-90) cc_final: 0.7690 (m-70) REVERT: A 60 GLU cc_start: 0.7806 (tp30) cc_final: 0.7382 (mm-30) REVERT: A 216 GLU cc_start: 0.8548 (tt0) cc_final: 0.8193 (mm-30) REVERT: A 224 ASP cc_start: 0.8246 (t70) cc_final: 0.7831 (t0) REVERT: B 66 GLU cc_start: 0.8719 (mm-30) cc_final: 0.7650 (tm-30) REVERT: B 112 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8583 (mt-10) REVERT: B 124 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8809 (pp) REVERT: B 365 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7543 (ttm170) REVERT: C 147 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7676 (p90) REVERT: D 60 GLU cc_start: 0.7973 (tp30) cc_final: 0.7675 (tp30) REVERT: D 100 LYS cc_start: 0.6720 (tptp) cc_final: 0.6430 (tptm) REVERT: D 101 GLU cc_start: 0.7955 (mp0) cc_final: 0.7515 (tp30) REVERT: D 112 GLU cc_start: 0.8860 (mm-30) cc_final: 0.7980 (mp0) REVERT: D 115 ASN cc_start: 0.9453 (OUTLIER) cc_final: 0.9229 (m110) REVERT: D 212 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7130 (t80) REVERT: E 73 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8105 (mmt) outliers start: 44 outliers final: 21 residues processed: 110 average time/residue: 1.1650 time to fit residues: 145.6035 Evaluate side-chains 99 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 73 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 66 optimal weight: 30.0000 chunk 77 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN D 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.094379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.061961 restraints weight = 46193.290| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.20 r_work: 0.2820 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17853 Z= 0.156 Angle : 0.518 10.673 24835 Z= 0.286 Chirality : 0.041 0.224 3003 Planarity : 0.003 0.043 2726 Dihedral : 19.943 179.885 3709 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.93 % Favored : 93.92 % Rotamer: Outliers : 3.04 % Allowed : 24.46 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.19), residues: 2008 helix: 2.66 (0.17), residues: 936 sheet: 1.19 (0.28), residues: 334 loop : -2.03 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 323 HIS 0.005 0.001 HIS D 394 PHE 0.012 0.001 PHE B 226 TYR 0.009 0.001 TYR D 188 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 818) hydrogen bonds : angle 3.68532 ( 2312) covalent geometry : bond 0.00358 (17853) covalent geometry : angle 0.51789 (24835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 71 time to evaluate : 1.656 Fit side-chains REVERT: A 53 HIS cc_start: 0.8429 (t-90) cc_final: 0.7690 (m-70) REVERT: A 60 GLU cc_start: 0.7806 (tp30) cc_final: 0.7287 (tp30) REVERT: A 66 GLU cc_start: 0.8993 (tp30) cc_final: 0.8746 (mm-30) REVERT: A 216 GLU cc_start: 0.8554 (tt0) cc_final: 0.8208 (mm-30) REVERT: A 224 ASP cc_start: 0.8292 (t70) cc_final: 0.7862 (t0) REVERT: B 46 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.6995 (p90) REVERT: B 66 GLU cc_start: 0.8684 (mm-30) cc_final: 0.7652 (tm-30) REVERT: B 112 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8585 (mt-10) REVERT: B 124 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8756 (pp) REVERT: B 216 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8479 (mm-30) REVERT: B 365 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7579 (ttm170) REVERT: C 147 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7724 (p90) REVERT: D 60 GLU cc_start: 0.7976 (tp30) cc_final: 0.7696 (tp30) REVERT: D 101 GLU cc_start: 0.8004 (mp0) cc_final: 0.7582 (tp30) REVERT: D 115 ASN cc_start: 0.9459 (OUTLIER) cc_final: 0.9248 (m110) REVERT: E 73 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8142 (mmt) outliers start: 42 outliers final: 22 residues processed: 104 average time/residue: 1.1143 time to fit residues: 132.4442 Evaluate side-chains 96 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain C residue -7 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 278 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 61 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 148 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.094781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.062449 restraints weight = 46202.792| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.25 r_work: 0.2834 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17853 Z= 0.141 Angle : 0.505 9.185 24835 Z= 0.280 Chirality : 0.040 0.223 3003 Planarity : 0.003 0.046 2726 Dihedral : 19.898 179.763 3709 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.93 % Favored : 93.92 % Rotamer: Outliers : 2.82 % Allowed : 24.89 % Favored : 72.29 % 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: 1.24 (0.19), residues: 2008 helix: 2.69 (0.17), residues: 935 sheet: 1.14 (0.27), residues: 337 loop : -2.00 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 323 HIS 0.005 0.001 HIS C 394 PHE 0.010 0.001 PHE B 226 TYR 0.009 0.001 TYR C 26 ARG 0.006 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 818) hydrogen bonds : angle 3.61765 ( 2312) covalent geometry : bond 0.00320 (17853) covalent geometry : angle 0.50498 (24835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 1.774 Fit side-chains REVERT: A 53 HIS cc_start: 0.8418 (t-90) cc_final: 0.7674 (m-70) REVERT: A 60 GLU cc_start: 0.7816 (tp30) cc_final: 0.7332 (tp30) REVERT: A 66 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8690 (mm-30) REVERT: A 216 GLU cc_start: 0.8512 (tt0) cc_final: 0.8163 (mm-30) REVERT: A 224 ASP cc_start: 0.8262 (t70) cc_final: 0.7862 (t0) REVERT: B 46 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6956 (p90) REVERT: B 66 GLU cc_start: 0.8677 (mm-30) cc_final: 0.7637 (tm-30) REVERT: B 112 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8578 (mt-10) REVERT: B 124 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8758 (pp) REVERT: B 216 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8527 (mm-30) REVERT: B 365 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7562 (ttm170) REVERT: C 147 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7685 (p90) REVERT: D 60 GLU cc_start: 0.7930 (tp30) cc_final: 0.7661 (tp30) REVERT: D 101 GLU cc_start: 0.8056 (mp0) cc_final: 0.7671 (tp30) REVERT: D 112 GLU cc_start: 0.8864 (mm-30) cc_final: 0.7982 (mp0) REVERT: D 115 ASN cc_start: 0.9461 (OUTLIER) cc_final: 0.9253 (m110) REVERT: E 73 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8130 (mmt) outliers start: 39 outliers final: 25 residues processed: 102 average time/residue: 1.1070 time to fit residues: 129.2319 Evaluate side-chains 101 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain C residue -7 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 286 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 108 optimal weight: 0.0570 chunk 110 optimal weight: 40.0000 chunk 164 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 419 HIS B 46 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.096175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063988 restraints weight = 46732.289| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.33 r_work: 0.2851 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17853 Z= 0.111 Angle : 0.483 7.883 24835 Z= 0.267 Chirality : 0.039 0.221 3003 Planarity : 0.003 0.047 2726 Dihedral : 19.807 177.977 3709 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % Rotamer: Outliers : 2.68 % Allowed : 24.96 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.19), residues: 2008 helix: 2.80 (0.17), residues: 934 sheet: 1.24 (0.27), residues: 336 loop : -1.96 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 323 HIS 0.004 0.001 HIS C 394 PHE 0.009 0.001 PHE C 226 TYR 0.006 0.001 TYR D 188 ARG 0.008 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 818) hydrogen bonds : angle 3.48982 ( 2312) covalent geometry : bond 0.00240 (17853) covalent geometry : angle 0.48294 (24835) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 1.784 Fit side-chains REVERT: A 53 HIS cc_start: 0.8343 (t-90) cc_final: 0.7660 (m-70) REVERT: A 60 GLU cc_start: 0.7651 (tp30) cc_final: 0.7255 (tp30) REVERT: A 212 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: A 224 ASP cc_start: 0.8102 (t70) cc_final: 0.7684 (t0) REVERT: B 46 HIS cc_start: 0.7108 (OUTLIER) cc_final: 0.6762 (p90) REVERT: B 66 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7572 (tm-30) REVERT: B 112 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 124 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8678 (pp) REVERT: B 216 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8551 (mm-30) REVERT: B 365 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7398 (ttm170) REVERT: C 147 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7651 (p90) REVERT: C 333 TYR cc_start: 0.8972 (p90) cc_final: 0.8754 (p90) REVERT: D 60 GLU cc_start: 0.7861 (tp30) cc_final: 0.7588 (tp30) REVERT: D 101 GLU cc_start: 0.7997 (mp0) cc_final: 0.7624 (tp30) REVERT: D 112 GLU cc_start: 0.8720 (mm-30) cc_final: 0.7854 (mp0) REVERT: D 115 ASN cc_start: 0.9449 (OUTLIER) cc_final: 0.9198 (m110) REVERT: E 73 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8081 (mmt) outliers start: 37 outliers final: 22 residues processed: 101 average time/residue: 1.0686 time to fit residues: 124.4763 Evaluate side-chains 99 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 12 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 chunk 115 optimal weight: 0.3980 chunk 168 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 53 optimal weight: 0.0170 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN E 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.095207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.062942 restraints weight = 46378.538| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.31 r_work: 0.2844 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17853 Z= 0.133 Angle : 0.500 8.524 24835 Z= 0.277 Chirality : 0.040 0.222 3003 Planarity : 0.003 0.048 2726 Dihedral : 19.802 178.907 3709 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.93 % Favored : 93.92 % Rotamer: Outliers : 2.60 % Allowed : 25.11 % Favored : 72.29 % 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: 1.32 (0.19), residues: 2008 helix: 2.76 (0.17), residues: 936 sheet: 1.15 (0.27), residues: 343 loop : -1.97 (0.20), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 323 HIS 0.009 0.001 HIS B 46 PHE 0.010 0.001 PHE B 226 TYR 0.011 0.001 TYR C 26 ARG 0.009 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 818) hydrogen bonds : angle 3.54912 ( 2312) covalent geometry : bond 0.00298 (17853) covalent geometry : angle 0.50016 (24835) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 1.653 Fit side-chains REVERT: A 53 HIS cc_start: 0.8439 (t-90) cc_final: 0.7767 (m-70) REVERT: A 60 GLU cc_start: 0.7778 (tp30) cc_final: 0.7357 (tp30) REVERT: A 216 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: A 224 ASP cc_start: 0.8182 (t70) cc_final: 0.7783 (t0) REVERT: B 46 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6939 (p90) REVERT: B 66 GLU cc_start: 0.8689 (mm-30) cc_final: 0.7640 (tm-30) REVERT: B 112 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 124 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8762 (pp) REVERT: B 216 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8557 (mm-30) REVERT: B 365 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7554 (ttm170) REVERT: C 147 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7682 (p90) REVERT: D 60 GLU cc_start: 0.7910 (tp30) cc_final: 0.7624 (tp30) REVERT: D 101 GLU cc_start: 0.8053 (mp0) cc_final: 0.7710 (tp30) REVERT: D 112 GLU cc_start: 0.8801 (mm-30) cc_final: 0.7947 (mp0) REVERT: D 115 ASN cc_start: 0.9455 (OUTLIER) cc_final: 0.9236 (m110) REVERT: E 73 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8092 (mmt) outliers start: 36 outliers final: 27 residues processed: 99 average time/residue: 1.0732 time to fit residues: 122.7628 Evaluate side-chains 103 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 286 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 138 optimal weight: 0.0980 chunk 149 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 191 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN D 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.096713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064666 restraints weight = 46480.598| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.18 r_work: 0.2886 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17853 Z= 0.106 Angle : 0.478 8.098 24835 Z= 0.265 Chirality : 0.039 0.219 3003 Planarity : 0.003 0.051 2726 Dihedral : 19.713 177.739 3709 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.43 % Favored : 94.42 % Rotamer: Outliers : 2.32 % Allowed : 25.47 % Favored : 72.21 % 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: 1.40 (0.19), residues: 2008 helix: 2.83 (0.17), residues: 934 sheet: 1.22 (0.27), residues: 342 loop : -1.94 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 323 HIS 0.007 0.001 HIS B 46 PHE 0.020 0.001 PHE B 45 TYR 0.007 0.001 TYR C 188 ARG 0.006 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 818) hydrogen bonds : angle 3.44441 ( 2312) covalent geometry : bond 0.00224 (17853) covalent geometry : angle 0.47810 (24835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10677.61 seconds wall clock time: 184 minutes 45.13 seconds (11085.13 seconds total)