Starting phenix.real_space_refine on Fri Jun 13 00:30:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eio_48088/06_2025/9eio_48088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eio_48088/06_2025/9eio_48088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eio_48088/06_2025/9eio_48088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eio_48088/06_2025/9eio_48088.map" model { file = "/net/cci-nas-00/data/ceres_data/9eio_48088/06_2025/9eio_48088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eio_48088/06_2025/9eio_48088.cif" } resolution = 3.62 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= 1.000 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 S 116 5.16 5 C 9358 2.51 5 N 2515 2.21 5 O 2653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14654 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2652 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2652 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2652 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2652 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1006 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "F" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1005 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "G" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1005 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1014 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.92, per 1000 atoms: 0.75 Number of scatterers: 14654 At special positions: 0 Unit cell: (144.48, 145.34, 100.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 116 16.00 O 2653 8.00 N 2515 7.00 C 9358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 371 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.9 seconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 118 through 145 removed outlier: 4.166A pdb=" N ARG A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.599A pdb=" N VAL A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 202 removed outlier: 3.943A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.551A pdb=" N CYS A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 275 removed outlier: 3.807A pdb=" N ARG A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.719A pdb=" N ARG A 287 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 288' Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.636A pdb=" N PHE A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.849A pdb=" N ARG A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 369 through 382 removed outlier: 4.361A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.805A pdb=" N VAL A 390 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.598A pdb=" N ILE A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 476 removed outlier: 4.034A pdb=" N HIS A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN A 462 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.633A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 158 removed outlier: 4.100A pdb=" N ILE B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 201 removed outlier: 4.092A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.761A pdb=" N ARG B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.719A pdb=" N PHE B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.896A pdb=" N ARG B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 358 removed outlier: 3.981A pdb=" N LEU B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.586A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 415 removed outlier: 3.700A pdb=" N HIS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 419 through 439 removed outlier: 4.151A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 474 removed outlier: 3.659A pdb=" N VAL B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N HIS B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B 462 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'C' and resid 119 through 134 removed outlier: 3.781A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.818A pdb=" N LEU C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 142 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 158 removed outlier: 3.592A pdb=" N VAL C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 201 removed outlier: 4.045A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.564A pdb=" N PHE C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 221 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 275 removed outlier: 3.687A pdb=" N ARG C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.966A pdb=" N ASN C 293 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.721A pdb=" N THR C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 321 removed outlier: 3.643A pdb=" N PHE C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 327 through 334 removed outlier: 3.850A pdb=" N ARG C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 371 through 382 removed outlier: 4.280A pdb=" N LEU C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 397 Processing helix chain 'C' and resid 402 through 415 removed outlier: 4.387A pdb=" N VAL C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N HIS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 419 through 439 removed outlier: 3.729A pdb=" N ALA C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 448 Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.855A pdb=" N LYS C 455 " --> pdb=" O LYS C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 476 removed outlier: 4.157A pdb=" N HIS C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN C 462 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU C 463 " --> pdb=" O ALA C 459 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 134 removed outlier: 4.214A pdb=" N ARG D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 158 removed outlier: 3.917A pdb=" N LEU D 140 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 141 " --> pdb=" O ASP D 137 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY D 146 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 147 " --> pdb=" O GLY D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 201 removed outlier: 4.043A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU D 183 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN D 201 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.619A pdb=" N ILE D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 260 through 264 removed outlier: 3.556A pdb=" N PHE D 264 " --> pdb=" O ILE D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 268 through 275 removed outlier: 3.693A pdb=" N ARG D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 300 through 310 removed outlier: 3.615A pdb=" N THR D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.681A pdb=" N ARG D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 371 through 382 removed outlier: 6.379A pdb=" N LEU D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 398 removed outlier: 3.957A pdb=" N VAL D 390 " --> pdb=" O CYS D 386 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 391 " --> pdb=" O THR D 387 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 415 removed outlier: 4.649A pdb=" N VAL D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 419 through 439 removed outlier: 3.791A pdb=" N TYR D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 477 removed outlier: 3.771A pdb=" N VAL D 449 " --> pdb=" O ASP D 445 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS D 452 " --> pdb=" O LYS D 448 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN D 462 " --> pdb=" O GLN D 458 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU D 463 " --> pdb=" O ALA D 459 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 469 " --> pdb=" O SER D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 8 Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.742A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.534A pdb=" N LEU E 32 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.882A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 removed outlier: 4.031A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 88 removed outlier: 4.256A pdb=" N ARG E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 101 through 111 Processing helix chain 'E' and resid 117 through 128 removed outlier: 5.975A pdb=" N MET E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.857A pdb=" N GLU E 140 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE E 141 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN E 143 " --> pdb=" O GLU E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 8 Processing helix chain 'F' and resid 9 through 19 removed outlier: 4.412A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 removed outlier: 3.769A pdb=" N SER F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU F 39 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY F 40 " --> pdb=" O MET F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 54 removed outlier: 4.131A pdb=" N GLU F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 101 through 111 Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 137 through 144 removed outlier: 4.316A pdb=" N GLU F 140 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE F 141 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 143 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.541A pdb=" N THR G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 53 Processing helix chain 'G' and resid 64 through 73 removed outlier: 3.801A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 119 through 128 removed outlier: 4.083A pdb=" N GLU G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU G 127 " --> pdb=" O GLU G 123 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA G 128 " --> pdb=" O MET G 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.682A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 36 Processing helix chain 'H' and resid 44 through 53 Processing helix chain 'H' and resid 64 through 73 removed outlier: 3.567A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 93 removed outlier: 4.240A pdb=" N GLU H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 112 removed outlier: 3.505A pdb=" N LEU H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 127 removed outlier: 4.050A pdb=" N GLU H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.601A pdb=" N ASP H 131 " --> pdb=" O ALA H 128 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4795 1.34 - 1.46: 2982 1.46 - 1.58: 6893 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 14870 Sorted by residual: bond pdb=" CA GLY G 134 " pdb=" C GLY G 134 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.60e+00 bond pdb=" N GLY G 134 " pdb=" CA GLY G 134 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.91e+00 bond pdb=" CB GLU C 430 " pdb=" CG GLU C 430 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" N GLN B 340 " pdb=" CA GLN B 340 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.05e+00 bond pdb=" CA LYS A 397 " pdb=" C LYS A 397 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.80e-02 3.09e+03 8.06e-01 ... (remaining 14865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 19271 1.14 - 2.28: 636 2.28 - 3.42: 123 3.42 - 4.56: 46 4.56 - 5.70: 16 Bond angle restraints: 20092 Sorted by residual: angle pdb=" N ILE A 257 " pdb=" CA ILE A 257 " pdb=" C ILE A 257 " ideal model delta sigma weight residual 112.96 108.16 4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" N ILE D 257 " pdb=" CA ILE D 257 " pdb=" C ILE D 257 " ideal model delta sigma weight residual 113.42 107.91 5.51 1.17e+00 7.31e-01 2.22e+01 angle pdb=" N ILE C 257 " pdb=" CA ILE C 257 " pdb=" C ILE C 257 " ideal model delta sigma weight residual 112.96 108.37 4.59 1.00e+00 1.00e+00 2.10e+01 angle pdb=" N THR C 343 " pdb=" CA THR C 343 " pdb=" C THR C 343 " ideal model delta sigma weight residual 112.94 107.90 5.04 1.41e+00 5.03e-01 1.28e+01 angle pdb=" C LEU B 122 " pdb=" CA LEU B 122 " pdb=" CB LEU B 122 " ideal model delta sigma weight residual 115.79 112.03 3.76 1.19e+00 7.06e-01 1.00e+01 ... (remaining 20087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8088 17.98 - 35.97: 705 35.97 - 53.95: 121 53.95 - 71.93: 19 71.93 - 89.92: 15 Dihedral angle restraints: 8948 sinusoidal: 3368 harmonic: 5580 Sorted by residual: dihedral pdb=" CB CYS A 333 " pdb=" SG CYS A 333 " pdb=" SG CYS A 371 " pdb=" CB CYS A 371 " ideal model delta sinusoidal sigma weight residual 93.00 27.64 65.36 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CB CYS C 333 " pdb=" SG CYS C 333 " pdb=" SG CYS C 371 " pdb=" CB CYS C 371 " ideal model delta sinusoidal sigma weight residual 93.00 29.97 63.03 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS B 333 " pdb=" SG CYS B 333 " pdb=" SG CYS B 371 " pdb=" CB CYS B 371 " ideal model delta sinusoidal sigma weight residual 93.00 32.88 60.12 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 8945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1331 0.030 - 0.060: 772 0.060 - 0.090: 210 0.090 - 0.120: 45 0.120 - 0.150: 11 Chirality restraints: 2369 Sorted by residual: chirality pdb=" CA VAL A 366 " pdb=" N VAL A 366 " pdb=" C VAL A 366 " pdb=" CB VAL A 366 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA VAL D 366 " pdb=" N VAL D 366 " pdb=" C VAL D 366 " pdb=" CB VAL D 366 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CG LEU C 174 " pdb=" CB LEU C 174 " pdb=" CD1 LEU C 174 " pdb=" CD2 LEU C 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2366 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 374 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C GLY D 374 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY D 374 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL D 375 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 366 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO D 367 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 228 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO D 229 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " -0.014 5.00e-02 4.00e+02 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 3769 2.79 - 3.38: 16026 3.38 - 3.97: 24135 3.97 - 4.55: 34087 4.55 - 5.14: 49952 Nonbonded interactions: 127969 Sorted by model distance: nonbonded pdb=" OE1 GLU B 334 " pdb=" OG1 THR B 343 " model vdw 2.208 3.040 nonbonded pdb=" O MET C 412 " pdb=" OG1 THR C 417 " model vdw 2.224 3.040 nonbonded pdb=" O SER B 278 " pdb=" OG1 THR B 282 " model vdw 2.240 3.040 nonbonded pdb=" O PHE B 281 " pdb=" NH2 ARG B 287 " model vdw 2.300 3.120 nonbonded pdb=" NE2 GLN C 470 " pdb=" OD1 ASN C 474 " model vdw 2.302 3.120 ... (remaining 127964 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 118 through 478) selection = chain 'B' selection = (chain 'C' and resid 118 through 478) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 3 through 100 or (resid 101 through 108 and (name N or nam \ e CA or name C or name O or name CB )) or resid 109 through 144 or resid 201 thr \ ough 202)) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and (resid 3 through 99 or (resid 100 through 108 and (name N or name \ CA or name C or name O or name CB )) or resid 109 through 144 or resid 201 thro \ ugh 202)) } 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 group one per residue 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: 9.230 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.240 Find NCS groups from input model: 0.670 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 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 0.045 14874 Z= 0.117 Angle : 0.535 5.700 20100 Z= 0.296 Chirality : 0.039 0.150 2369 Planarity : 0.002 0.026 2529 Dihedral : 14.219 89.917 5312 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.19), residues: 1900 helix: -0.95 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -2.10 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 351 HIS 0.006 0.001 HIS C 452 PHE 0.010 0.001 PHE D 456 TYR 0.012 0.001 TYR D 362 ARG 0.003 0.000 ARG C 429 Details of bonding type rmsd hydrogen bonds : bond 0.10688 ( 703) hydrogen bonds : angle 4.51008 ( 2052) SS BOND : bond 0.00428 ( 4) SS BOND : angle 0.20057 ( 8) covalent geometry : bond 0.00250 (14870) covalent geometry : angle 0.53515 (20092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.5562 (m-30) cc_final: 0.5306 (m-30) REVERT: C 413 ASP cc_start: 0.7785 (t0) cc_final: 0.7561 (t0) REVERT: E 24 ASP cc_start: 0.6718 (p0) cc_final: 0.5232 (t0) REVERT: F 83 GLU cc_start: 0.6409 (pm20) cc_final: 0.6023 (pm20) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2636 time to fit residues: 134.3622 Evaluate side-chains 305 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.0370 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 96 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 ASN D 470 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.278449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.263049 restraints weight = 16588.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.259264 restraints weight = 24152.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.255683 restraints weight = 24335.393| |-----------------------------------------------------------------------------| r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14874 Z= 0.110 Angle : 0.546 7.277 20100 Z= 0.289 Chirality : 0.038 0.154 2369 Planarity : 0.003 0.039 2529 Dihedral : 4.309 26.426 2049 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.04 % Allowed : 10.88 % Favored : 87.08 % 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: -1.87 (0.20), residues: 1900 helix: -0.77 (0.15), residues: 1287 sheet: None (None), residues: 0 loop : -2.02 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 351 HIS 0.003 0.000 HIS B 461 PHE 0.015 0.001 PHE H 16 TYR 0.017 0.001 TYR A 435 ARG 0.007 0.000 ARG D 287 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 703) hydrogen bonds : angle 3.82954 ( 2052) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.27105 ( 8) covalent geometry : bond 0.00239 (14870) covalent geometry : angle 0.54647 (20092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 305 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 162 ASP cc_start: 0.5295 (m-30) cc_final: 0.5041 (m-30) REVERT: D 294 LYS cc_start: 0.6516 (mmtt) cc_final: 0.6263 (mmtt) REVERT: E 22 ASP cc_start: 0.6075 (p0) cc_final: 0.5791 (p0) REVERT: E 24 ASP cc_start: 0.6716 (p0) cc_final: 0.5329 (t0) REVERT: E 36 MET cc_start: 0.7647 (mtp) cc_final: 0.7302 (mtp) REVERT: F 83 GLU cc_start: 0.6494 (pm20) cc_final: 0.6100 (pm20) REVERT: H 20 ASP cc_start: 0.4615 (t0) cc_final: 0.4412 (t0) REVERT: H 22 ASP cc_start: 0.5886 (p0) cc_final: 0.5320 (p0) REVERT: H 24 ASP cc_start: 0.6340 (p0) cc_final: 0.3368 (t0) outliers start: 30 outliers final: 17 residues processed: 315 average time/residue: 0.2604 time to fit residues: 119.7516 Evaluate side-chains 306 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 289 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 23 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 177 optimal weight: 0.0170 chunk 143 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN B 470 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.276407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.260693 restraints weight = 16490.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.255750 restraints weight = 23565.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.252895 restraints weight = 22275.336| |-----------------------------------------------------------------------------| r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14874 Z= 0.119 Angle : 0.539 7.503 20100 Z= 0.285 Chirality : 0.038 0.145 2369 Planarity : 0.003 0.025 2529 Dihedral : 4.278 24.558 2049 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.52 % Allowed : 13.32 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1900 helix: -0.72 (0.15), residues: 1287 sheet: None (None), residues: 0 loop : -1.95 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 351 HIS 0.003 0.000 HIS D 461 PHE 0.018 0.001 PHE F 68 TYR 0.015 0.001 TYR H 138 ARG 0.007 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 703) hydrogen bonds : angle 3.78393 ( 2052) SS BOND : bond 0.00437 ( 4) SS BOND : angle 0.27413 ( 8) covalent geometry : bond 0.00272 (14870) covalent geometry : angle 0.53914 (20092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8299 (ptp) REVERT: B 162 ASP cc_start: 0.5255 (m-30) cc_final: 0.5045 (m-30) REVERT: D 316 LEU cc_start: 0.8431 (tt) cc_final: 0.8097 (tp) REVERT: E 22 ASP cc_start: 0.5565 (p0) cc_final: 0.5345 (p0) REVERT: E 24 ASP cc_start: 0.6749 (p0) cc_final: 0.5457 (t0) REVERT: E 36 MET cc_start: 0.7708 (mtp) cc_final: 0.7478 (mtp) REVERT: E 72 MET cc_start: 0.7195 (mmm) cc_final: 0.6805 (mmt) REVERT: F 71 MET cc_start: 0.8248 (tmm) cc_final: 0.7145 (tmm) REVERT: F 83 GLU cc_start: 0.6617 (pm20) cc_final: 0.6013 (pm20) REVERT: H 22 ASP cc_start: 0.5844 (p0) cc_final: 0.5355 (p0) REVERT: H 24 ASP cc_start: 0.6565 (p0) cc_final: 0.3556 (t0) outliers start: 37 outliers final: 24 residues processed: 305 average time/residue: 0.3151 time to fit residues: 144.2052 Evaluate side-chains 308 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 75 optimal weight: 0.4980 chunk 163 optimal weight: 0.6980 chunk 126 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN B 470 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.276791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.261365 restraints weight = 16455.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.256916 restraints weight = 23048.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.253002 restraints weight = 21939.342| |-----------------------------------------------------------------------------| r_work (final): 0.4765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14874 Z= 0.113 Angle : 0.525 7.102 20100 Z= 0.278 Chirality : 0.037 0.145 2369 Planarity : 0.003 0.027 2529 Dihedral : 4.209 24.254 2049 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.13 % Allowed : 15.23 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.20), residues: 1900 helix: -0.55 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : -1.96 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 351 HIS 0.002 0.000 HIS D 461 PHE 0.025 0.001 PHE H 68 TYR 0.019 0.001 TYR A 435 ARG 0.004 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 703) hydrogen bonds : angle 3.73940 ( 2052) SS BOND : bond 0.00384 ( 4) SS BOND : angle 0.23869 ( 8) covalent geometry : bond 0.00258 (14870) covalent geometry : angle 0.52504 (20092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 289 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8749 (mt) cc_final: 0.8504 (tt) REVERT: A 365 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8299 (ptp) REVERT: B 162 ASP cc_start: 0.5176 (m-30) cc_final: 0.4972 (m-30) REVERT: B 470 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7308 (tp40) REVERT: D 316 LEU cc_start: 0.8534 (tt) cc_final: 0.8188 (tp) REVERT: E 24 ASP cc_start: 0.6720 (p0) cc_final: 0.5510 (t0) REVERT: E 36 MET cc_start: 0.7624 (mtp) cc_final: 0.7334 (mtp) REVERT: E 72 MET cc_start: 0.7184 (mmm) cc_final: 0.6762 (mmt) REVERT: E 112 LEU cc_start: 0.5429 (OUTLIER) cc_final: 0.4804 (tp) REVERT: F 71 MET cc_start: 0.8288 (tmm) cc_final: 0.7252 (tmm) REVERT: F 83 GLU cc_start: 0.6566 (pm20) cc_final: 0.6062 (pm20) REVERT: H 22 ASP cc_start: 0.5805 (p0) cc_final: 0.5309 (p0) REVERT: H 24 ASP cc_start: 0.6432 (p0) cc_final: 0.3337 (t0) outliers start: 46 outliers final: 25 residues processed: 309 average time/residue: 0.2992 time to fit residues: 134.5507 Evaluate side-chains 313 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 138 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.274686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.258814 restraints weight = 16571.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.253693 restraints weight = 22036.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.249371 restraints weight = 21538.981| |-----------------------------------------------------------------------------| r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14874 Z= 0.132 Angle : 0.547 6.936 20100 Z= 0.289 Chirality : 0.038 0.149 2369 Planarity : 0.003 0.032 2529 Dihedral : 4.288 24.028 2049 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.20 % Allowed : 16.59 % Favored : 80.22 % 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: -1.65 (0.20), residues: 1900 helix: -0.59 (0.15), residues: 1256 sheet: None (None), residues: 0 loop : -1.94 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 351 HIS 0.003 0.000 HIS B 461 PHE 0.013 0.001 PHE B 456 TYR 0.011 0.001 TYR B 362 ARG 0.004 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 703) hydrogen bonds : angle 3.78338 ( 2052) SS BOND : bond 0.00503 ( 4) SS BOND : angle 0.30639 ( 8) covalent geometry : bond 0.00312 (14870) covalent geometry : angle 0.54705 (20092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7532 (mt) REVERT: A 316 LEU cc_start: 0.8763 (mt) cc_final: 0.8514 (tt) REVERT: A 470 GLN cc_start: 0.7845 (tp40) cc_final: 0.7597 (tp40) REVERT: D 316 LEU cc_start: 0.8483 (tt) cc_final: 0.8186 (tp) REVERT: E 22 ASP cc_start: 0.5875 (p0) cc_final: 0.5368 (p0) REVERT: E 24 ASP cc_start: 0.6952 (p0) cc_final: 0.5501 (t0) REVERT: E 36 MET cc_start: 0.7585 (mtp) cc_final: 0.7328 (mtp) REVERT: E 72 MET cc_start: 0.7323 (mmm) cc_final: 0.6915 (mmt) REVERT: E 84 GLU cc_start: 0.6280 (mm-30) cc_final: 0.5969 (mp0) REVERT: E 112 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.5015 (mt) REVERT: F 71 MET cc_start: 0.8340 (tmm) cc_final: 0.7335 (tmm) REVERT: F 83 GLU cc_start: 0.6494 (pm20) cc_final: 0.5994 (pm20) REVERT: G 72 MET cc_start: 0.8167 (tpt) cc_final: 0.7763 (mmt) REVERT: H 22 ASP cc_start: 0.5844 (p0) cc_final: 0.5336 (p0) REVERT: H 24 ASP cc_start: 0.6468 (p0) cc_final: 0.3773 (t70) outliers start: 47 outliers final: 30 residues processed: 310 average time/residue: 0.3107 time to fit residues: 142.8563 Evaluate side-chains 316 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 0.0060 chunk 22 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 158 optimal weight: 0.1980 chunk 20 optimal weight: 0.0020 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.278960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.265267 restraints weight = 16520.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.261235 restraints weight = 22898.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.257727 restraints weight = 21027.266| |-----------------------------------------------------------------------------| r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14874 Z= 0.095 Angle : 0.504 7.430 20100 Z= 0.268 Chirality : 0.037 0.148 2369 Planarity : 0.002 0.028 2529 Dihedral : 4.032 23.841 2049 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.45 % Allowed : 17.95 % Favored : 79.61 % 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: -1.50 (0.20), residues: 1900 helix: -0.49 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -1.86 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 351 HIS 0.002 0.000 HIS A 461 PHE 0.013 0.001 PHE B 456 TYR 0.007 0.001 TYR B 268 ARG 0.004 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.02524 ( 703) hydrogen bonds : angle 3.57602 ( 2052) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.22297 ( 8) covalent geometry : bond 0.00207 (14870) covalent geometry : angle 0.50427 (20092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7469 (mt) REVERT: A 316 LEU cc_start: 0.8604 (mt) cc_final: 0.8354 (tt) REVERT: C 210 MET cc_start: 0.7497 (mtm) cc_final: 0.7200 (mtp) REVERT: D 316 LEU cc_start: 0.8289 (tt) cc_final: 0.7972 (tp) REVERT: E 20 ASP cc_start: 0.4143 (t0) cc_final: 0.3839 (t0) REVERT: E 22 ASP cc_start: 0.5732 (p0) cc_final: 0.5332 (p0) REVERT: E 24 ASP cc_start: 0.6701 (p0) cc_final: 0.5323 (t0) REVERT: E 36 MET cc_start: 0.7350 (mtp) cc_final: 0.7139 (mtp) REVERT: E 37 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6898 (mmm160) REVERT: E 72 MET cc_start: 0.7184 (mmm) cc_final: 0.6937 (mmp) REVERT: E 112 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.5125 (mt) REVERT: F 83 GLU cc_start: 0.6498 (pm20) cc_final: 0.6100 (pm20) REVERT: G 72 MET cc_start: 0.8129 (tpt) cc_final: 0.7826 (tpt) REVERT: H 22 ASP cc_start: 0.5585 (p0) cc_final: 0.5141 (p0) REVERT: H 24 ASP cc_start: 0.6384 (p0) cc_final: 0.3711 (t70) outliers start: 36 outliers final: 26 residues processed: 308 average time/residue: 0.2474 time to fit residues: 112.3699 Evaluate side-chains 313 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 158 optimal weight: 0.1980 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.275387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.258895 restraints weight = 16601.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.254746 restraints weight = 24241.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.251877 restraints weight = 20564.661| |-----------------------------------------------------------------------------| r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14874 Z= 0.132 Angle : 0.544 8.151 20100 Z= 0.287 Chirality : 0.038 0.153 2369 Planarity : 0.003 0.071 2529 Dihedral : 4.189 24.446 2049 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.52 % Allowed : 18.97 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.58 (0.20), residues: 1900 helix: -0.58 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -1.83 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 351 HIS 0.008 0.001 HIS C 190 PHE 0.018 0.001 PHE H 68 TYR 0.010 0.001 TYR B 362 ARG 0.005 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 703) hydrogen bonds : angle 3.69203 ( 2052) SS BOND : bond 0.00500 ( 4) SS BOND : angle 0.29804 ( 8) covalent geometry : bond 0.00310 (14870) covalent geometry : angle 0.54423 (20092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7531 (mt) REVERT: A 316 LEU cc_start: 0.8811 (mt) cc_final: 0.8562 (tt) REVERT: D 316 LEU cc_start: 0.8424 (tt) cc_final: 0.8095 (tp) REVERT: E 20 ASP cc_start: 0.4336 (t0) cc_final: 0.4022 (t0) REVERT: E 22 ASP cc_start: 0.5642 (p0) cc_final: 0.5153 (p0) REVERT: E 24 ASP cc_start: 0.6922 (p0) cc_final: 0.5441 (t0) REVERT: E 37 ARG cc_start: 0.7129 (mtp85) cc_final: 0.6904 (mmm160) REVERT: E 72 MET cc_start: 0.7113 (mmm) cc_final: 0.6740 (mmt) REVERT: E 112 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.5179 (mt) REVERT: F 83 GLU cc_start: 0.6598 (pm20) cc_final: 0.6171 (pm20) REVERT: G 72 MET cc_start: 0.8091 (tpt) cc_final: 0.7757 (tpt) REVERT: H 22 ASP cc_start: 0.5623 (p0) cc_final: 0.5202 (p0) REVERT: H 24 ASP cc_start: 0.6469 (p0) cc_final: 0.3827 (t70) outliers start: 37 outliers final: 29 residues processed: 309 average time/residue: 0.3479 time to fit residues: 159.7278 Evaluate side-chains 315 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 159 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.274331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.258218 restraints weight = 16441.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.253894 restraints weight = 24207.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.249601 restraints weight = 21508.132| |-----------------------------------------------------------------------------| r_work (final): 0.4742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14874 Z= 0.139 Angle : 0.562 9.047 20100 Z= 0.296 Chirality : 0.039 0.158 2369 Planarity : 0.003 0.032 2529 Dihedral : 4.269 24.856 2049 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.52 % Allowed : 19.44 % Favored : 78.04 % 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: -1.67 (0.20), residues: 1900 helix: -0.73 (0.15), residues: 1312 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 351 HIS 0.006 0.001 HIS C 190 PHE 0.012 0.001 PHE G 68 TYR 0.011 0.001 TYR B 362 ARG 0.002 0.000 ARG B 471 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 703) hydrogen bonds : angle 3.75114 ( 2052) SS BOND : bond 0.00539 ( 4) SS BOND : angle 0.31301 ( 8) covalent geometry : bond 0.00334 (14870) covalent geometry : angle 0.56185 (20092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8772 (mt) cc_final: 0.8526 (tt) REVERT: E 20 ASP cc_start: 0.4513 (t0) cc_final: 0.4219 (t0) REVERT: E 22 ASP cc_start: 0.5767 (p0) cc_final: 0.5253 (p0) REVERT: E 24 ASP cc_start: 0.7025 (p0) cc_final: 0.5522 (t0) REVERT: E 72 MET cc_start: 0.7081 (mmm) cc_final: 0.6768 (mmt) REVERT: E 83 GLU cc_start: 0.6909 (pm20) cc_final: 0.6137 (tp30) REVERT: E 112 LEU cc_start: 0.5547 (OUTLIER) cc_final: 0.5103 (mt) REVERT: F 83 GLU cc_start: 0.6661 (pm20) cc_final: 0.6248 (pm20) REVERT: G 80 ASP cc_start: 0.7238 (p0) cc_final: 0.6988 (p0) REVERT: H 22 ASP cc_start: 0.5723 (p0) cc_final: 0.5345 (p0) REVERT: H 24 ASP cc_start: 0.6539 (p0) cc_final: 0.3984 (t70) outliers start: 37 outliers final: 28 residues processed: 306 average time/residue: 0.2519 time to fit residues: 114.3761 Evaluate side-chains 319 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 70 optimal weight: 0.0020 chunk 171 optimal weight: 0.1980 chunk 174 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 470 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.276336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.260999 restraints weight = 16503.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.257154 restraints weight = 22884.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.252735 restraints weight = 22939.147| |-----------------------------------------------------------------------------| r_work (final): 0.4769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14874 Z= 0.112 Angle : 0.547 11.422 20100 Z= 0.289 Chirality : 0.037 0.159 2369 Planarity : 0.003 0.031 2529 Dihedral : 4.146 24.240 2049 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.47 % Favored : 92.47 % Rotamer: Outliers : 2.18 % Allowed : 19.44 % Favored : 78.38 % 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: -1.54 (0.20), residues: 1900 helix: -0.61 (0.15), residues: 1312 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 351 HIS 0.005 0.000 HIS C 190 PHE 0.019 0.001 PHE H 68 TYR 0.008 0.001 TYR A 120 ARG 0.002 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 703) hydrogen bonds : angle 3.65160 ( 2052) SS BOND : bond 0.00337 ( 4) SS BOND : angle 0.21561 ( 8) covalent geometry : bond 0.00257 (14870) covalent geometry : angle 0.54684 (20092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 289 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8782 (mt) cc_final: 0.8471 (tt) REVERT: D 174 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7160 (mp) REVERT: D 316 LEU cc_start: 0.8194 (tt) cc_final: 0.7891 (tp) REVERT: E 22 ASP cc_start: 0.5635 (p0) cc_final: 0.5317 (p0) REVERT: E 24 ASP cc_start: 0.6853 (p0) cc_final: 0.5350 (t0) REVERT: E 72 MET cc_start: 0.7041 (mmm) cc_final: 0.6753 (mmt) REVERT: E 83 GLU cc_start: 0.6861 (pm20) cc_final: 0.6179 (tp30) REVERT: E 112 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5148 (mt) REVERT: F 83 GLU cc_start: 0.6713 (pm20) cc_final: 0.6019 (tp30) REVERT: H 22 ASP cc_start: 0.5703 (p0) cc_final: 0.5412 (p0) REVERT: H 24 ASP cc_start: 0.6480 (p0) cc_final: 0.3951 (t70) outliers start: 32 outliers final: 28 residues processed: 303 average time/residue: 0.2548 time to fit residues: 114.3547 Evaluate side-chains 310 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 206 TRP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 187 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 470 GLN D 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.273992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.260131 restraints weight = 16526.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.256370 restraints weight = 23723.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.251462 restraints weight = 22999.355| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14874 Z= 0.145 Angle : 0.593 10.967 20100 Z= 0.309 Chirality : 0.039 0.170 2369 Planarity : 0.003 0.033 2529 Dihedral : 4.271 25.005 2049 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.00 % Rotamer: Outliers : 2.31 % Allowed : 19.31 % Favored : 78.38 % 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: -1.62 (0.20), residues: 1900 helix: -0.69 (0.15), residues: 1312 sheet: None (None), residues: 0 loop : -1.68 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 351 HIS 0.006 0.001 HIS C 190 PHE 0.022 0.001 PHE E 68 TYR 0.011 0.001 TYR B 362 ARG 0.002 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 703) hydrogen bonds : angle 3.74870 ( 2052) SS BOND : bond 0.00545 ( 4) SS BOND : angle 0.31151 ( 8) covalent geometry : bond 0.00351 (14870) covalent geometry : angle 0.59347 (20092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 283 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.8742 (mt) cc_final: 0.8453 (tt) REVERT: D 174 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7191 (mp) REVERT: D 316 LEU cc_start: 0.8174 (tt) cc_final: 0.7876 (tp) REVERT: E 22 ASP cc_start: 0.5603 (p0) cc_final: 0.5296 (p0) REVERT: E 24 ASP cc_start: 0.6562 (p0) cc_final: 0.5078 (t0) REVERT: E 72 MET cc_start: 0.7129 (mmm) cc_final: 0.6892 (mmt) REVERT: E 83 GLU cc_start: 0.6877 (pm20) cc_final: 0.6208 (tp30) REVERT: E 112 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5134 (mt) REVERT: F 83 GLU cc_start: 0.6701 (pm20) cc_final: 0.6063 (tp30) REVERT: H 22 ASP cc_start: 0.5695 (p0) cc_final: 0.5434 (p0) REVERT: H 24 ASP cc_start: 0.6532 (p0) cc_final: 0.4020 (t70) outliers start: 34 outliers final: 30 residues processed: 299 average time/residue: 0.2550 time to fit residues: 112.9362 Evaluate side-chains 314 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain H residue 50 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 96 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 150 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 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 = 0.4945 r_free = 0.4945 target = 0.274689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.260954 restraints weight = 16596.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.256388 restraints weight = 24011.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.253341 restraints weight = 25452.713| |-----------------------------------------------------------------------------| r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 14874 Z= 0.208 Angle : 0.932 59.199 20100 Z= 0.562 Chirality : 0.039 0.266 2369 Planarity : 0.005 0.133 2529 Dihedral : 4.353 37.980 2049 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.95 % Rotamer: Outliers : 2.04 % Allowed : 19.58 % Favored : 78.38 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.62 (0.20), residues: 1900 helix: -0.69 (0.15), residues: 1312 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 351 HIS 0.005 0.001 HIS C 190 PHE 0.011 0.001 PHE E 68 TYR 0.011 0.001 TYR B 362 ARG 0.002 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 703) hydrogen bonds : angle 3.74652 ( 2052) SS BOND : bond 0.00459 ( 4) SS BOND : angle 0.32166 ( 8) covalent geometry : bond 0.00415 (14870) covalent geometry : angle 0.93185 (20092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4964.31 seconds wall clock time: 89 minutes 26.90 seconds (5366.90 seconds total)