Starting phenix.real_space_refine on Sat May 17 03:47:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qxk_18730/05_2025/8qxk_18730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qxk_18730/05_2025/8qxk_18730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qxk_18730/05_2025/8qxk_18730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qxk_18730/05_2025/8qxk_18730.map" model { file = "/net/cci-nas-00/data/ceres_data/8qxk_18730/05_2025/8qxk_18730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qxk_18730/05_2025/8qxk_18730.cif" } resolution = 2.66 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= 0.003 sd= 0.158 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 36 5.49 5 Mg 12 5.21 5 S 80 5.16 5 C 9694 2.51 5 N 2646 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15323 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3738 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3729 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 3742 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3734 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 458, 3734 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3813 Chain: "D" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3738 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 11.26, per 1000 atoms: 0.73 Number of scatterers: 15323 At special positions: 0 Unit cell: (119.88, 104.76, 93.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 80 16.00 P 36 15.00 Mg 12 11.99 O 2851 8.00 N 2646 7.00 C 9694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.5 seconds 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3442 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 16 sheets defined 60.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 removed outlier: 3.518A pdb=" N ILE A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.766A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.000A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 removed outlier: 3.524A pdb=" N GLN A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 214 through 220 removed outlier: 4.146A pdb=" N ASP A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.598A pdb=" N LEU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 248 Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.574A pdb=" N TYR A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.113A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.856A pdb=" N SER A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.683A pdb=" N TRP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 410 through 414 removed outlier: 4.200A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 432 removed outlier: 4.131A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.911A pdb=" N TYR A 473 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.716A pdb=" N VAL A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 573 removed outlier: 3.541A pdb=" N ARG A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 147 removed outlier: 3.517A pdb=" N ILE C 147 " --> pdb=" O LEU C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.765A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 3.998A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.653A pdb=" N GLN C 190 " --> pdb=" O PRO C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 214 through 220 removed outlier: 4.189A pdb=" N ASP C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.590A pdb=" N LEU C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 248 Processing helix chain 'C' and resid 250 through 257 removed outlier: 3.590A pdb=" N TYR C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 removed outlier: 4.233A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.906A pdb=" N SER C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.681A pdb=" N TRP C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 324 " --> pdb=" O CYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 394 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.615A pdb=" N ALA C 412 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 413 " --> pdb=" O SER C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 423 No H-bonds generated for 'chain 'C' and resid 421 through 423' Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.123A pdb=" N LEU C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 475 through 482 Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 533 through 538 removed outlier: 3.656A pdb=" N VAL C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 574 removed outlier: 3.635A pdb=" N ALA C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 removed outlier: 3.514A pdb=" N ILE B 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.766A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.997A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 removed outlier: 3.618A pdb=" N GLN B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.180A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.601A pdb=" N LEU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 248 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.567A pdb=" N TYR B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 274 removed outlier: 4.148A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.884A pdb=" N SER B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.699A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.628A pdb=" N ALA B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.124A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 469 through 474 removed outlier: 4.107A pdb=" N TYR B 473 " --> pdb=" O ARG B 470 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU B 474 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.684A pdb=" N VAL B 537 " --> pdb=" O THR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 removed outlier: 3.516A pdb=" N ILE D 147 " --> pdb=" O LEU D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 147' Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.761A pdb=" N TYR D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 186 removed outlier: 3.996A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 removed outlier: 3.551A pdb=" N GLN D 190 " --> pdb=" O PRO D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 214 through 220 removed outlier: 4.129A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.602A pdb=" N LEU D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 248 Processing helix chain 'D' and resid 250 through 257 removed outlier: 3.578A pdb=" N TYR D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 removed outlier: 4.309A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.882A pdb=" N SER D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.682A pdb=" N TRP D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 324 " --> pdb=" O CYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 355 through 373 Processing helix chain 'D' and resid 376 through 394 Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 410 through 414 removed outlier: 4.171A pdb=" N ILE D 413 " --> pdb=" O SER D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.135A pdb=" N LEU D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.947A pdb=" N TYR D 473 " --> pdb=" O ARG D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.699A pdb=" N VAL D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 574 removed outlier: 3.650A pdb=" N ALA D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 342 removed outlier: 8.343A pdb=" N TYR A 521 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA A 351 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 459 removed outlier: 6.994A pdb=" N VAL A 552 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 459 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 550 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 120 Processing sheet with id=AA6, first strand: chain 'C' and resid 339 through 342 removed outlier: 8.333A pdb=" N TYR C 521 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 351 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'C' and resid 455 through 459 removed outlier: 6.980A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 339 through 343 removed outlier: 8.342A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'B' and resid 455 through 459 removed outlier: 6.986A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 120 Processing sheet with id=AB5, first strand: chain 'D' and resid 339 through 342 removed outlier: 8.341A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA D 351 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AB7, first strand: chain 'D' and resid 455 through 459 removed outlier: 6.975A pdb=" N VAL D 552 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU D 459 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 550 " --> pdb=" O GLU D 459 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1908 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: 4.21 Time building geometry restraints manager: 4.93 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: 4943 1.34 - 1.46: 3456 1.46 - 1.58: 7104 1.58 - 1.69: 57 1.69 - 1.81: 120 Bond restraints: 15680 Sorted by residual: bond pdb=" C4 DCP C 706 " pdb=" C5 DCP C 706 " ideal model delta sigma weight residual 1.426 1.388 0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" C4 DCP A 706 " pdb=" C5 DCP A 706 " ideal model delta sigma weight residual 1.426 1.388 0.038 1.20e-02 6.94e+03 9.90e+00 bond pdb=" O1A DCP B 707 " pdb=" PA DCP B 707 " ideal model delta sigma weight residual 1.477 1.508 -0.031 1.00e-02 1.00e+04 9.86e+00 bond pdb=" C4 DCP B 707 " pdb=" C5 DCP B 707 " ideal model delta sigma weight residual 1.426 1.389 0.037 1.20e-02 6.94e+03 9.74e+00 bond pdb=" C4 DCP D 707 " pdb=" C5 DCP D 707 " ideal model delta sigma weight residual 1.426 1.389 0.037 1.20e-02 6.94e+03 9.69e+00 ... (remaining 15675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 21180 3.94 - 7.88: 62 7.88 - 11.82: 0 11.82 - 15.76: 4 15.76 - 19.70: 4 Bond angle restraints: 21250 Sorted by residual: angle pdb=" PB DCP D 707 " pdb=" O3B DCP D 707 " pdb=" PG DCP D 707 " ideal model delta sigma weight residual 139.87 120.17 19.70 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PB DCP B 707 " pdb=" O3B DCP B 707 " pdb=" PG DCP B 707 " ideal model delta sigma weight residual 139.87 120.36 19.51 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PB DCP A 706 " pdb=" O3B DCP A 706 " pdb=" PG DCP A 706 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB DCP C 706 " pdb=" O3B DCP C 706 " pdb=" PG DCP C 706 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PA DCP C 706 " pdb=" O3A DCP C 706 " pdb=" PB DCP C 706 " ideal model delta sigma weight residual 136.83 122.46 14.37 1.00e+00 1.00e+00 2.06e+02 ... (remaining 21245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 9116 33.50 - 67.01: 321 67.01 - 100.51: 61 100.51 - 134.01: 4 134.01 - 167.51: 4 Dihedral angle restraints: 9506 sinusoidal: 4146 harmonic: 5360 Sorted by residual: dihedral pdb=" O3A GTP D 702 " pdb=" O3B GTP D 702 " pdb=" PB GTP D 702 " pdb=" PG GTP D 702 " ideal model delta sinusoidal sigma weight residual 303.79 136.28 167.51 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O3A GTP B 702 " pdb=" O3B GTP B 702 " pdb=" PB GTP B 702 " pdb=" PG GTP B 702 " ideal model delta sinusoidal sigma weight residual 303.79 136.57 167.22 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O3A GTP C 701 " pdb=" O3B GTP C 701 " pdb=" PB GTP C 701 " pdb=" PG GTP C 701 " ideal model delta sinusoidal sigma weight residual 303.79 136.99 166.80 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 9503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1768 0.048 - 0.096: 341 0.096 - 0.145: 115 0.145 - 0.193: 9 0.193 - 0.241: 8 Chirality restraints: 2241 Sorted by residual: chirality pdb=" C3' DTP D 701 " pdb=" C2' DTP D 701 " pdb=" C4' DTP D 701 " pdb=" O3' DTP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3' DTP C 707 " pdb=" C2' DTP C 707 " pdb=" C4' DTP C 707 " pdb=" O3' DTP C 707 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DTP B 701 " pdb=" C2' DTP B 701 " pdb=" C4' DTP B 701 " pdb=" O3' DTP B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2238 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCP B 707 " -0.017 2.00e-02 2.50e+03 6.56e-02 9.68e+01 pdb=" C2 DCP B 707 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DCP B 707 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DCP B 707 " -0.116 2.00e-02 2.50e+03 pdb=" C6 DCP B 707 " 0.061 2.00e-02 2.50e+03 pdb=" N1 DCP B 707 " 0.059 2.00e-02 2.50e+03 pdb=" N3 DCP B 707 " 0.098 2.00e-02 2.50e+03 pdb=" N4 DCP B 707 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DCP B 707 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP C 706 " 0.019 2.00e-02 2.50e+03 6.50e-02 9.50e+01 pdb=" C2 DCP C 706 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DCP C 706 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DCP C 706 " 0.115 2.00e-02 2.50e+03 pdb=" C6 DCP C 706 " -0.062 2.00e-02 2.50e+03 pdb=" N1 DCP C 706 " -0.059 2.00e-02 2.50e+03 pdb=" N3 DCP C 706 " -0.096 2.00e-02 2.50e+03 pdb=" N4 DCP C 706 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DCP C 706 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP A 706 " -0.016 2.00e-02 2.50e+03 6.49e-02 9.47e+01 pdb=" C2 DCP A 706 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DCP A 706 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DCP A 706 " -0.115 2.00e-02 2.50e+03 pdb=" C6 DCP A 706 " 0.059 2.00e-02 2.50e+03 pdb=" N1 DCP A 706 " 0.057 2.00e-02 2.50e+03 pdb=" N3 DCP A 706 " 0.098 2.00e-02 2.50e+03 pdb=" N4 DCP A 706 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DCP A 706 " -0.089 2.00e-02 2.50e+03 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 110 2.55 - 3.14: 11263 3.14 - 3.73: 22390 3.73 - 4.31: 33339 4.31 - 4.90: 55855 Nonbonded interactions: 122957 Sorted by model distance: nonbonded pdb=" O1B GTP C 701 " pdb="MG MG C 705 " model vdw 1.965 2.170 nonbonded pdb=" O1B GTP A 701 " pdb="MG MG A 705 " model vdw 1.968 2.170 nonbonded pdb=" O1B GTP D 702 " pdb="MG MG D 706 " model vdw 1.969 2.170 nonbonded pdb=" O1B GTP B 702 " pdb="MG MG B 706 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR B 463 " pdb=" OE1 GLN B 465 " model vdw 1.990 3.040 ... (remaining 122952 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 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 483 or (resid 484 and (name N \ or name CA or name C or name O or name CB )) or resid 485 through 527 or resid 5 \ 29 through 576 or (resid 577 and (name N or name CA or name C or name O or name \ CB )) or resid 578 or resid 704 through 705)) selection = (chain 'B' and (resid 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 527 or resid 529 through 576 o \ r (resid 577 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 78 or resid 704 through 705)) selection = (chain 'C' and (resid 114 through 483 or (resid 484 and (name N or name CA or na \ me C or name O or name CB )) or resid 485 through 527 or resid 529 through 578 o \ r resid 704 through 705)) selection = (chain 'D' and (resid 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 483 or (resid 484 and (name N \ or name CA or name C or name O or name CB )) or resid 485 through 527 or resid 5 \ 29 through 576 or (resid 577 and (name N or name CA or name C or name O or name \ CB )) or resid 578 or resid 704 through 705)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.080 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.060 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:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.011 0.900 15682 Z= 1.035 Angle : 0.736 19.702 21250 Z= 0.506 Chirality : 0.046 0.241 2241 Planarity : 0.005 0.066 2688 Dihedral : 17.510 167.514 6064 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1817 helix: 0.63 (0.19), residues: 896 sheet: 1.15 (0.48), residues: 120 loop : -1.20 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 572 HIS 0.005 0.001 HIS A 233 PHE 0.015 0.001 PHE B 165 TYR 0.021 0.002 TYR B 473 ARG 0.005 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.17575 ( 704) hydrogen bonds : angle 5.98286 ( 1908) covalent geometry : bond 0.00350 (15680) covalent geometry : angle 0.73638 (21250) Misc. bond : bond 0.89843 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.670 Fit side-chains REVERT: A 311 ASP cc_start: 0.8353 (t0) cc_final: 0.8120 (t0) REVERT: A 461 GLN cc_start: 0.7502 (tt0) cc_final: 0.7125 (tt0) REVERT: B 311 ASP cc_start: 0.8356 (t0) cc_final: 0.8068 (t0) REVERT: B 372 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7127 (mtm180) REVERT: D 311 ASP cc_start: 0.8433 (t0) cc_final: 0.8226 (t0) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 1.5751 time to fit residues: 393.7258 Evaluate side-chains 180 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 293 ASN A 527 ASN A 548 GLN C 293 ASN C 527 ASN B 293 ASN B 527 ASN D 215 HIS D 293 ASN D 527 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.162789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.135747 restraints weight = 17715.426| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.26 r_work: 0.3180 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15682 Z= 0.166 Angle : 0.647 8.405 21250 Z= 0.343 Chirality : 0.047 0.203 2241 Planarity : 0.005 0.043 2688 Dihedral : 15.685 171.716 2306 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.18 % Allowed : 8.05 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 1817 helix: 0.89 (0.18), residues: 900 sheet: 1.51 (0.47), residues: 120 loop : -1.17 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 PHE 0.016 0.002 PHE B 165 TYR 0.033 0.002 TYR B 315 ARG 0.004 0.000 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.06715 ( 704) hydrogen bonds : angle 4.63202 ( 1908) covalent geometry : bond 0.00368 (15680) covalent geometry : angle 0.64666 (21250) Misc. bond : bond 0.00122 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.690 Fit side-chains REVERT: A 251 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8204 (mmtp) REVERT: A 461 GLN cc_start: 0.7447 (tt0) cc_final: 0.7058 (tt0) REVERT: A 475 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.6717 (t) REVERT: A 494 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7678 (tmmm) REVERT: C 134 ARG cc_start: 0.8499 (tpt-90) cc_final: 0.8254 (tpt90) REVERT: C 494 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7648 (tmmm) REVERT: B 494 LYS cc_start: 0.8160 (mppt) cc_final: 0.7543 (mmtm) REVERT: D 494 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7015 (tttt) outliers start: 19 outliers final: 6 residues processed: 194 average time/residue: 1.5667 time to fit residues: 329.5924 Evaluate side-chains 177 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 42 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 133 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN B 345 ASN B 527 ASN D 215 HIS D 527 ASN D 535 ASN D 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.162774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.133933 restraints weight = 15923.278| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.20 r_work: 0.3242 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15682 Z= 0.152 Angle : 0.604 8.349 21250 Z= 0.318 Chirality : 0.046 0.165 2241 Planarity : 0.004 0.038 2688 Dihedral : 15.026 176.159 2306 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.36 % Allowed : 9.79 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1817 helix: 1.11 (0.18), residues: 880 sheet: 1.55 (0.47), residues: 120 loop : -1.01 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 PHE 0.015 0.002 PHE B 165 TYR 0.031 0.002 TYR B 315 ARG 0.002 0.000 ARG B 470 Details of bonding type rmsd hydrogen bonds : bond 0.06335 ( 704) hydrogen bonds : angle 4.50118 ( 1908) covalent geometry : bond 0.00333 (15680) covalent geometry : angle 0.60415 (21250) Misc. bond : bond 0.00140 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.844 Fit side-chains REVERT: A 372 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.6885 (mtp180) REVERT: A 461 GLN cc_start: 0.7459 (tt0) cc_final: 0.7077 (tt0) REVERT: A 475 SER cc_start: 0.7522 (p) cc_final: 0.6721 (t) REVERT: A 478 LYS cc_start: 0.7544 (mtmm) cc_final: 0.7233 (mttt) REVERT: A 494 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7616 (tmmm) REVERT: C 134 ARG cc_start: 0.8408 (tpt-90) cc_final: 0.8127 (tpt90) REVERT: C 494 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7596 (tmmm) REVERT: B 429 GLU cc_start: 0.8420 (tt0) cc_final: 0.8181 (tm-30) REVERT: B 478 LYS cc_start: 0.7525 (mtmm) cc_final: 0.7245 (mttt) REVERT: B 494 LYS cc_start: 0.8217 (mppt) cc_final: 0.7573 (mmtm) REVERT: B 501 ASP cc_start: 0.7905 (t70) cc_final: 0.7674 (t70) REVERT: D 429 GLU cc_start: 0.8418 (tt0) cc_final: 0.8091 (tm-30) REVERT: D 494 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7001 (tttt) outliers start: 22 outliers final: 11 residues processed: 197 average time/residue: 1.5041 time to fit residues: 322.4702 Evaluate side-chains 184 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 126 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN D 215 HIS D 527 ASN D 535 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.161398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.133969 restraints weight = 21695.156| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.44 r_work: 0.3141 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15682 Z= 0.159 Angle : 0.616 8.890 21250 Z= 0.324 Chirality : 0.046 0.163 2241 Planarity : 0.004 0.038 2688 Dihedral : 14.926 179.716 2306 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 10.04 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1817 helix: 1.09 (0.18), residues: 880 sheet: 1.54 (0.48), residues: 120 loop : -1.00 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 PHE 0.015 0.002 PHE B 165 TYR 0.028 0.002 TYR B 315 ARG 0.002 0.000 ARG B 470 Details of bonding type rmsd hydrogen bonds : bond 0.06500 ( 704) hydrogen bonds : angle 4.48264 ( 1908) covalent geometry : bond 0.00352 (15680) covalent geometry : angle 0.61626 (21250) Misc. bond : bond 0.00127 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 1.702 Fit side-chains REVERT: A 218 ASP cc_start: 0.8221 (p0) cc_final: 0.7871 (p0) REVERT: A 372 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6796 (mtp180) REVERT: A 461 GLN cc_start: 0.7455 (tt0) cc_final: 0.7062 (tt0) REVERT: A 475 SER cc_start: 0.7512 (p) cc_final: 0.6726 (t) REVERT: A 478 LYS cc_start: 0.7522 (mtmm) cc_final: 0.7216 (mttt) REVERT: A 494 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7653 (tmmm) REVERT: A 575 ASP cc_start: 0.7603 (t0) cc_final: 0.7318 (m-30) REVERT: C 218 ASP cc_start: 0.8182 (p0) cc_final: 0.7860 (p0) REVERT: C 494 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7672 (tmmm) REVERT: B 218 ASP cc_start: 0.8163 (p0) cc_final: 0.7839 (p0) REVERT: B 429 GLU cc_start: 0.8371 (tt0) cc_final: 0.8137 (tm-30) REVERT: B 478 LYS cc_start: 0.7482 (mtmm) cc_final: 0.7211 (mttt) REVERT: B 494 LYS cc_start: 0.8239 (mppt) cc_final: 0.7610 (mmmm) REVERT: D 429 GLU cc_start: 0.8350 (tt0) cc_final: 0.8023 (tm-30) REVERT: D 494 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7103 (ttpt) outliers start: 42 outliers final: 16 residues processed: 214 average time/residue: 1.4604 time to fit residues: 341.5481 Evaluate side-chains 192 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN A 536 GLN C 527 ASN C 535 ASN C 536 GLN C 539 GLN B 345 ASN B 527 ASN B 536 GLN D 215 HIS D 527 ASN D 535 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.163027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.135731 restraints weight = 17922.047| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.36 r_work: 0.3204 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15682 Z= 0.140 Angle : 0.577 8.338 21250 Z= 0.303 Chirality : 0.045 0.152 2241 Planarity : 0.004 0.037 2688 Dihedral : 14.335 173.178 2306 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer: Outliers : 2.04 % Allowed : 10.97 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1817 helix: 1.21 (0.18), residues: 880 sheet: 1.54 (0.48), residues: 120 loop : -0.93 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 572 HIS 0.007 0.001 HIS A 233 PHE 0.015 0.001 PHE B 165 TYR 0.027 0.002 TYR B 315 ARG 0.002 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.05814 ( 704) hydrogen bonds : angle 4.38413 ( 1908) covalent geometry : bond 0.00300 (15680) covalent geometry : angle 0.57744 (21250) Misc. bond : bond 0.00097 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.664 Fit side-chains REVERT: A 185 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6764 (ttpt) REVERT: A 242 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: A 372 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6768 (mtp180) REVERT: A 475 SER cc_start: 0.7531 (OUTLIER) cc_final: 0.6757 (t) REVERT: A 478 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7282 (mttt) REVERT: A 494 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7664 (tmmm) REVERT: A 575 ASP cc_start: 0.7661 (t0) cc_final: 0.7347 (m-30) REVERT: C 218 ASP cc_start: 0.8246 (p0) cc_final: 0.7800 (p0) REVERT: C 429 GLU cc_start: 0.8559 (tt0) cc_final: 0.8335 (tm-30) REVERT: C 494 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7686 (tmmm) REVERT: B 429 GLU cc_start: 0.8486 (tt0) cc_final: 0.8264 (tm-30) REVERT: B 478 LYS cc_start: 0.7477 (mtmm) cc_final: 0.7228 (mttt) REVERT: B 494 LYS cc_start: 0.8226 (mppt) cc_final: 0.7623 (mmmm) REVERT: D 429 GLU cc_start: 0.8500 (tt0) cc_final: 0.8207 (tm-30) REVERT: D 478 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7145 (mttt) REVERT: D 494 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7102 (ttpt) REVERT: D 575 ASP cc_start: 0.7583 (t0) cc_final: 0.7378 (m-30) outliers start: 33 outliers final: 19 residues processed: 218 average time/residue: 1.4118 time to fit residues: 336.8822 Evaluate side-chains 197 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 117 optimal weight: 0.2980 chunk 151 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN D 527 ASN D 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.160544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.133506 restraints weight = 14744.973| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.22 r_work: 0.3196 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15682 Z= 0.184 Angle : 0.650 9.559 21250 Z= 0.339 Chirality : 0.047 0.166 2241 Planarity : 0.005 0.039 2688 Dihedral : 14.792 166.335 2306 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 2.42 % Allowed : 11.34 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1817 helix: 1.01 (0.18), residues: 880 sheet: 1.56 (0.48), residues: 120 loop : -0.99 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 PHE 0.014 0.002 PHE C 363 TYR 0.028 0.002 TYR B 315 ARG 0.003 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.07095 ( 704) hydrogen bonds : angle 4.51849 ( 1908) covalent geometry : bond 0.00420 (15680) covalent geometry : angle 0.64970 (21250) Misc. bond : bond 0.00172 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.818 Fit side-chains REVERT: A 242 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: A 372 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.6807 (mtp180) REVERT: A 478 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7251 (mttt) REVERT: A 494 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7734 (tmmm) REVERT: A 575 ASP cc_start: 0.7643 (t0) cc_final: 0.7357 (m-30) REVERT: C 218 ASP cc_start: 0.8249 (p0) cc_final: 0.7766 (p0) REVERT: C 429 GLU cc_start: 0.8533 (tt0) cc_final: 0.8299 (tm-30) REVERT: C 494 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7708 (tmmm) REVERT: B 429 GLU cc_start: 0.8454 (tt0) cc_final: 0.8228 (tm-30) REVERT: B 478 LYS cc_start: 0.7499 (mtmm) cc_final: 0.7229 (mttt) REVERT: B 494 LYS cc_start: 0.8258 (mppt) cc_final: 0.7683 (mmmm) REVERT: B 502 VAL cc_start: 0.8440 (m) cc_final: 0.8031 (t) REVERT: D 429 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: D 478 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7190 (mttt) REVERT: D 494 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7143 (ttpt) REVERT: D 575 ASP cc_start: 0.7602 (t0) cc_final: 0.7373 (m-30) outliers start: 39 outliers final: 24 residues processed: 210 average time/residue: 1.4152 time to fit residues: 325.1432 Evaluate side-chains 205 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 139 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.164295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.138289 restraints weight = 16438.451| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.21 r_work: 0.3255 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15682 Z= 0.127 Angle : 0.556 7.980 21250 Z= 0.291 Chirality : 0.044 0.141 2241 Planarity : 0.004 0.037 2688 Dihedral : 13.690 158.741 2306 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.98 % Allowed : 12.39 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1817 helix: 1.29 (0.18), residues: 880 sheet: 1.62 (0.48), residues: 120 loop : -0.83 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 572 HIS 0.006 0.001 HIS A 233 PHE 0.014 0.001 PHE B 165 TYR 0.024 0.002 TYR B 315 ARG 0.002 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 704) hydrogen bonds : angle 4.31704 ( 1908) covalent geometry : bond 0.00269 (15680) covalent geometry : angle 0.55594 (21250) Misc. bond : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.806 Fit side-chains REVERT: A 185 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6802 (ttpt) REVERT: A 242 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: A 311 ASP cc_start: 0.8806 (t0) cc_final: 0.8475 (t0) REVERT: A 372 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6709 (mtp180) REVERT: A 470 ARG cc_start: 0.7100 (mmm160) cc_final: 0.6638 (tpp-160) REVERT: A 475 SER cc_start: 0.7543 (OUTLIER) cc_final: 0.6772 (t) REVERT: A 478 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7348 (mttt) REVERT: A 494 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7744 (tmmm) REVERT: C 185 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6608 (ttpt) REVERT: C 429 GLU cc_start: 0.8548 (tt0) cc_final: 0.8330 (tm-30) REVERT: C 494 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7723 (tmmm) REVERT: B 311 ASP cc_start: 0.8784 (t0) cc_final: 0.8477 (t0) REVERT: B 429 GLU cc_start: 0.8453 (tt0) cc_final: 0.8228 (tm-30) REVERT: B 478 LYS cc_start: 0.7489 (mtmm) cc_final: 0.7217 (mttt) REVERT: B 494 LYS cc_start: 0.8231 (mppt) cc_final: 0.7659 (mmmm) REVERT: B 502 VAL cc_start: 0.8328 (m) cc_final: 0.7970 (t) REVERT: D 429 GLU cc_start: 0.8531 (tt0) cc_final: 0.8246 (tm-30) REVERT: D 478 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7138 (mttt) REVERT: D 494 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7121 (ttpt) REVERT: D 539 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8392 (mm-40) outliers start: 32 outliers final: 15 residues processed: 216 average time/residue: 1.4347 time to fit residues: 338.0754 Evaluate side-chains 200 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 22 optimal weight: 0.0070 chunk 82 optimal weight: 0.0270 chunk 165 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.160675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.131701 restraints weight = 18549.384| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.48 r_work: 0.3170 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15682 Z= 0.180 Angle : 0.644 9.415 21250 Z= 0.336 Chirality : 0.047 0.172 2241 Planarity : 0.005 0.040 2688 Dihedral : 14.203 160.786 2306 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 2.42 % Allowed : 12.52 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1817 helix: 1.06 (0.18), residues: 880 sheet: 1.60 (0.48), residues: 120 loop : -0.92 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 572 HIS 0.007 0.002 HIS C 233 PHE 0.014 0.002 PHE C 363 TYR 0.027 0.002 TYR B 315 ARG 0.003 0.000 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.06959 ( 704) hydrogen bonds : angle 4.48315 ( 1908) covalent geometry : bond 0.00411 (15680) covalent geometry : angle 0.64398 (21250) Misc. bond : bond 0.00174 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.773 Fit side-chains REVERT: A 242 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: A 372 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6852 (mtp180) REVERT: A 429 GLU cc_start: 0.8493 (tt0) cc_final: 0.8212 (tm-30) REVERT: A 470 ARG cc_start: 0.7122 (mmm160) cc_final: 0.6611 (tpp-160) REVERT: A 478 LYS cc_start: 0.7638 (mtmm) cc_final: 0.7351 (mttt) REVERT: C 429 GLU cc_start: 0.8589 (tt0) cc_final: 0.8355 (tm-30) REVERT: C 494 LYS cc_start: 0.8032 (ttpt) cc_final: 0.7714 (tmmm) REVERT: B 429 GLU cc_start: 0.8495 (tt0) cc_final: 0.8273 (tm-30) REVERT: B 478 LYS cc_start: 0.7483 (mtmm) cc_final: 0.7209 (mttt) REVERT: B 494 LYS cc_start: 0.8223 (mppt) cc_final: 0.7659 (mmmm) REVERT: B 502 VAL cc_start: 0.8471 (m) cc_final: 0.8060 (t) REVERT: D 429 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: D 478 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7180 (mttt) REVERT: D 494 LYS cc_start: 0.7911 (mtpp) cc_final: 0.7152 (ttpt) outliers start: 39 outliers final: 24 residues processed: 207 average time/residue: 1.4063 time to fit residues: 318.7527 Evaluate side-chains 202 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 328 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.161792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.132861 restraints weight = 16387.387| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.23 r_work: 0.3165 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15682 Z= 0.154 Angle : 0.603 8.903 21250 Z= 0.316 Chirality : 0.046 0.155 2241 Planarity : 0.004 0.039 2688 Dihedral : 13.961 160.439 2306 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 2.04 % Allowed : 13.32 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1817 helix: 1.14 (0.18), residues: 880 sheet: 1.58 (0.48), residues: 120 loop : -0.88 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 572 HIS 0.007 0.002 HIS A 233 PHE 0.013 0.002 PHE B 165 TYR 0.028 0.002 TYR C 331 ARG 0.002 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.06235 ( 704) hydrogen bonds : angle 4.42533 ( 1908) covalent geometry : bond 0.00340 (15680) covalent geometry : angle 0.60285 (21250) Misc. bond : bond 0.00124 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.800 Fit side-chains REVERT: A 242 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: A 372 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6864 (mtp180) REVERT: A 429 GLU cc_start: 0.8539 (tt0) cc_final: 0.8266 (tm-30) REVERT: A 470 ARG cc_start: 0.7111 (mmm160) cc_final: 0.6601 (tpp-160) REVERT: A 478 LYS cc_start: 0.7592 (mtmm) cc_final: 0.7297 (mttt) REVERT: A 494 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7598 (tmmm) REVERT: C 429 GLU cc_start: 0.8645 (tt0) cc_final: 0.8422 (tm-30) REVERT: C 494 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7684 (tmmm) REVERT: B 429 GLU cc_start: 0.8558 (tt0) cc_final: 0.8343 (tm-30) REVERT: B 478 LYS cc_start: 0.7443 (mtmm) cc_final: 0.7181 (mttt) REVERT: B 494 LYS cc_start: 0.8184 (mppt) cc_final: 0.7603 (mmmm) REVERT: B 502 VAL cc_start: 0.8418 (m) cc_final: 0.7992 (t) REVERT: D 429 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: D 478 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7131 (mttt) REVERT: D 494 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7135 (ttpt) REVERT: D 539 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8442 (mm-40) outliers start: 33 outliers final: 26 residues processed: 206 average time/residue: 1.3856 time to fit residues: 312.5851 Evaluate side-chains 207 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.158021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129421 restraints weight = 15001.895| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.16 r_work: 0.3125 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15682 Z= 0.242 Angle : 0.732 10.338 21250 Z= 0.383 Chirality : 0.050 0.186 2241 Planarity : 0.005 0.046 2688 Dihedral : 15.210 160.540 2306 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 2.35 % Allowed : 13.14 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1817 helix: 0.65 (0.18), residues: 904 sheet: 1.52 (0.47), residues: 120 loop : -1.09 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.009 0.002 HIS B 162 PHE 0.019 0.003 PHE C 363 TYR 0.029 0.003 TYR C 315 ARG 0.004 0.001 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.08337 ( 704) hydrogen bonds : angle 4.65199 ( 1908) covalent geometry : bond 0.00571 (15680) covalent geometry : angle 0.73183 (21250) Misc. bond : bond 0.00264 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 1.702 Fit side-chains REVERT: A 242 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: A 372 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6938 (mtp180) REVERT: A 429 GLU cc_start: 0.8548 (tt0) cc_final: 0.8272 (tm-30) REVERT: A 478 LYS cc_start: 0.7643 (mtmm) cc_final: 0.7339 (mttt) REVERT: A 494 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7661 (tmmm) REVERT: C 429 GLU cc_start: 0.8644 (tt0) cc_final: 0.8418 (tm-30) REVERT: B 429 GLU cc_start: 0.8531 (tt0) cc_final: 0.8324 (tm-30) REVERT: B 478 LYS cc_start: 0.7518 (mtmm) cc_final: 0.7238 (mttt) REVERT: B 494 LYS cc_start: 0.8227 (mppt) cc_final: 0.7626 (mmmm) REVERT: B 502 VAL cc_start: 0.8555 (m) cc_final: 0.8137 (t) REVERT: D 429 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: D 478 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7224 (mttt) REVERT: D 494 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7202 (ttpt) outliers start: 38 outliers final: 25 residues processed: 203 average time/residue: 1.4430 time to fit residues: 319.5471 Evaluate side-chains 198 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 32 optimal weight: 0.9990 chunk 145 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 328 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.163489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136655 restraints weight = 18040.394| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.27 r_work: 0.3212 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15682 Z= 0.127 Angle : 0.561 7.885 21250 Z= 0.294 Chirality : 0.044 0.139 2241 Planarity : 0.004 0.039 2688 Dihedral : 13.998 156.153 2306 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.80 % Allowed : 13.94 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1817 helix: 1.21 (0.18), residues: 880 sheet: 1.56 (0.47), residues: 120 loop : -0.86 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 285 HIS 0.006 0.001 HIS C 233 PHE 0.014 0.001 PHE B 165 TYR 0.029 0.002 TYR C 331 ARG 0.002 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 704) hydrogen bonds : angle 4.34255 ( 1908) covalent geometry : bond 0.00266 (15680) covalent geometry : angle 0.56105 (21250) Misc. bond : bond 0.00066 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11472.11 seconds wall clock time: 197 minutes 49.35 seconds (11869.35 seconds total)