Starting phenix.real_space_refine on Tue May 20 08:44:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3u_44156/05_2025/9b3u_44156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3u_44156/05_2025/9b3u_44156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3u_44156/05_2025/9b3u_44156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3u_44156/05_2025/9b3u_44156.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3u_44156/05_2025/9b3u_44156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3u_44156/05_2025/9b3u_44156.cif" } resolution = 2.4 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= 0.004 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 C 12992 2.51 5 N 3305 2.21 5 O 3425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19842 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4863 Classifications: {'peptide': 606} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 587} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4921 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 588} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4921 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 588} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4921 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 588} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'PEX': 1, 'RTO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.90, per 1000 atoms: 0.65 Number of scatterers: 19842 At special positions: 0 Unit cell: (138.61, 138.61, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 4 15.00 O 3425 8.00 N 3305 7.00 C 12992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 2.5 seconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4562 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 4 sheets defined 66.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.696A pdb=" N SER A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.556A pdb=" N GLN A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.556A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.847A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 324 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Proline residue: A 325 - end of helix No H-bonds generated for 'chain 'A' and resid 320 through 327' Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 388 Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.907A pdb=" N PHE A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 492 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.504A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 529 removed outlier: 3.547A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 559 removed outlier: 3.882A pdb=" N LEU A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.991A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 717 removed outlier: 3.737A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.696A pdb=" N SER B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.556A pdb=" N GLN B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.556A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 320 through 327 removed outlier: 3.847A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN B 324 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Proline residue: B 325 - end of helix No H-bonds generated for 'chain 'B' and resid 320 through 327' Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 377 through 388 Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.907A pdb=" N PHE B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 492 Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.504A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 529 removed outlier: 3.547A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.882A pdb=" N LEU B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.991A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 606 No H-bonds generated for 'chain 'B' and resid 604 through 606' Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 717 removed outlier: 3.737A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.696A pdb=" N SER C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 196 through 200 removed outlier: 3.556A pdb=" N GLN C 200 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.556A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.847A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 324 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Proline residue: C 325 - end of helix No H-bonds generated for 'chain 'C' and resid 320 through 327' Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 388 Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.907A pdb=" N PHE C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.504A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 529 removed outlier: 3.547A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 559 removed outlier: 3.882A pdb=" N LEU C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 603 removed outlier: 3.991A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 606 No H-bonds generated for 'chain 'C' and resid 604 through 606' Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 717 removed outlier: 3.737A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.696A pdb=" N SER D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 196 through 200 removed outlier: 3.556A pdb=" N GLN D 200 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.556A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 320 through 327 removed outlier: 3.847A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 324 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Proline residue: D 325 - end of helix No H-bonds generated for 'chain 'D' and resid 320 through 327' Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 462 through 467 removed outlier: 3.907A pdb=" N PHE D 467 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 492 Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.504A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.547A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.882A pdb=" N LEU D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 603 removed outlier: 3.991A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 606 No H-bonds generated for 'chain 'D' and resid 604 through 606' Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 717 removed outlier: 3.737A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.957A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.957A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.957A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.957A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3168 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: 6.90 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3738 1.33 - 1.45: 5016 1.45 - 1.58: 11371 1.58 - 1.70: 12 1.70 - 1.83: 176 Bond restraints: 20313 Sorted by residual: bond pdb=" N ARG C 86 " pdb=" CA ARG C 86 " ideal model delta sigma weight residual 1.454 1.501 -0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" N ARG B 86 " pdb=" CA ARG B 86 " ideal model delta sigma weight residual 1.454 1.501 -0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" N ARG A 86 " pdb=" CA ARG A 86 " ideal model delta sigma weight residual 1.454 1.501 -0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" N ARG D 86 " pdb=" CA ARG D 86 " ideal model delta sigma weight residual 1.454 1.501 -0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" N ARG D 619 " pdb=" CA ARG D 619 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.21e-02 6.83e+03 1.28e+01 ... (remaining 20308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 20679 1.96 - 3.92: 6262 3.92 - 5.88: 499 5.88 - 7.84: 40 7.84 - 9.81: 20 Bond angle restraints: 27500 Sorted by residual: angle pdb=" N ARG B 617 " pdb=" CA ARG B 617 " pdb=" C ARG B 617 " ideal model delta sigma weight residual 110.32 100.51 9.81 1.59e+00 3.96e-01 3.80e+01 angle pdb=" N ARG C 617 " pdb=" CA ARG C 617 " pdb=" C ARG C 617 " ideal model delta sigma weight residual 110.32 100.51 9.81 1.59e+00 3.96e-01 3.80e+01 angle pdb=" N ARG A 617 " pdb=" CA ARG A 617 " pdb=" C ARG A 617 " ideal model delta sigma weight residual 110.32 100.51 9.81 1.59e+00 3.96e-01 3.80e+01 angle pdb=" N ARG D 617 " pdb=" CA ARG D 617 " pdb=" C ARG D 617 " ideal model delta sigma weight residual 110.32 100.51 9.81 1.59e+00 3.96e-01 3.80e+01 angle pdb=" C ARG C 193 " pdb=" CA ARG C 193 " pdb=" CB ARG C 193 " ideal model delta sigma weight residual 111.22 102.54 8.68 1.72e+00 3.38e-01 2.55e+01 ... (remaining 27495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 11508 23.36 - 46.71: 398 46.71 - 70.06: 92 70.06 - 93.41: 8 93.41 - 116.76: 8 Dihedral angle restraints: 12014 sinusoidal: 4941 harmonic: 7073 Sorted by residual: dihedral pdb=" CA PHE C 209 " pdb=" C PHE C 209 " pdb=" N GLY C 210 " pdb=" CA GLY C 210 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA PHE B 209 " pdb=" C PHE B 209 " pdb=" N GLY B 210 " pdb=" CA GLY B 210 " ideal model delta harmonic sigma weight residual 180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA PHE D 209 " pdb=" C PHE D 209 " pdb=" N GLY D 210 " pdb=" CA GLY D 210 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 12011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1729 0.068 - 0.135: 1023 0.135 - 0.203: 252 0.203 - 0.270: 60 0.270 - 0.338: 24 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA ARG B 617 " pdb=" N ARG B 617 " pdb=" C ARG B 617 " pdb=" CB ARG B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA ARG A 617 " pdb=" N ARG A 617 " pdb=" C ARG A 617 " pdb=" CB ARG A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA ARG D 617 " pdb=" N ARG D 617 " pdb=" C ARG D 617 " pdb=" CB ARG D 617 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 3085 not shown) Planarity restraints: 3376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 509 " 0.128 2.00e-02 2.50e+03 6.70e-02 1.12e+02 pdb=" CG TRP C 509 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP C 509 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP C 509 " -0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP C 509 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP C 509 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 509 " -0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 509 " 0.072 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 509 " -0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP C 509 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 509 " 0.128 2.00e-02 2.50e+03 6.70e-02 1.12e+02 pdb=" CG TRP D 509 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP D 509 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP D 509 " -0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP D 509 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP D 509 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 509 " -0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 509 " 0.072 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 509 " -0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP D 509 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 509 " -0.128 2.00e-02 2.50e+03 6.70e-02 1.12e+02 pdb=" CG TRP B 509 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP B 509 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B 509 " 0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP B 509 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP B 509 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 509 " 0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 509 " -0.072 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 509 " 0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP B 509 " -0.080 2.00e-02 2.50e+03 ... (remaining 3373 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 7853 2.94 - 3.43: 20132 3.43 - 3.92: 35487 3.92 - 4.41: 38674 4.41 - 4.90: 64793 Nonbonded interactions: 166939 Sorted by model distance: nonbonded pdb=" C ASP A 258 " pdb=" OD1 ASP A 258 " model vdw 2.455 3.270 nonbonded pdb=" C ASP B 258 " pdb=" OD1 ASP B 258 " model vdw 2.455 3.270 nonbonded pdb=" C ASP D 258 " pdb=" OD1 ASP D 258 " model vdw 2.455 3.270 nonbonded pdb=" C ASP C 258 " pdb=" OD1 ASP C 258 " model vdw 2.455 3.270 nonbonded pdb=" OE1 GLU C 708 " pdb=" OG1 THR D 205 " model vdw 2.482 3.040 ... (remaining 166934 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 74 through 719 or resid 801)) selection = (chain 'B' and ((resid 74 and (name N or name CA or name C or name O )) or resid \ 75 through 87 or (resid 88 and (name N or name CA or name C or name O )) or res \ id 89 or (resid 90 through 91 and (name N or name CA or name C or name O )) or r \ esid 92 through 96 or (resid 97 and (name N or name CA or name C or name O )) or \ resid 98 through 128 or (resid 129 and (name N or name CA or name C or name O ) \ ) or resid 130 through 143 or (resid 144 and (name N or name CA or name C or nam \ e O )) or resid 145 through 261 or (resid 262 and (name N or name CA or name C o \ r name O )) or resid 263 through 490 or (resid 491 and (name N or name CA or nam \ e C or name O )) or resid 492 through 680 or (resid 681 and (name N or name CA o \ r name C or name O )) or resid 682 through 693 or (resid 694 and (name N or name \ CA or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2)) or resid 699 through 719 or resid 801)) selection = (chain 'C' and ((resid 74 and (name N or name CA or name C or name O )) or resid \ 75 through 87 or (resid 88 and (name N or name CA or name C or name O )) or res \ id 89 or (resid 90 through 91 and (name N or name CA or name C or name O )) or r \ esid 92 through 96 or (resid 97 and (name N or name CA or name C or name O )) or \ resid 98 through 128 or (resid 129 and (name N or name CA or name C or name O ) \ ) or resid 130 through 143 or (resid 144 and (name N or name CA or name C or nam \ e O )) or resid 145 through 261 or (resid 262 and (name N or name CA or name C o \ r name O )) or resid 263 through 490 or (resid 491 and (name N or name CA or nam \ e C or name O )) or resid 492 through 680 or (resid 681 and (name N or name CA o \ r name C or name O )) or resid 682 through 693 or (resid 694 and (name N or name \ CA or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2)) or resid 699 through 719 or resid 801)) selection = (chain 'D' and ((resid 74 and (name N or name CA or name C or name O )) or resid \ 75 through 87 or (resid 88 and (name N or name CA or name C or name O )) or res \ id 89 or (resid 90 through 91 and (name N or name CA or name C or name O )) or r \ esid 92 through 96 or (resid 97 and (name N or name CA or name C or name O )) or \ resid 98 through 128 or (resid 129 and (name N or name CA or name C or name O ) \ ) or resid 130 through 143 or (resid 144 and (name N or name CA or name C or nam \ e O )) or resid 145 through 261 or (resid 262 and (name N or name CA or name C o \ r name O )) or resid 263 through 490 or (resid 491 and (name N or name CA or nam \ e C or name O )) or resid 492 through 680 or (resid 681 and (name N or name CA o \ r name C or name O )) or resid 682 through 693 or (resid 694 and (name N or name \ CA or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2)) or resid 699 through 719 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 45.420 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 : 0.012 0.057 20313 Z= 0.752 Angle : 1.726 9.805 27500 Z= 1.164 Chirality : 0.088 0.338 3088 Planarity : 0.014 0.121 3376 Dihedral : 13.685 116.760 7452 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.19 % Allowed : 2.03 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2394 helix: -0.54 (0.12), residues: 1432 sheet: 0.09 (0.45), residues: 120 loop : 0.49 (0.24), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.136 0.028 TRP A 386 HIS 0.011 0.002 HIS B 269 PHE 0.047 0.012 PHE C 198 TYR 0.098 0.016 TYR C 403 ARG 0.008 0.001 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.14773 ( 1104) hydrogen bonds : angle 6.14075 ( 3168) covalent geometry : bond 0.01217 (20313) covalent geometry : angle 1.72567 (27500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 383 time to evaluate : 2.216 Fit side-chains REVERT: A 123 LYS cc_start: 0.7170 (tttt) cc_final: 0.6703 (tptt) REVERT: A 221 LYS cc_start: 0.7855 (pttt) cc_final: 0.7481 (mmtt) REVERT: A 294 GLN cc_start: 0.8018 (mt0) cc_final: 0.7655 (mt0) REVERT: A 331 THR cc_start: 0.8847 (t) cc_final: 0.8600 (m) REVERT: A 358 GLU cc_start: 0.8245 (tt0) cc_final: 0.7768 (mt-10) REVERT: A 380 LYS cc_start: 0.8057 (tttt) cc_final: 0.7822 (ttpt) REVERT: A 392 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.7774 (ttt180) REVERT: A 540 PHE cc_start: 0.7877 (t80) cc_final: 0.7654 (t80) REVERT: A 549 PHE cc_start: 0.8469 (m-80) cc_final: 0.7337 (t80) REVERT: A 690 LYS cc_start: 0.7917 (tttt) cc_final: 0.7283 (ttpt) REVERT: B 123 LYS cc_start: 0.7172 (tttt) cc_final: 0.6705 (tptt) REVERT: B 221 LYS cc_start: 0.7855 (pttt) cc_final: 0.7481 (mmtt) REVERT: B 294 GLN cc_start: 0.8017 (mt0) cc_final: 0.7651 (mt0) REVERT: B 331 THR cc_start: 0.8847 (t) cc_final: 0.8599 (m) REVERT: B 380 LYS cc_start: 0.8056 (tttt) cc_final: 0.7822 (ttpt) REVERT: B 392 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7774 (ttt180) REVERT: B 540 PHE cc_start: 0.7877 (t80) cc_final: 0.7654 (t80) REVERT: B 549 PHE cc_start: 0.8469 (m-80) cc_final: 0.7336 (t80) REVERT: B 690 LYS cc_start: 0.7919 (tttt) cc_final: 0.7286 (ttpt) REVERT: C 123 LYS cc_start: 0.7172 (tttt) cc_final: 0.6704 (tptt) REVERT: C 221 LYS cc_start: 0.7856 (pttt) cc_final: 0.7481 (mmtt) REVERT: C 294 GLN cc_start: 0.8019 (mt0) cc_final: 0.7651 (mt0) REVERT: C 331 THR cc_start: 0.8848 (t) cc_final: 0.8600 (m) REVERT: C 380 LYS cc_start: 0.8057 (tttt) cc_final: 0.7822 (ttpt) REVERT: C 392 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7776 (ttt180) REVERT: C 540 PHE cc_start: 0.7877 (t80) cc_final: 0.7652 (t80) REVERT: C 549 PHE cc_start: 0.8468 (m-80) cc_final: 0.7337 (t80) REVERT: C 690 LYS cc_start: 0.7920 (tttt) cc_final: 0.7286 (ttpt) REVERT: D 123 LYS cc_start: 0.7169 (tttt) cc_final: 0.6701 (tptt) REVERT: D 221 LYS cc_start: 0.7855 (pttt) cc_final: 0.7481 (mmtt) REVERT: D 294 GLN cc_start: 0.8020 (mt0) cc_final: 0.7653 (mt0) REVERT: D 331 THR cc_start: 0.8848 (t) cc_final: 0.8601 (m) REVERT: D 380 LYS cc_start: 0.8056 (tttt) cc_final: 0.7822 (ttpt) REVERT: D 392 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7773 (ttt180) REVERT: D 540 PHE cc_start: 0.7878 (t80) cc_final: 0.7653 (t80) REVERT: D 549 PHE cc_start: 0.8469 (m-80) cc_final: 0.7335 (t80) REVERT: D 690 LYS cc_start: 0.7917 (tttt) cc_final: 0.7283 (ttpt) outliers start: 4 outliers final: 0 residues processed: 387 average time/residue: 1.3769 time to fit residues: 595.8548 Evaluate side-chains 309 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 186 ASN A 191 HIS A 203 GLN A 222 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS B 156 GLN B 186 ASN B 191 HIS B 203 GLN B 222 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS C 156 GLN C 186 ASN C 191 HIS C 203 GLN C 222 GLN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS D 156 GLN D 186 ASN D 191 HIS D 203 GLN D 222 GLN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127066 restraints weight = 19468.840| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.54 r_work: 0.3232 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20313 Z= 0.123 Angle : 0.510 6.464 27500 Z= 0.274 Chirality : 0.039 0.136 3088 Planarity : 0.004 0.035 3376 Dihedral : 10.267 99.469 2858 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.13 % Allowed : 7.73 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2394 helix: 1.42 (0.13), residues: 1480 sheet: 0.49 (0.50), residues: 120 loop : 0.70 (0.26), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 333 HIS 0.005 0.001 HIS B 251 PHE 0.012 0.001 PHE A 319 TYR 0.009 0.002 TYR A 343 ARG 0.006 0.001 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 1104) hydrogen bonds : angle 3.93371 ( 3168) covalent geometry : bond 0.00269 (20313) covalent geometry : angle 0.50963 (27500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 311 time to evaluate : 2.115 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6915 (tttt) cc_final: 0.6317 (tptt) REVERT: A 221 LYS cc_start: 0.8097 (pttt) cc_final: 0.7208 (mmtt) REVERT: A 223 TRP cc_start: 0.7572 (t-100) cc_final: 0.6653 (m100) REVERT: A 289 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 331 THR cc_start: 0.8687 (t) cc_final: 0.8400 (m) REVERT: A 332 GLU cc_start: 0.8359 (tt0) cc_final: 0.8044 (tt0) REVERT: A 352 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7101 (pm20) REVERT: A 353 LYS cc_start: 0.8386 (tptt) cc_final: 0.7992 (tppp) REVERT: A 358 GLU cc_start: 0.8283 (tt0) cc_final: 0.7446 (mt-10) REVERT: A 380 LYS cc_start: 0.7982 (tttt) cc_final: 0.7332 (tttp) REVERT: A 384 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 392 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7406 (ttp-170) REVERT: A 495 GLU cc_start: 0.7864 (pt0) cc_final: 0.7503 (pt0) REVERT: A 528 MET cc_start: 0.7231 (mtt) cc_final: 0.6990 (mtp) REVERT: A 535 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.7227 (ttp-170) REVERT: A 549 PHE cc_start: 0.8227 (m-80) cc_final: 0.6815 (t80) REVERT: A 690 LYS cc_start: 0.7808 (tttt) cc_final: 0.6909 (ttpt) REVERT: B 123 LYS cc_start: 0.6902 (tttt) cc_final: 0.6305 (tptt) REVERT: B 221 LYS cc_start: 0.8101 (pttt) cc_final: 0.7177 (mmtt) REVERT: B 223 TRP cc_start: 0.7574 (t-100) cc_final: 0.6650 (m100) REVERT: B 289 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7536 (mm-30) REVERT: B 331 THR cc_start: 0.8680 (t) cc_final: 0.8399 (m) REVERT: B 332 GLU cc_start: 0.8358 (tt0) cc_final: 0.8040 (tt0) REVERT: B 352 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: B 353 LYS cc_start: 0.8408 (tptt) cc_final: 0.8012 (tppp) REVERT: B 358 GLU cc_start: 0.8270 (tt0) cc_final: 0.7435 (mt-10) REVERT: B 380 LYS cc_start: 0.7997 (tttt) cc_final: 0.7343 (tttp) REVERT: B 384 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: B 495 GLU cc_start: 0.7834 (pt0) cc_final: 0.7464 (pt0) REVERT: B 528 MET cc_start: 0.7238 (mtt) cc_final: 0.6996 (mtp) REVERT: B 535 ARG cc_start: 0.7599 (ttp-170) cc_final: 0.7329 (ttp-170) REVERT: B 549 PHE cc_start: 0.8226 (m-80) cc_final: 0.6824 (t80) REVERT: B 690 LYS cc_start: 0.7799 (tttt) cc_final: 0.6895 (ttpt) REVERT: C 123 LYS cc_start: 0.6894 (tttt) cc_final: 0.6297 (tptt) REVERT: C 221 LYS cc_start: 0.8102 (pttt) cc_final: 0.7181 (mmtt) REVERT: C 223 TRP cc_start: 0.7586 (t-100) cc_final: 0.6666 (m100) REVERT: C 289 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 331 THR cc_start: 0.8692 (t) cc_final: 0.8396 (m) REVERT: C 332 GLU cc_start: 0.8363 (tt0) cc_final: 0.8047 (tt0) REVERT: C 352 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: C 353 LYS cc_start: 0.8395 (tptt) cc_final: 0.7995 (tppp) REVERT: C 358 GLU cc_start: 0.8277 (tt0) cc_final: 0.7432 (mt-10) REVERT: C 380 LYS cc_start: 0.7991 (tttt) cc_final: 0.7335 (tttp) REVERT: C 384 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: C 495 GLU cc_start: 0.7843 (pt0) cc_final: 0.7475 (pt0) REVERT: C 528 MET cc_start: 0.7229 (mtt) cc_final: 0.6987 (mtp) REVERT: C 535 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7356 (ttp-170) REVERT: C 549 PHE cc_start: 0.8227 (m-80) cc_final: 0.6823 (t80) REVERT: C 690 LYS cc_start: 0.7801 (tttt) cc_final: 0.6898 (ttpt) REVERT: D 123 LYS cc_start: 0.6909 (tttt) cc_final: 0.6311 (tptt) REVERT: D 221 LYS cc_start: 0.8100 (pttt) cc_final: 0.7178 (mmtt) REVERT: D 223 TRP cc_start: 0.7575 (t-100) cc_final: 0.6662 (m100) REVERT: D 289 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7533 (mm-30) REVERT: D 331 THR cc_start: 0.8687 (t) cc_final: 0.8414 (m) REVERT: D 332 GLU cc_start: 0.8352 (tt0) cc_final: 0.8038 (tt0) REVERT: D 352 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: D 353 LYS cc_start: 0.8401 (tptt) cc_final: 0.8008 (tppp) REVERT: D 358 GLU cc_start: 0.8271 (tt0) cc_final: 0.7442 (mt-10) REVERT: D 380 LYS cc_start: 0.7980 (tttt) cc_final: 0.7326 (tttp) REVERT: D 384 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: D 495 GLU cc_start: 0.7846 (pt0) cc_final: 0.7480 (pt0) REVERT: D 528 MET cc_start: 0.7234 (mtt) cc_final: 0.6989 (mtp) REVERT: D 535 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7336 (ttp-170) REVERT: D 549 PHE cc_start: 0.8223 (m-80) cc_final: 0.6811 (t80) REVERT: D 690 LYS cc_start: 0.7804 (tttt) cc_final: 0.6905 (ttpt) outliers start: 24 outliers final: 4 residues processed: 323 average time/residue: 1.3958 time to fit residues: 503.4975 Evaluate side-chains 280 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 268 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 494 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 221 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 276 GLN A 452 GLN B 186 ASN B 276 GLN C 186 ASN C 276 GLN D 186 ASN D 276 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.160877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122889 restraints weight = 19386.905| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.52 r_work: 0.3211 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20313 Z= 0.156 Angle : 0.515 7.428 27500 Z= 0.273 Chirality : 0.040 0.124 3088 Planarity : 0.004 0.038 3376 Dihedral : 10.092 94.338 2858 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.65 % Allowed : 8.44 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2394 helix: 1.70 (0.13), residues: 1468 sheet: 0.56 (0.51), residues: 120 loop : 0.71 (0.25), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 333 HIS 0.007 0.002 HIS C 651 PHE 0.013 0.002 PHE D 319 TYR 0.011 0.002 TYR D 228 ARG 0.003 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 1104) hydrogen bonds : angle 3.81549 ( 3168) covalent geometry : bond 0.00365 (20313) covalent geometry : angle 0.51456 (27500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 2.594 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.7024 (tttt) cc_final: 0.6601 (tptp) REVERT: A 221 LYS cc_start: 0.8092 (pttt) cc_final: 0.6963 (mmtt) REVERT: A 223 TRP cc_start: 0.7525 (t-100) cc_final: 0.6684 (m100) REVERT: A 289 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7563 (mp0) REVERT: A 352 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: A 353 LYS cc_start: 0.8351 (tptt) cc_final: 0.7945 (tppp) REVERT: A 358 GLU cc_start: 0.8253 (tt0) cc_final: 0.7375 (mt-10) REVERT: A 495 GLU cc_start: 0.7812 (pt0) cc_final: 0.7477 (pt0) REVERT: A 528 MET cc_start: 0.7427 (mtt) cc_final: 0.7201 (mtp) REVERT: A 535 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7141 (ttp-170) REVERT: A 549 PHE cc_start: 0.8177 (m-80) cc_final: 0.6741 (t80) REVERT: A 609 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 690 LYS cc_start: 0.7853 (tttt) cc_final: 0.6888 (ttpt) REVERT: B 123 LYS cc_start: 0.6994 (tttt) cc_final: 0.6592 (tptp) REVERT: B 221 LYS cc_start: 0.8090 (pttt) cc_final: 0.6960 (mmtt) REVERT: B 223 TRP cc_start: 0.7531 (t-100) cc_final: 0.6692 (m100) REVERT: B 289 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7559 (mp0) REVERT: B 352 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: B 353 LYS cc_start: 0.8353 (tptt) cc_final: 0.7950 (tppp) REVERT: B 358 GLU cc_start: 0.8240 (tt0) cc_final: 0.7364 (mt-10) REVERT: B 495 GLU cc_start: 0.7792 (pt0) cc_final: 0.7448 (pt0) REVERT: B 528 MET cc_start: 0.7442 (mtt) cc_final: 0.7215 (mtp) REVERT: B 549 PHE cc_start: 0.8182 (m-80) cc_final: 0.6746 (t80) REVERT: B 609 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 647 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 690 LYS cc_start: 0.7833 (tttt) cc_final: 0.6883 (ttpt) REVERT: C 123 LYS cc_start: 0.6978 (tttt) cc_final: 0.6577 (tptp) REVERT: C 221 LYS cc_start: 0.8088 (pttt) cc_final: 0.6963 (mmtt) REVERT: C 223 TRP cc_start: 0.7529 (t-100) cc_final: 0.6691 (m100) REVERT: C 289 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7557 (mp0) REVERT: C 352 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: C 353 LYS cc_start: 0.8347 (tptt) cc_final: 0.7939 (tppp) REVERT: C 358 GLU cc_start: 0.8252 (tt0) cc_final: 0.7366 (mt-10) REVERT: C 495 GLU cc_start: 0.7798 (pt0) cc_final: 0.7455 (pt0) REVERT: C 528 MET cc_start: 0.7430 (mtt) cc_final: 0.7200 (mtp) REVERT: C 549 PHE cc_start: 0.8180 (m-80) cc_final: 0.6742 (t80) REVERT: C 609 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 647 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7494 (mt-10) REVERT: C 690 LYS cc_start: 0.7840 (tttt) cc_final: 0.6894 (ttpt) REVERT: D 123 LYS cc_start: 0.6992 (tttt) cc_final: 0.6587 (tptp) REVERT: D 221 LYS cc_start: 0.8091 (pttt) cc_final: 0.6959 (mmtt) REVERT: D 223 TRP cc_start: 0.7534 (t-100) cc_final: 0.6695 (m100) REVERT: D 289 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7556 (mp0) REVERT: D 352 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: D 353 LYS cc_start: 0.8357 (tptt) cc_final: 0.7951 (tppp) REVERT: D 358 GLU cc_start: 0.8249 (tt0) cc_final: 0.7373 (mt-10) REVERT: D 495 GLU cc_start: 0.7809 (pt0) cc_final: 0.7455 (pt0) REVERT: D 549 PHE cc_start: 0.8184 (m-80) cc_final: 0.6746 (t80) REVERT: D 609 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7706 (mm-30) REVERT: D 647 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7482 (mt-10) REVERT: D 690 LYS cc_start: 0.7839 (tttt) cc_final: 0.6894 (ttpt) outliers start: 35 outliers final: 11 residues processed: 294 average time/residue: 1.2866 time to fit residues: 427.0434 Evaluate side-chains 279 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 264 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 538 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 132 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 186 ASN C 186 ASN D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120734 restraints weight = 19457.791| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.61 r_work: 0.3187 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20313 Z= 0.176 Angle : 0.526 7.329 27500 Z= 0.277 Chirality : 0.041 0.128 3088 Planarity : 0.004 0.041 3376 Dihedral : 10.039 93.557 2858 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.54 % Allowed : 8.11 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.18), residues: 2394 helix: 1.64 (0.13), residues: 1468 sheet: 0.52 (0.50), residues: 120 loop : 0.56 (0.25), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 333 HIS 0.006 0.002 HIS A 651 PHE 0.013 0.002 PHE B 394 TYR 0.014 0.002 TYR D 525 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 1104) hydrogen bonds : angle 3.80074 ( 3168) covalent geometry : bond 0.00414 (20313) covalent geometry : angle 0.52579 (27500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 266 time to evaluate : 2.149 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6947 (tttt) cc_final: 0.6497 (tptp) REVERT: A 223 TRP cc_start: 0.7570 (t-100) cc_final: 0.6664 (m100) REVERT: A 352 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: A 353 LYS cc_start: 0.8313 (tptt) cc_final: 0.7898 (tppp) REVERT: A 358 GLU cc_start: 0.8281 (tt0) cc_final: 0.7399 (mt-10) REVERT: A 392 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7397 (ttp-170) REVERT: A 495 GLU cc_start: 0.7801 (pt0) cc_final: 0.7428 (pt0) REVERT: A 549 PHE cc_start: 0.8188 (m-80) cc_final: 0.6724 (t80) REVERT: A 609 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7661 (mm-30) REVERT: A 650 ASN cc_start: 0.7811 (m-40) cc_final: 0.7144 (p0) REVERT: A 690 LYS cc_start: 0.7829 (tttt) cc_final: 0.6872 (ttpt) REVERT: B 123 LYS cc_start: 0.6936 (tttt) cc_final: 0.6488 (tptp) REVERT: B 223 TRP cc_start: 0.7566 (t-100) cc_final: 0.6658 (m100) REVERT: B 352 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: B 353 LYS cc_start: 0.8317 (tptt) cc_final: 0.7903 (tppp) REVERT: B 358 GLU cc_start: 0.8269 (tt0) cc_final: 0.7386 (mt-10) REVERT: B 495 GLU cc_start: 0.7805 (pt0) cc_final: 0.7397 (pt0) REVERT: B 549 PHE cc_start: 0.8192 (m-80) cc_final: 0.6732 (t80) REVERT: B 609 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 647 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: B 650 ASN cc_start: 0.7819 (m-40) cc_final: 0.7151 (p0) REVERT: B 690 LYS cc_start: 0.7827 (tttt) cc_final: 0.6855 (ttpt) REVERT: C 123 LYS cc_start: 0.6927 (tttt) cc_final: 0.6483 (tptp) REVERT: C 223 TRP cc_start: 0.7570 (t-100) cc_final: 0.6664 (m100) REVERT: C 352 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: C 353 LYS cc_start: 0.8313 (tptt) cc_final: 0.7892 (tppp) REVERT: C 358 GLU cc_start: 0.8279 (tt0) cc_final: 0.7393 (mt-10) REVERT: C 495 GLU cc_start: 0.7816 (pt0) cc_final: 0.7410 (pt0) REVERT: C 549 PHE cc_start: 0.8200 (m-80) cc_final: 0.6741 (t80) REVERT: C 609 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 647 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: C 650 ASN cc_start: 0.7819 (m-40) cc_final: 0.7146 (p0) REVERT: C 690 LYS cc_start: 0.7828 (tttt) cc_final: 0.6854 (ttpt) REVERT: D 123 LYS cc_start: 0.6940 (tttt) cc_final: 0.6491 (tptp) REVERT: D 223 TRP cc_start: 0.7568 (t-100) cc_final: 0.6659 (m100) REVERT: D 352 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: D 353 LYS cc_start: 0.8306 (tptt) cc_final: 0.7891 (tppp) REVERT: D 358 GLU cc_start: 0.8266 (tt0) cc_final: 0.7388 (mt-10) REVERT: D 495 GLU cc_start: 0.7782 (pt0) cc_final: 0.7396 (pt0) REVERT: D 549 PHE cc_start: 0.8202 (m-80) cc_final: 0.6740 (t80) REVERT: D 609 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7678 (mm-30) REVERT: D 647 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: D 650 ASN cc_start: 0.7822 (m-40) cc_final: 0.7156 (p0) REVERT: D 690 LYS cc_start: 0.7832 (tttt) cc_final: 0.6863 (ttpt) outliers start: 54 outliers final: 27 residues processed: 301 average time/residue: 1.2647 time to fit residues: 430.8227 Evaluate side-chains 283 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 294 GLN A 452 GLN B 186 ASN B 294 GLN C 186 ASN C 294 GLN D 186 ASN D 294 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.161280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123419 restraints weight = 19477.428| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.52 r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20313 Z= 0.125 Angle : 0.458 5.620 27500 Z= 0.244 Chirality : 0.038 0.116 3088 Planarity : 0.004 0.040 3376 Dihedral : 9.586 82.806 2858 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.36 % Allowed : 8.44 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.18), residues: 2394 helix: 1.88 (0.13), residues: 1464 sheet: 0.53 (0.50), residues: 120 loop : 0.67 (0.25), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 333 HIS 0.004 0.001 HIS C 251 PHE 0.010 0.001 PHE A 394 TYR 0.016 0.002 TYR A 525 ARG 0.002 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1104) hydrogen bonds : angle 3.64893 ( 3168) covalent geometry : bond 0.00285 (20313) covalent geometry : angle 0.45782 (27500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 2.194 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6817 (tttt) cc_final: 0.6356 (tptp) REVERT: A 221 LYS cc_start: 0.8284 (ptmt) cc_final: 0.6997 (mmtt) REVERT: A 223 TRP cc_start: 0.7436 (t-100) cc_final: 0.6611 (m100) REVERT: A 289 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7537 (mp0) REVERT: A 352 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: A 353 LYS cc_start: 0.8328 (tptt) cc_final: 0.7923 (tppp) REVERT: A 358 GLU cc_start: 0.8253 (tt0) cc_final: 0.7381 (mt-10) REVERT: A 392 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7317 (ttp-170) REVERT: A 495 GLU cc_start: 0.7766 (pt0) cc_final: 0.7366 (pt0) REVERT: A 549 PHE cc_start: 0.8095 (m-80) cc_final: 0.6689 (t80) REVERT: A 609 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 687 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.7035 (mtm-85) REVERT: A 690 LYS cc_start: 0.7845 (tttt) cc_final: 0.6853 (ttpt) REVERT: B 123 LYS cc_start: 0.6818 (tttt) cc_final: 0.6360 (tptp) REVERT: B 221 LYS cc_start: 0.8263 (ptmt) cc_final: 0.6994 (mmtt) REVERT: B 223 TRP cc_start: 0.7429 (t-100) cc_final: 0.6602 (m100) REVERT: B 289 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7538 (mp0) REVERT: B 352 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: B 353 LYS cc_start: 0.8334 (tptt) cc_final: 0.7932 (tppp) REVERT: B 358 GLU cc_start: 0.8239 (tt0) cc_final: 0.7364 (mt-10) REVERT: B 392 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7326 (ttp-170) REVERT: B 495 GLU cc_start: 0.7752 (pt0) cc_final: 0.7378 (pt0) REVERT: B 549 PHE cc_start: 0.8079 (m-80) cc_final: 0.6662 (t80) REVERT: B 609 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 647 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: B 687 ARG cc_start: 0.7328 (mtm-85) cc_final: 0.7032 (mtm-85) REVERT: B 690 LYS cc_start: 0.7798 (tttt) cc_final: 0.6790 (ttpt) REVERT: C 123 LYS cc_start: 0.6805 (tttt) cc_final: 0.6350 (tptp) REVERT: C 221 LYS cc_start: 0.8262 (ptmt) cc_final: 0.6992 (mmtt) REVERT: C 223 TRP cc_start: 0.7423 (t-100) cc_final: 0.6607 (m100) REVERT: C 289 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7522 (mp0) REVERT: C 352 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: C 353 LYS cc_start: 0.8326 (tptt) cc_final: 0.7924 (tppp) REVERT: C 358 GLU cc_start: 0.8247 (tt0) cc_final: 0.7367 (mt-10) REVERT: C 392 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7323 (ttp-170) REVERT: C 495 GLU cc_start: 0.7762 (pt0) cc_final: 0.7385 (pt0) REVERT: C 549 PHE cc_start: 0.8087 (m-80) cc_final: 0.6664 (t80) REVERT: C 609 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7695 (mm-30) REVERT: C 647 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: C 687 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.7050 (mtm-85) REVERT: C 690 LYS cc_start: 0.7803 (tttt) cc_final: 0.6799 (ttpt) REVERT: D 123 LYS cc_start: 0.6802 (tttt) cc_final: 0.6343 (tptp) REVERT: D 221 LYS cc_start: 0.8263 (ptmt) cc_final: 0.6991 (mmtt) REVERT: D 223 TRP cc_start: 0.7428 (t-100) cc_final: 0.6604 (m100) REVERT: D 289 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7525 (mp0) REVERT: D 352 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: D 353 LYS cc_start: 0.8323 (tptt) cc_final: 0.7921 (tppp) REVERT: D 358 GLU cc_start: 0.8244 (tt0) cc_final: 0.7371 (mt-10) REVERT: D 392 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7311 (ttp-170) REVERT: D 495 GLU cc_start: 0.7723 (pt0) cc_final: 0.7374 (pt0) REVERT: D 549 PHE cc_start: 0.8090 (m-80) cc_final: 0.6664 (t80) REVERT: D 609 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 647 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: D 687 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.7037 (mtm-85) REVERT: D 690 LYS cc_start: 0.7807 (tttt) cc_final: 0.6806 (ttpt) outliers start: 50 outliers final: 19 residues processed: 298 average time/residue: 1.3050 time to fit residues: 437.8424 Evaluate side-chains 275 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 161 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 226 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122122 restraints weight = 19397.743| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.55 r_work: 0.3215 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20313 Z= 0.129 Angle : 0.460 5.599 27500 Z= 0.245 Chirality : 0.038 0.117 3088 Planarity : 0.004 0.040 3376 Dihedral : 9.264 72.519 2858 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.17 % Allowed : 8.67 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.18), residues: 2394 helix: 1.90 (0.13), residues: 1464 sheet: 0.55 (0.50), residues: 120 loop : 0.71 (0.25), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 333 HIS 0.005 0.001 HIS A 251 PHE 0.011 0.001 PHE B 394 TYR 0.018 0.002 TYR B 525 ARG 0.004 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1104) hydrogen bonds : angle 3.62028 ( 3168) covalent geometry : bond 0.00298 (20313) covalent geometry : angle 0.46015 (27500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 2.184 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6655 (tttt) cc_final: 0.5808 (tptp) REVERT: A 221 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7011 (mmtt) REVERT: A 223 TRP cc_start: 0.7464 (t-100) cc_final: 0.6711 (m100) REVERT: A 289 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7558 (mp0) REVERT: A 331 THR cc_start: 0.8767 (t) cc_final: 0.8459 (m) REVERT: A 352 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: A 353 LYS cc_start: 0.8336 (tptt) cc_final: 0.7922 (tppp) REVERT: A 358 GLU cc_start: 0.8250 (tt0) cc_final: 0.7344 (mt-10) REVERT: A 392 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7313 (ttp-170) REVERT: A 495 GLU cc_start: 0.7790 (pt0) cc_final: 0.7385 (pt0) REVERT: A 530 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6739 (mt0) REVERT: A 549 PHE cc_start: 0.8040 (m-10) cc_final: 0.6665 (t80) REVERT: A 609 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 687 ARG cc_start: 0.7259 (mtm-85) cc_final: 0.6948 (mtm-85) REVERT: A 690 LYS cc_start: 0.7770 (tttt) cc_final: 0.6841 (ttpp) REVERT: B 123 LYS cc_start: 0.6647 (tttt) cc_final: 0.6149 (tptp) REVERT: B 221 LYS cc_start: 0.8303 (ptmt) cc_final: 0.6999 (mmtt) REVERT: B 223 TRP cc_start: 0.7456 (t-100) cc_final: 0.6703 (m100) REVERT: B 289 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7556 (mp0) REVERT: B 331 THR cc_start: 0.8763 (t) cc_final: 0.8465 (m) REVERT: B 352 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: B 353 LYS cc_start: 0.8339 (tptt) cc_final: 0.7929 (tppp) REVERT: B 358 GLU cc_start: 0.8242 (tt0) cc_final: 0.7338 (mt-10) REVERT: B 392 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7321 (ttp-170) REVERT: B 495 GLU cc_start: 0.7763 (pt0) cc_final: 0.7408 (pt0) REVERT: B 530 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6773 (mt0) REVERT: B 549 PHE cc_start: 0.8041 (m-10) cc_final: 0.6664 (t80) REVERT: B 609 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 647 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: B 687 ARG cc_start: 0.7246 (mtm-85) cc_final: 0.6943 (mtm-85) REVERT: B 690 LYS cc_start: 0.7744 (tttt) cc_final: 0.6806 (ttpp) REVERT: C 123 LYS cc_start: 0.6638 (tttt) cc_final: 0.6143 (tptp) REVERT: C 221 LYS cc_start: 0.8304 (ptmt) cc_final: 0.7000 (mmtt) REVERT: C 223 TRP cc_start: 0.7457 (t-100) cc_final: 0.6707 (m100) REVERT: C 289 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7538 (mp0) REVERT: C 331 THR cc_start: 0.8761 (t) cc_final: 0.8467 (m) REVERT: C 352 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: C 353 LYS cc_start: 0.8339 (tptt) cc_final: 0.7929 (tppp) REVERT: C 358 GLU cc_start: 0.8245 (tt0) cc_final: 0.7340 (mt-10) REVERT: C 392 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7311 (ttp-170) REVERT: C 495 GLU cc_start: 0.7773 (pt0) cc_final: 0.7417 (pt0) REVERT: C 530 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6767 (mt0) REVERT: C 549 PHE cc_start: 0.8054 (m-10) cc_final: 0.6677 (t80) REVERT: C 609 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7687 (mm-30) REVERT: C 647 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: C 687 ARG cc_start: 0.7254 (mtm-85) cc_final: 0.6949 (mtm-85) REVERT: C 690 LYS cc_start: 0.7741 (tttt) cc_final: 0.6805 (ttpp) REVERT: D 123 LYS cc_start: 0.6636 (tttt) cc_final: 0.6137 (tptp) REVERT: D 221 LYS cc_start: 0.8302 (ptmt) cc_final: 0.6995 (mmtt) REVERT: D 223 TRP cc_start: 0.7459 (t-100) cc_final: 0.6709 (m100) REVERT: D 289 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7545 (mp0) REVERT: D 331 THR cc_start: 0.8763 (t) cc_final: 0.8480 (m) REVERT: D 352 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: D 353 LYS cc_start: 0.8334 (tptt) cc_final: 0.7925 (tppp) REVERT: D 358 GLU cc_start: 0.8243 (tt0) cc_final: 0.7344 (mt-10) REVERT: D 392 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7298 (ttp-170) REVERT: D 495 GLU cc_start: 0.7721 (pt0) cc_final: 0.7342 (pt0) REVERT: D 530 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6763 (mt0) REVERT: D 549 PHE cc_start: 0.8051 (m-10) cc_final: 0.6669 (t80) REVERT: D 609 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 647 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: D 687 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6934 (mtm-85) REVERT: D 690 LYS cc_start: 0.7748 (tttt) cc_final: 0.6813 (ttpp) outliers start: 46 outliers final: 15 residues processed: 292 average time/residue: 1.3228 time to fit residues: 435.0094 Evaluate side-chains 274 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 530 GLN Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120548 restraints weight = 19355.313| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.55 r_work: 0.3222 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20313 Z= 0.162 Angle : 0.501 6.350 27500 Z= 0.264 Chirality : 0.039 0.126 3088 Planarity : 0.004 0.042 3376 Dihedral : 9.676 77.303 2858 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.17 % Allowed : 9.00 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.18), residues: 2394 helix: 1.83 (0.13), residues: 1464 sheet: 0.57 (0.50), residues: 120 loop : 0.55 (0.25), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 333 HIS 0.005 0.001 HIS D 251 PHE 0.013 0.001 PHE B 394 TYR 0.021 0.002 TYR B 525 ARG 0.003 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 1104) hydrogen bonds : angle 3.71049 ( 3168) covalent geometry : bond 0.00379 (20313) covalent geometry : angle 0.50101 (27500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 2.295 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6729 (tttt) cc_final: 0.6246 (tptp) REVERT: A 221 LYS cc_start: 0.8334 (ptmt) cc_final: 0.7003 (mmtt) REVERT: A 223 TRP cc_start: 0.7434 (t-100) cc_final: 0.6683 (m100) REVERT: A 289 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7480 (mp0) REVERT: A 352 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: A 353 LYS cc_start: 0.8323 (tptt) cc_final: 0.7895 (tppp) REVERT: A 358 GLU cc_start: 0.8224 (tt0) cc_final: 0.7285 (mt-10) REVERT: A 392 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7289 (ttp-170) REVERT: A 495 GLU cc_start: 0.7789 (pt0) cc_final: 0.7438 (pt0) REVERT: A 530 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6732 (mt0) REVERT: A 535 ARG cc_start: 0.7648 (tmm160) cc_final: 0.7350 (ttp-170) REVERT: A 549 PHE cc_start: 0.8035 (m-10) cc_final: 0.6594 (t80) REVERT: A 609 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 650 ASN cc_start: 0.7792 (m-40) cc_final: 0.7092 (p0) REVERT: A 690 LYS cc_start: 0.7767 (tttt) cc_final: 0.6817 (ttpp) REVERT: B 123 LYS cc_start: 0.6737 (tttt) cc_final: 0.6256 (tptp) REVERT: B 221 LYS cc_start: 0.8344 (ptmt) cc_final: 0.6980 (mmtt) REVERT: B 223 TRP cc_start: 0.7437 (t-100) cc_final: 0.6685 (m100) REVERT: B 289 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7482 (mp0) REVERT: B 352 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: B 353 LYS cc_start: 0.8338 (tptt) cc_final: 0.7917 (tppp) REVERT: B 358 GLU cc_start: 0.8224 (tt0) cc_final: 0.7287 (mt-10) REVERT: B 392 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7288 (ttp-170) REVERT: B 495 GLU cc_start: 0.7779 (pt0) cc_final: 0.7424 (pt0) REVERT: B 530 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6401 (mt0) REVERT: B 549 PHE cc_start: 0.8051 (m-10) cc_final: 0.6595 (t80) REVERT: B 609 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 647 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: B 650 ASN cc_start: 0.7798 (m-40) cc_final: 0.7096 (p0) REVERT: B 690 LYS cc_start: 0.7747 (tttt) cc_final: 0.6783 (ttpp) REVERT: C 123 LYS cc_start: 0.6730 (tttt) cc_final: 0.6202 (tptp) REVERT: C 221 LYS cc_start: 0.8348 (ptmt) cc_final: 0.6985 (mmtt) REVERT: C 223 TRP cc_start: 0.7437 (t-100) cc_final: 0.6687 (m100) REVERT: C 289 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7466 (mp0) REVERT: C 352 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: C 353 LYS cc_start: 0.8337 (tptt) cc_final: 0.7914 (tppp) REVERT: C 358 GLU cc_start: 0.8230 (tt0) cc_final: 0.7295 (mt-10) REVERT: C 392 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7289 (ttp-170) REVERT: C 495 GLU cc_start: 0.7790 (pt0) cc_final: 0.7435 (pt0) REVERT: C 530 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6395 (mt0) REVERT: C 549 PHE cc_start: 0.8045 (m-10) cc_final: 0.6599 (t80) REVERT: C 609 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7563 (mm-30) REVERT: C 647 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: C 650 ASN cc_start: 0.7802 (m-40) cc_final: 0.7100 (p0) REVERT: C 690 LYS cc_start: 0.7749 (tttt) cc_final: 0.6787 (ttpp) REVERT: D 123 LYS cc_start: 0.6723 (tttt) cc_final: 0.6240 (tptp) REVERT: D 221 LYS cc_start: 0.8340 (ptmt) cc_final: 0.6973 (mmtt) REVERT: D 223 TRP cc_start: 0.7436 (t-100) cc_final: 0.6683 (m100) REVERT: D 289 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7464 (mp0) REVERT: D 352 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: D 353 LYS cc_start: 0.8324 (tptt) cc_final: 0.7901 (tppp) REVERT: D 358 GLU cc_start: 0.8228 (tt0) cc_final: 0.7294 (mt-10) REVERT: D 392 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7277 (ttp-170) REVERT: D 495 GLU cc_start: 0.7780 (pt0) cc_final: 0.7424 (pt0) REVERT: D 528 MET cc_start: 0.7626 (mtt) cc_final: 0.7379 (mtp) REVERT: D 530 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6778 (mt0) REVERT: D 549 PHE cc_start: 0.8053 (m-10) cc_final: 0.6590 (t80) REVERT: D 609 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 647 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: D 650 ASN cc_start: 0.7794 (m-40) cc_final: 0.7095 (p0) REVERT: D 690 LYS cc_start: 0.7758 (tttt) cc_final: 0.6802 (ttpp) outliers start: 46 outliers final: 19 residues processed: 289 average time/residue: 1.2957 time to fit residues: 423.9309 Evaluate side-chains 282 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 530 GLN Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 222 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121176 restraints weight = 19369.961| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.56 r_work: 0.3203 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20313 Z= 0.142 Angle : 0.480 5.804 27500 Z= 0.253 Chirality : 0.039 0.119 3088 Planarity : 0.004 0.041 3376 Dihedral : 9.477 73.974 2858 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.12 % Allowed : 9.33 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.18), residues: 2394 helix: 1.89 (0.13), residues: 1465 sheet: 0.54 (0.49), residues: 120 loop : 0.66 (0.25), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 333 HIS 0.005 0.001 HIS A 251 PHE 0.012 0.001 PHE B 394 TYR 0.021 0.002 TYR A 525 ARG 0.004 0.000 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 1104) hydrogen bonds : angle 3.67706 ( 3168) covalent geometry : bond 0.00331 (20313) covalent geometry : angle 0.48014 (27500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 2.354 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6678 (tttt) cc_final: 0.5820 (tptp) REVERT: A 221 LYS cc_start: 0.8342 (ptmt) cc_final: 0.7039 (mmtt) REVERT: A 223 TRP cc_start: 0.7436 (t-100) cc_final: 0.6762 (m100) REVERT: A 289 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7551 (mp0) REVERT: A 352 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6966 (pm20) REVERT: A 353 LYS cc_start: 0.8358 (tptt) cc_final: 0.7942 (tppp) REVERT: A 358 GLU cc_start: 0.8278 (tt0) cc_final: 0.7380 (mt-10) REVERT: A 384 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: A 392 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7347 (ttp-170) REVERT: A 495 GLU cc_start: 0.7836 (pt0) cc_final: 0.7464 (pt0) REVERT: A 530 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6809 (mt0) REVERT: A 535 ARG cc_start: 0.7655 (tmm160) cc_final: 0.7368 (ttp-170) REVERT: A 549 PHE cc_start: 0.8057 (m-10) cc_final: 0.6684 (t80) REVERT: A 609 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 640 MET cc_start: 0.8781 (ttp) cc_final: 0.8519 (tmm) REVERT: A 650 ASN cc_start: 0.7821 (m-40) cc_final: 0.7141 (p0) REVERT: A 690 LYS cc_start: 0.7782 (tttt) cc_final: 0.6840 (ttpp) REVERT: B 123 LYS cc_start: 0.6664 (tttt) cc_final: 0.5809 (tptp) REVERT: B 221 LYS cc_start: 0.8353 (ptmt) cc_final: 0.7003 (mmtt) REVERT: B 223 TRP cc_start: 0.7429 (t-100) cc_final: 0.6757 (m100) REVERT: B 289 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7543 (mp0) REVERT: B 352 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: B 353 LYS cc_start: 0.8370 (tptt) cc_final: 0.7960 (tppp) REVERT: B 358 GLU cc_start: 0.8281 (tt0) cc_final: 0.7390 (mt-10) REVERT: B 384 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: B 392 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7353 (ttp-170) REVERT: B 495 GLU cc_start: 0.7827 (pt0) cc_final: 0.7468 (pt0) REVERT: B 530 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6467 (mt0) REVERT: B 549 PHE cc_start: 0.8043 (m-10) cc_final: 0.6653 (t80) REVERT: B 609 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 647 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: B 650 ASN cc_start: 0.7840 (m-40) cc_final: 0.7162 (p0) REVERT: B 690 LYS cc_start: 0.7755 (tttt) cc_final: 0.6716 (ttpt) REVERT: C 123 LYS cc_start: 0.6657 (tttt) cc_final: 0.5805 (tptp) REVERT: C 221 LYS cc_start: 0.8353 (ptmt) cc_final: 0.7006 (mmtt) REVERT: C 223 TRP cc_start: 0.7427 (t-100) cc_final: 0.6758 (m100) REVERT: C 289 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7524 (mp0) REVERT: C 352 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: C 353 LYS cc_start: 0.8374 (tptt) cc_final: 0.7958 (tppp) REVERT: C 358 GLU cc_start: 0.8283 (tt0) cc_final: 0.7389 (mt-10) REVERT: C 384 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: C 392 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7349 (ttp-170) REVERT: C 495 GLU cc_start: 0.7833 (pt0) cc_final: 0.7471 (pt0) REVERT: C 530 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6456 (mt0) REVERT: C 549 PHE cc_start: 0.8052 (m-10) cc_final: 0.6660 (t80) REVERT: C 609 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7640 (mm-30) REVERT: C 647 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: C 650 ASN cc_start: 0.7836 (m-40) cc_final: 0.7156 (p0) REVERT: C 690 LYS cc_start: 0.7761 (tttt) cc_final: 0.6727 (ttpt) REVERT: D 123 LYS cc_start: 0.6659 (tttt) cc_final: 0.5802 (tptp) REVERT: D 221 LYS cc_start: 0.8355 (ptmt) cc_final: 0.7002 (mmtt) REVERT: D 223 TRP cc_start: 0.7432 (t-100) cc_final: 0.6765 (m100) REVERT: D 289 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7537 (mp0) REVERT: D 352 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: D 353 LYS cc_start: 0.8358 (tptt) cc_final: 0.7948 (tppp) REVERT: D 358 GLU cc_start: 0.8280 (tt0) cc_final: 0.7387 (mt-10) REVERT: D 384 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: D 392 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7338 (ttp-170) REVERT: D 495 GLU cc_start: 0.7811 (pt0) cc_final: 0.7385 (pt0) REVERT: D 528 MET cc_start: 0.7695 (mtt) cc_final: 0.7458 (mtp) REVERT: D 530 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6479 (mt0) REVERT: D 549 PHE cc_start: 0.8049 (m-10) cc_final: 0.6654 (t80) REVERT: D 609 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7637 (mm-30) REVERT: D 647 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: D 650 ASN cc_start: 0.7830 (m-40) cc_final: 0.7155 (p0) REVERT: D 690 LYS cc_start: 0.7769 (tttt) cc_final: 0.6738 (ttpt) outliers start: 45 outliers final: 18 residues processed: 281 average time/residue: 1.2825 time to fit residues: 407.4633 Evaluate side-chains 280 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 530 GLN Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS A 452 GLN B 363 HIS C 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119916 restraints weight = 19292.739| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.58 r_work: 0.3188 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20313 Z= 0.165 Angle : 0.510 6.203 27500 Z= 0.267 Chirality : 0.040 0.185 3088 Planarity : 0.004 0.042 3376 Dihedral : 9.767 79.675 2858 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.31 % Allowed : 9.38 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 2394 helix: 1.83 (0.13), residues: 1464 sheet: 0.50 (0.48), residues: 120 loop : 0.52 (0.25), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 333 HIS 0.005 0.001 HIS C 251 PHE 0.013 0.001 PHE B 394 TYR 0.022 0.002 TYR B 525 ARG 0.004 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1104) hydrogen bonds : angle 3.75364 ( 3168) covalent geometry : bond 0.00388 (20313) covalent geometry : angle 0.51026 (27500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 2.151 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6664 (tttt) cc_final: 0.5805 (tptp) REVERT: A 221 LYS cc_start: 0.8401 (ptmt) cc_final: 0.7089 (mmtt) REVERT: A 223 TRP cc_start: 0.7487 (t-100) cc_final: 0.6735 (m100) REVERT: A 289 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7553 (mp0) REVERT: A 352 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: A 353 LYS cc_start: 0.8372 (tptt) cc_final: 0.7973 (tppp) REVERT: A 358 GLU cc_start: 0.8277 (tt0) cc_final: 0.7391 (mt-10) REVERT: A 384 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: A 392 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7413 (ttp-170) REVERT: A 495 GLU cc_start: 0.7863 (pt0) cc_final: 0.7551 (pt0) REVERT: A 529 ILE cc_start: 0.5110 (OUTLIER) cc_final: 0.4418 (mm) REVERT: A 530 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6604 (mt0) REVERT: A 549 PHE cc_start: 0.8122 (m-10) cc_final: 0.6709 (t80) REVERT: A 609 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 640 MET cc_start: 0.8776 (ttp) cc_final: 0.8522 (tmm) REVERT: A 650 ASN cc_start: 0.7845 (m-40) cc_final: 0.7162 (p0) REVERT: A 690 LYS cc_start: 0.7849 (tttt) cc_final: 0.6844 (ttpp) REVERT: B 123 LYS cc_start: 0.6655 (tttt) cc_final: 0.5799 (tptp) REVERT: B 223 TRP cc_start: 0.7478 (t-100) cc_final: 0.6733 (m100) REVERT: B 266 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6956 (pp) REVERT: B 289 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7554 (mp0) REVERT: B 352 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: B 353 LYS cc_start: 0.8383 (tptt) cc_final: 0.7988 (tppp) REVERT: B 358 GLU cc_start: 0.8275 (tt0) cc_final: 0.7387 (mt-10) REVERT: B 384 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: B 392 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7417 (ttp-170) REVERT: B 495 GLU cc_start: 0.7861 (pt0) cc_final: 0.7499 (pt0) REVERT: B 529 ILE cc_start: 0.5125 (OUTLIER) cc_final: 0.4403 (mm) REVERT: B 530 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6569 (mt0) REVERT: B 549 PHE cc_start: 0.8125 (m-10) cc_final: 0.6708 (t80) REVERT: B 609 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7659 (mm-30) REVERT: B 647 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: B 650 ASN cc_start: 0.7857 (m-40) cc_final: 0.7167 (p0) REVERT: B 690 LYS cc_start: 0.7844 (tttt) cc_final: 0.6839 (ttpp) REVERT: C 123 LYS cc_start: 0.6641 (tttt) cc_final: 0.5787 (tptp) REVERT: C 223 TRP cc_start: 0.7486 (t-100) cc_final: 0.6739 (m100) REVERT: C 266 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6956 (pp) REVERT: C 289 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7534 (mp0) REVERT: C 352 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: C 353 LYS cc_start: 0.8377 (tptt) cc_final: 0.7979 (tppp) REVERT: C 358 GLU cc_start: 0.8278 (tt0) cc_final: 0.7379 (mt-10) REVERT: C 384 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: C 392 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7414 (ttp-170) REVERT: C 495 GLU cc_start: 0.7872 (pt0) cc_final: 0.7509 (pt0) REVERT: C 529 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4400 (mm) REVERT: C 530 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6557 (mt0) REVERT: C 549 PHE cc_start: 0.8132 (m-10) cc_final: 0.6715 (t80) REVERT: C 609 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7632 (mm-30) REVERT: C 647 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: C 650 ASN cc_start: 0.7855 (m-40) cc_final: 0.7165 (p0) REVERT: C 690 LYS cc_start: 0.7849 (tttt) cc_final: 0.6846 (ttpp) REVERT: D 123 LYS cc_start: 0.6641 (tttt) cc_final: 0.5785 (tptp) REVERT: D 223 TRP cc_start: 0.7484 (t-100) cc_final: 0.6737 (m100) REVERT: D 266 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6960 (pp) REVERT: D 289 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7546 (mp0) REVERT: D 352 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: D 353 LYS cc_start: 0.8368 (tptt) cc_final: 0.7973 (tppp) REVERT: D 358 GLU cc_start: 0.8285 (tt0) cc_final: 0.7391 (mt-10) REVERT: D 384 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: D 392 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7379 (ttp-170) REVERT: D 495 GLU cc_start: 0.7840 (pt0) cc_final: 0.7507 (pt0) REVERT: D 528 MET cc_start: 0.7757 (mtt) cc_final: 0.7537 (mtp) REVERT: D 530 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6604 (mt0) REVERT: D 549 PHE cc_start: 0.8127 (m-10) cc_final: 0.6707 (t80) REVERT: D 609 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7623 (mm-30) REVERT: D 647 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: D 650 ASN cc_start: 0.7854 (m-40) cc_final: 0.7166 (p0) REVERT: D 690 LYS cc_start: 0.7852 (tttt) cc_final: 0.6852 (ttpp) outliers start: 49 outliers final: 19 residues processed: 292 average time/residue: 1.2974 time to fit residues: 428.6914 Evaluate side-chains 292 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 530 GLN Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 0.0980 chunk 185 optimal weight: 0.0040 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124241 restraints weight = 19348.123| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.56 r_work: 0.3269 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20313 Z= 0.097 Angle : 0.431 4.523 27500 Z= 0.228 Chirality : 0.037 0.173 3088 Planarity : 0.004 0.040 3376 Dihedral : 8.754 64.188 2858 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.18 % Allowed : 10.46 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.18), residues: 2394 helix: 2.16 (0.13), residues: 1460 sheet: 0.86 (0.50), residues: 120 loop : 0.80 (0.25), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 333 HIS 0.003 0.001 HIS C 251 PHE 0.012 0.001 PHE A 547 TYR 0.019 0.001 TYR A 525 ARG 0.005 0.000 ARG B 388 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 1104) hydrogen bonds : angle 3.55868 ( 3168) covalent geometry : bond 0.00213 (20313) covalent geometry : angle 0.43055 (27500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 2.396 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6513 (tttt) cc_final: 0.5741 (tptp) REVERT: A 221 LYS cc_start: 0.8240 (ptmt) cc_final: 0.6974 (mmtt) REVERT: A 223 TRP cc_start: 0.7401 (t-100) cc_final: 0.6787 (m100) REVERT: A 289 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7474 (mp0) REVERT: A 331 THR cc_start: 0.8747 (t) cc_final: 0.8498 (m) REVERT: A 352 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: A 353 LYS cc_start: 0.8318 (tptt) cc_final: 0.7908 (tppp) REVERT: A 358 GLU cc_start: 0.8202 (tt0) cc_final: 0.7293 (mt-10) REVERT: A 384 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: A 392 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7308 (ttp-170) REVERT: A 495 GLU cc_start: 0.7760 (pt0) cc_final: 0.7385 (pt0) REVERT: A 530 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6657 (mt0) REVERT: A 549 PHE cc_start: 0.7918 (m-10) cc_final: 0.6600 (t80) REVERT: A 609 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 687 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.7003 (mtm-85) REVERT: A 690 LYS cc_start: 0.7836 (tttt) cc_final: 0.6830 (ttpp) REVERT: B 123 LYS cc_start: 0.6505 (tttt) cc_final: 0.5741 (tptp) REVERT: B 221 LYS cc_start: 0.8218 (ptmt) cc_final: 0.6902 (mmtt) REVERT: B 223 TRP cc_start: 0.7386 (t-100) cc_final: 0.6781 (m100) REVERT: B 289 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7479 (mp0) REVERT: B 331 THR cc_start: 0.8739 (t) cc_final: 0.8493 (m) REVERT: B 352 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: B 353 LYS cc_start: 0.8332 (tptt) cc_final: 0.7926 (tppp) REVERT: B 358 GLU cc_start: 0.8206 (tt0) cc_final: 0.7293 (mt-10) REVERT: B 384 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: B 392 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7314 (ttp-170) REVERT: B 495 GLU cc_start: 0.7729 (pt0) cc_final: 0.7346 (pt0) REVERT: B 530 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6266 (mt0) REVERT: B 549 PHE cc_start: 0.7918 (m-10) cc_final: 0.6596 (t80) REVERT: B 609 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 647 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: B 687 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.6973 (mtm-85) REVERT: B 690 LYS cc_start: 0.7808 (tttt) cc_final: 0.6716 (ttpt) REVERT: C 123 LYS cc_start: 0.6484 (tttt) cc_final: 0.5721 (tptp) REVERT: C 221 LYS cc_start: 0.8227 (ptmt) cc_final: 0.6912 (mmtt) REVERT: C 223 TRP cc_start: 0.7391 (t-100) cc_final: 0.6785 (m100) REVERT: C 289 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7448 (mp0) REVERT: C 331 THR cc_start: 0.8732 (t) cc_final: 0.8477 (m) REVERT: C 352 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: C 353 LYS cc_start: 0.8330 (tptt) cc_final: 0.7919 (tppp) REVERT: C 358 GLU cc_start: 0.8215 (tt0) cc_final: 0.7298 (mt-10) REVERT: C 384 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: C 392 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7320 (ttp-170) REVERT: C 495 GLU cc_start: 0.7740 (pt0) cc_final: 0.7346 (pt0) REVERT: C 530 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6267 (mt0) REVERT: C 549 PHE cc_start: 0.7920 (m-10) cc_final: 0.6597 (t80) REVERT: C 609 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7644 (mm-30) REVERT: C 647 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: C 687 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6995 (mtm-85) REVERT: C 690 LYS cc_start: 0.7814 (tttt) cc_final: 0.6722 (ttpt) REVERT: D 123 LYS cc_start: 0.6499 (tttt) cc_final: 0.5732 (tptp) REVERT: D 221 LYS cc_start: 0.8221 (ptmt) cc_final: 0.6901 (mmtt) REVERT: D 223 TRP cc_start: 0.7394 (t-100) cc_final: 0.6787 (m100) REVERT: D 289 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7469 (mp0) REVERT: D 331 THR cc_start: 0.8738 (t) cc_final: 0.8489 (m) REVERT: D 352 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: D 353 LYS cc_start: 0.8322 (tptt) cc_final: 0.7911 (tppp) REVERT: D 358 GLU cc_start: 0.8222 (tt0) cc_final: 0.7303 (mt-10) REVERT: D 384 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: D 392 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7301 (ttp-170) REVERT: D 495 GLU cc_start: 0.7758 (pt0) cc_final: 0.7401 (pt0) REVERT: D 530 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: D 549 PHE cc_start: 0.7922 (m-10) cc_final: 0.6598 (t80) REVERT: D 609 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7638 (mm-30) REVERT: D 647 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: D 687 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.7009 (mtm-85) REVERT: D 690 LYS cc_start: 0.7824 (tttt) cc_final: 0.6734 (ttpt) outliers start: 25 outliers final: 0 residues processed: 267 average time/residue: 1.3741 time to fit residues: 412.1017 Evaluate side-chains 265 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 530 GLN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 132 optimal weight: 0.0670 chunk 35 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN C 452 GLN D 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124208 restraints weight = 19438.084| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.57 r_work: 0.3208 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20313 Z= 0.101 Angle : 0.435 4.795 27500 Z= 0.230 Chirality : 0.037 0.213 3088 Planarity : 0.004 0.039 3376 Dihedral : 8.596 63.618 2858 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.94 % Allowed : 10.65 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.18), residues: 2394 helix: 2.16 (0.13), residues: 1464 sheet: 1.05 (0.52), residues: 120 loop : 0.87 (0.26), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 333 HIS 0.004 0.001 HIS D 251 PHE 0.011 0.001 PHE A 547 TYR 0.023 0.001 TYR D 525 ARG 0.005 0.000 ARG B 388 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 1104) hydrogen bonds : angle 3.52717 ( 3168) covalent geometry : bond 0.00224 (20313) covalent geometry : angle 0.43475 (27500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17435.76 seconds wall clock time: 300 minutes 36.70 seconds (18036.70 seconds total)