Starting phenix.real_space_refine on Thu Sep 18 19:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3u_44156/09_2025/9b3u_44156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3u_44156/09_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_44156/09_2025/9b3u_44156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3u_44156/09_2025/9b3u_44156.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3u_44156/09_2025/9b3u_44156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3u_44156/09_2025/9b3u_44156.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 6, 'TRP:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1} 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: {'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: 4.58, per 1000 atoms: 0.23 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: 1.63 Conformation dependent library (CDL) restraints added in 801.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.64 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: 3.49 Time building geometry restraints manager: 2.19 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 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 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 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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.330 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.020 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:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG B 328 TYR 0.098 0.016 TYR C 403 PHE 0.047 0.012 PHE C 198 TRP 0.136 0.028 TRP A 386 HIS 0.011 0.002 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.01217 (20313) covalent geometry : angle 1.72567 (27500) hydrogen bonds : bond 0.14773 ( 1104) hydrogen bonds : angle 6.14075 ( 3168) *********************** 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 : 0.793 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: 0.7515 time to fit residues: 323.2989 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 : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 683 HIS C 156 GLN C 186 ASN C 191 HIS C 203 GLN C 222 GLN 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 = 0.3875 r_free = 0.3875 target = 0.164447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126769 restraints weight = 19391.708| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.54 r_work: 0.3231 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20313 Z= 0.124 Angle : 0.512 6.860 27500 Z= 0.274 Chirality : 0.040 0.141 3088 Planarity : 0.004 0.035 3376 Dihedral : 10.270 99.436 2858 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.18), residues: 2394 helix: 1.43 (0.13), residues: 1484 sheet: 0.45 (0.50), residues: 120 loop : 0.75 (0.26), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 339 TYR 0.010 0.002 TYR A 343 PHE 0.013 0.001 PHE A 319 TRP 0.012 0.001 TRP C 333 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00281 (20313) covalent geometry : angle 0.51241 (27500) hydrogen bonds : bond 0.03651 ( 1104) hydrogen bonds : angle 3.93432 ( 3168) *********************** 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 330 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 306 time to evaluate : 0.852 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.6910 (tttt) cc_final: 0.6332 (tptt) REVERT: A 221 LYS cc_start: 0.8120 (pttt) cc_final: 0.7209 (mmtt) REVERT: A 223 TRP cc_start: 0.7586 (t-100) cc_final: 0.6613 (m100) REVERT: A 235 GLN cc_start: 0.7294 (tt0) cc_final: 0.7079 (tt0) REVERT: A 289 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 331 THR cc_start: 0.8676 (t) cc_final: 0.8412 (m) REVERT: A 352 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: A 353 LYS cc_start: 0.8410 (tptt) cc_final: 0.8013 (tppp) REVERT: A 358 GLU cc_start: 0.8305 (tt0) cc_final: 0.7469 (mt-10) REVERT: A 392 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7430 (ttp-170) REVERT: A 495 GLU cc_start: 0.7877 (pt0) cc_final: 0.7517 (pt0) REVERT: A 528 MET cc_start: 0.7275 (mtt) cc_final: 0.7022 (mtp) REVERT: A 535 ARG cc_start: 0.7611 (ttp-170) cc_final: 0.7250 (ttp-170) REVERT: A 549 PHE cc_start: 0.8233 (m-80) cc_final: 0.6833 (t80) REVERT: A 690 LYS cc_start: 0.7814 (tttt) cc_final: 0.6919 (ttpt) REVERT: B 123 LYS cc_start: 0.6908 (tttt) cc_final: 0.6329 (tptt) REVERT: B 221 LYS cc_start: 0.8124 (pttt) cc_final: 0.7176 (mmtt) REVERT: B 223 TRP cc_start: 0.7586 (t-100) cc_final: 0.6612 (m100) REVERT: B 235 GLN cc_start: 0.7287 (tt0) cc_final: 0.7068 (tt0) REVERT: B 289 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 331 THR cc_start: 0.8672 (t) cc_final: 0.8411 (m) REVERT: B 352 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: B 353 LYS cc_start: 0.8432 (tptt) cc_final: 0.8037 (tppp) REVERT: B 358 GLU cc_start: 0.8288 (tt0) cc_final: 0.7461 (mt-10) REVERT: B 495 GLU cc_start: 0.7853 (pt0) cc_final: 0.7484 (pt0) REVERT: B 528 MET cc_start: 0.7287 (mtt) cc_final: 0.7036 (mtp) REVERT: B 535 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7266 (ttp-170) REVERT: B 549 PHE cc_start: 0.8220 (m-80) cc_final: 0.6836 (t80) REVERT: B 690 LYS cc_start: 0.7765 (tttt) cc_final: 0.6871 (ttpt) REVERT: C 123 LYS cc_start: 0.6898 (tttt) cc_final: 0.6319 (tptt) REVERT: C 221 LYS cc_start: 0.8123 (pttt) cc_final: 0.7180 (mmtt) REVERT: C 223 TRP cc_start: 0.7592 (t-100) cc_final: 0.6621 (m100) REVERT: C 235 GLN cc_start: 0.7284 (tt0) cc_final: 0.7070 (tt0) REVERT: C 289 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7525 (mm-30) REVERT: C 331 THR cc_start: 0.8682 (t) cc_final: 0.8408 (m) REVERT: C 352 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7136 (pm20) REVERT: C 353 LYS cc_start: 0.8418 (tptt) cc_final: 0.8019 (tppp) REVERT: C 358 GLU cc_start: 0.8300 (tt0) cc_final: 0.7461 (mt-10) REVERT: C 495 GLU cc_start: 0.7861 (pt0) cc_final: 0.7494 (pt0) REVERT: C 528 MET cc_start: 0.7285 (mtt) cc_final: 0.7033 (mtp) REVERT: C 535 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7286 (ttp-170) REVERT: C 549 PHE cc_start: 0.8219 (m-80) cc_final: 0.6831 (t80) REVERT: C 690 LYS cc_start: 0.7766 (tttt) cc_final: 0.6874 (ttpt) REVERT: D 123 LYS cc_start: 0.6912 (tttt) cc_final: 0.6331 (tptt) REVERT: D 221 LYS cc_start: 0.8124 (pttt) cc_final: 0.7178 (mmtt) REVERT: D 223 TRP cc_start: 0.7589 (t-100) cc_final: 0.6625 (m100) REVERT: D 235 GLN cc_start: 0.7288 (tt0) cc_final: 0.7074 (tt0) REVERT: D 289 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7534 (mm-30) REVERT: D 331 THR cc_start: 0.8676 (t) cc_final: 0.8427 (m) REVERT: D 352 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7136 (pm20) REVERT: D 353 LYS cc_start: 0.8423 (tptt) cc_final: 0.8028 (tppp) REVERT: D 358 GLU cc_start: 0.8282 (tt0) cc_final: 0.7458 (mt-10) REVERT: D 380 LYS cc_start: 0.8016 (tttt) cc_final: 0.7816 (tttp) REVERT: D 495 GLU cc_start: 0.7830 (pt0) cc_final: 0.7454 (pt0) REVERT: D 528 MET cc_start: 0.7284 (mtt) cc_final: 0.7036 (mtp) REVERT: D 535 ARG cc_start: 0.7607 (ttp-170) cc_final: 0.7268 (ttp-170) REVERT: D 549 PHE cc_start: 0.8216 (m-80) cc_final: 0.6825 (t80) REVERT: D 690 LYS cc_start: 0.7768 (tttt) cc_final: 0.6876 (ttpt) outliers start: 24 outliers final: 8 residues processed: 318 average time/residue: 0.7227 time to fit residues: 256.0819 Evaluate side-chains 267 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 255 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 103 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 156 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.161673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123648 restraints weight = 19606.195| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.53 r_work: 0.3239 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20313 Z= 0.138 Angle : 0.494 7.045 27500 Z= 0.264 Chirality : 0.039 0.120 3088 Planarity : 0.004 0.038 3376 Dihedral : 9.926 90.640 2858 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.65 % Allowed : 7.92 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.18), residues: 2394 helix: 1.79 (0.13), residues: 1468 sheet: 0.60 (0.51), residues: 120 loop : 0.79 (0.25), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 193 TYR 0.011 0.002 TYR A 228 PHE 0.013 0.001 PHE D 319 TRP 0.013 0.001 TRP D 333 HIS 0.006 0.001 HIS A 651 Details of bonding type rmsd covalent geometry : bond 0.00319 (20313) covalent geometry : angle 0.49429 (27500) hydrogen bonds : bond 0.03819 ( 1104) hydrogen bonds : angle 3.76405 ( 3168) *********************** 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 287 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.854 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6870 (tttt) cc_final: 0.6470 (tptp) REVERT: A 221 LYS cc_start: 0.7995 (pttt) cc_final: 0.6832 (mmtt) REVERT: A 223 TRP cc_start: 0.7473 (t-100) cc_final: 0.6598 (m100) REVERT: A 289 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7527 (mp0) REVERT: A 331 THR cc_start: 0.8751 (t) cc_final: 0.8443 (m) REVERT: A 352 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: A 353 LYS cc_start: 0.8295 (tptt) cc_final: 0.7871 (tppp) REVERT: A 358 GLU cc_start: 0.8205 (tt0) cc_final: 0.7282 (mt-10) REVERT: A 495 GLU cc_start: 0.7772 (pt0) cc_final: 0.7443 (pt0) REVERT: A 528 MET cc_start: 0.7360 (mtt) cc_final: 0.7127 (mtp) REVERT: A 535 ARG cc_start: 0.7612 (ttp-170) cc_final: 0.7091 (ttp-170) REVERT: A 549 PHE cc_start: 0.8090 (m-80) cc_final: 0.6602 (t80) REVERT: A 609 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 687 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.6943 (mtm-85) REVERT: A 690 LYS cc_start: 0.7727 (tttt) cc_final: 0.6777 (ttpt) REVERT: B 123 LYS cc_start: 0.6855 (tttt) cc_final: 0.6457 (tptp) REVERT: B 221 LYS cc_start: 0.7990 (pttt) cc_final: 0.6825 (mmtt) REVERT: B 223 TRP cc_start: 0.7471 (t-100) cc_final: 0.6600 (m100) REVERT: B 289 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7522 (mp0) REVERT: B 331 THR cc_start: 0.8748 (t) cc_final: 0.8440 (m) REVERT: B 352 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: B 353 LYS cc_start: 0.8305 (tptt) cc_final: 0.7886 (tppp) REVERT: B 358 GLU cc_start: 0.8192 (tt0) cc_final: 0.7279 (mt-10) REVERT: B 495 GLU cc_start: 0.7786 (pt0) cc_final: 0.7418 (pt0) REVERT: B 528 MET cc_start: 0.7366 (mtt) cc_final: 0.7131 (mtp) REVERT: B 549 PHE cc_start: 0.8097 (m-80) cc_final: 0.6628 (t80) REVERT: B 690 LYS cc_start: 0.7790 (tttt) cc_final: 0.6823 (ttpt) REVERT: C 123 LYS cc_start: 0.6843 (tttt) cc_final: 0.6446 (tptp) REVERT: C 221 LYS cc_start: 0.7990 (pttt) cc_final: 0.6828 (mmtt) REVERT: C 223 TRP cc_start: 0.7473 (t-100) cc_final: 0.6599 (m100) REVERT: C 289 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7525 (mp0) REVERT: C 331 THR cc_start: 0.8743 (t) cc_final: 0.8439 (m) REVERT: C 352 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: C 353 LYS cc_start: 0.8293 (tptt) cc_final: 0.7870 (tppp) REVERT: C 358 GLU cc_start: 0.8205 (tt0) cc_final: 0.7275 (mt-10) REVERT: C 495 GLU cc_start: 0.7793 (pt0) cc_final: 0.7421 (pt0) REVERT: C 528 MET cc_start: 0.7359 (mtt) cc_final: 0.7124 (mtp) REVERT: C 549 PHE cc_start: 0.8096 (m-80) cc_final: 0.6619 (t80) REVERT: C 690 LYS cc_start: 0.7793 (tttt) cc_final: 0.6828 (ttpt) REVERT: D 123 LYS cc_start: 0.6863 (tttt) cc_final: 0.6463 (tptp) REVERT: D 221 LYS cc_start: 0.7991 (pttt) cc_final: 0.6826 (mmtt) REVERT: D 223 TRP cc_start: 0.7479 (t-100) cc_final: 0.6611 (m100) REVERT: D 289 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7519 (mp0) REVERT: D 331 THR cc_start: 0.8741 (t) cc_final: 0.8448 (m) REVERT: D 352 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: D 353 LYS cc_start: 0.8300 (tptt) cc_final: 0.7880 (tppp) REVERT: D 358 GLU cc_start: 0.8194 (tt0) cc_final: 0.7273 (mt-10) REVERT: D 495 GLU cc_start: 0.7771 (pt0) cc_final: 0.7412 (pt0) REVERT: D 528 MET cc_start: 0.7342 (mtt) cc_final: 0.7111 (mtp) REVERT: D 549 PHE cc_start: 0.8099 (m-80) cc_final: 0.6629 (t80) REVERT: D 690 LYS cc_start: 0.7795 (tttt) cc_final: 0.6834 (ttpt) outliers start: 35 outliers final: 7 residues processed: 274 average time/residue: 0.6944 time to fit residues: 213.1582 Evaluate side-chains 243 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 232 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 494 THR 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 C residue 88 VAL Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 494 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 169 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 164 optimal weight: 0.5980 chunk 176 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 452 GLN B 186 ASN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125193 restraints weight = 19537.363| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.62 r_work: 0.3249 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2833 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 : 0.429 5.347 27500 Z= 0.230 Chirality : 0.037 0.109 3088 Planarity : 0.004 0.038 3376 Dihedral : 9.181 76.722 2858 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.46 % Allowed : 9.52 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.18), residues: 2394 helix: 1.95 (0.14), residues: 1482 sheet: 0.54 (0.51), residues: 120 loop : 0.97 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.009 0.001 TYR A 228 PHE 0.011 0.001 PHE A 547 TRP 0.013 0.001 TRP A 333 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00224 (20313) covalent geometry : angle 0.42922 (27500) hydrogen bonds : bond 0.03261 ( 1104) hydrogen bonds : angle 3.57512 ( 3168) *********************** 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 287 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.883 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6793 (tttt) cc_final: 0.6327 (tptp) REVERT: A 221 LYS cc_start: 0.7934 (pttt) cc_final: 0.6784 (mmtt) REVERT: A 223 TRP cc_start: 0.7497 (t-100) cc_final: 0.6689 (m100) REVERT: A 289 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7551 (mp0) REVERT: A 331 THR cc_start: 0.8748 (t) cc_final: 0.8480 (m) REVERT: A 352 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: A 353 LYS cc_start: 0.8326 (tptt) cc_final: 0.7913 (tppp) REVERT: A 358 GLU cc_start: 0.8265 (tt0) cc_final: 0.7954 (tt0) REVERT: A 495 GLU cc_start: 0.7778 (pt0) cc_final: 0.7399 (pt0) REVERT: A 528 MET cc_start: 0.7360 (mtt) cc_final: 0.7120 (mtp) REVERT: A 549 PHE cc_start: 0.7991 (m-80) cc_final: 0.6645 (t80) REVERT: A 609 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 687 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.6958 (mtm-85) REVERT: A 690 LYS cc_start: 0.7844 (tttt) cc_final: 0.6899 (ttpt) REVERT: B 123 LYS cc_start: 0.6778 (tttt) cc_final: 0.6313 (tptp) REVERT: B 221 LYS cc_start: 0.7932 (pttt) cc_final: 0.6779 (mmtt) REVERT: B 223 TRP cc_start: 0.7491 (t-100) cc_final: 0.6690 (m100) REVERT: B 289 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7557 (mp0) REVERT: B 331 THR cc_start: 0.8737 (t) cc_final: 0.8500 (m) REVERT: B 352 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: B 353 LYS cc_start: 0.8344 (tptt) cc_final: 0.7928 (tppp) REVERT: B 358 GLU cc_start: 0.8253 (tt0) cc_final: 0.7348 (mt-10) REVERT: B 495 GLU cc_start: 0.7741 (pt0) cc_final: 0.7388 (pt0) REVERT: B 528 MET cc_start: 0.7371 (mtt) cc_final: 0.7133 (mtp) REVERT: B 549 PHE cc_start: 0.7993 (m-80) cc_final: 0.6667 (t80) REVERT: B 609 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 687 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.7040 (mtm-85) REVERT: B 690 LYS cc_start: 0.7785 (tttt) cc_final: 0.6839 (ttpt) REVERT: B 706 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7996 (ttm-80) REVERT: C 123 LYS cc_start: 0.6759 (tttt) cc_final: 0.6294 (tptp) REVERT: C 221 LYS cc_start: 0.7933 (pttt) cc_final: 0.6785 (mmtt) REVERT: C 223 TRP cc_start: 0.7488 (t-100) cc_final: 0.6692 (m100) REVERT: C 289 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7550 (mp0) REVERT: C 331 THR cc_start: 0.8738 (t) cc_final: 0.8486 (m) REVERT: C 352 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: C 353 LYS cc_start: 0.8341 (tptt) cc_final: 0.7923 (tppp) REVERT: C 358 GLU cc_start: 0.8245 (tt0) cc_final: 0.7336 (mt-10) REVERT: C 495 GLU cc_start: 0.7749 (pt0) cc_final: 0.7395 (pt0) REVERT: C 528 MET cc_start: 0.7361 (mtt) cc_final: 0.7119 (mtp) REVERT: C 549 PHE cc_start: 0.7996 (m-80) cc_final: 0.6669 (t80) REVERT: C 609 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7693 (mm-30) REVERT: C 687 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7049 (mtm-85) REVERT: C 690 LYS cc_start: 0.7784 (tttt) cc_final: 0.6840 (ttpt) REVERT: C 706 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7996 (ttm-80) REVERT: D 123 LYS cc_start: 0.6791 (tttt) cc_final: 0.6324 (tptp) REVERT: D 221 LYS cc_start: 0.7933 (pttt) cc_final: 0.6781 (mmtt) REVERT: D 223 TRP cc_start: 0.7497 (t-100) cc_final: 0.6705 (m100) REVERT: D 289 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7558 (mp0) REVERT: D 331 THR cc_start: 0.8737 (t) cc_final: 0.8496 (m) REVERT: D 352 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: D 353 LYS cc_start: 0.8340 (tptt) cc_final: 0.7923 (tppp) REVERT: D 358 GLU cc_start: 0.8257 (tt0) cc_final: 0.7353 (mt-10) REVERT: D 495 GLU cc_start: 0.7717 (pt0) cc_final: 0.7327 (pt0) REVERT: D 528 MET cc_start: 0.7358 (mtt) cc_final: 0.7132 (mtp) REVERT: D 549 PHE cc_start: 0.7999 (m-80) cc_final: 0.6672 (t80) REVERT: D 609 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 687 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.7038 (mtm-85) REVERT: D 690 LYS cc_start: 0.7789 (tttt) cc_final: 0.6845 (ttpt) REVERT: D 706 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.7976 (ttm-80) outliers start: 31 outliers final: 7 residues processed: 275 average time/residue: 0.7207 time to fit residues: 221.7273 Evaluate side-chains 244 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 233 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 494 THR 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 C residue 88 VAL Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 494 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 173 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124323 restraints weight = 19398.149| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.55 r_work: 0.3241 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20313 Z= 0.109 Angle : 0.434 5.400 27500 Z= 0.232 Chirality : 0.037 0.113 3088 Planarity : 0.004 0.039 3376 Dihedral : 8.839 66.184 2858 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.65 % Allowed : 9.43 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.18), residues: 2394 helix: 2.07 (0.14), residues: 1464 sheet: 0.67 (0.51), residues: 120 loop : 0.87 (0.25), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 339 TYR 0.010 0.001 TYR A 228 PHE 0.010 0.001 PHE A 467 TRP 0.013 0.001 TRP A 333 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00246 (20313) covalent geometry : angle 0.43355 (27500) hydrogen bonds : bond 0.03358 ( 1104) hydrogen bonds : angle 3.52265 ( 3168) *********************** 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 277 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.656 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6780 (tttt) cc_final: 0.5992 (tptp) REVERT: A 221 LYS cc_start: 0.7943 (pttt) cc_final: 0.6779 (mmtt) REVERT: A 223 TRP cc_start: 0.7494 (t-100) cc_final: 0.6776 (m100) REVERT: A 289 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7537 (mp0) REVERT: A 331 THR cc_start: 0.8778 (t) cc_final: 0.8490 (m) REVERT: A 352 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: A 353 LYS cc_start: 0.8299 (tptt) cc_final: 0.7897 (tppp) REVERT: A 358 GLU cc_start: 0.8246 (tt0) cc_final: 0.7940 (tt0) REVERT: A 495 GLU cc_start: 0.7740 (pt0) cc_final: 0.7366 (pt0) REVERT: A 535 ARG cc_start: 0.7607 (ttp-170) cc_final: 0.7376 (tmm160) REVERT: A 549 PHE cc_start: 0.7985 (m-10) cc_final: 0.6639 (t80) REVERT: A 609 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 687 ARG cc_start: 0.7168 (mtm-85) cc_final: 0.6883 (mtm-85) REVERT: A 690 LYS cc_start: 0.7852 (tttt) cc_final: 0.6866 (ttpt) REVERT: B 123 LYS cc_start: 0.6761 (tttt) cc_final: 0.5972 (tptp) REVERT: B 221 LYS cc_start: 0.7938 (pttt) cc_final: 0.6770 (mmtt) REVERT: B 223 TRP cc_start: 0.7483 (t-100) cc_final: 0.6759 (m100) REVERT: B 289 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7529 (mp0) REVERT: B 331 THR cc_start: 0.8744 (t) cc_final: 0.8508 (m) REVERT: B 352 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: B 353 LYS cc_start: 0.8313 (tptt) cc_final: 0.7913 (tppp) REVERT: B 358 GLU cc_start: 0.8235 (tt0) cc_final: 0.7929 (tt0) REVERT: B 495 GLU cc_start: 0.7719 (pt0) cc_final: 0.7391 (pt0) REVERT: B 549 PHE cc_start: 0.7986 (m-10) cc_final: 0.6642 (t80) REVERT: B 609 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 687 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.7007 (mtm-85) REVERT: B 690 LYS cc_start: 0.7820 (tttt) cc_final: 0.6823 (ttpt) REVERT: C 123 LYS cc_start: 0.6750 (tttt) cc_final: 0.5961 (tptp) REVERT: C 221 LYS cc_start: 0.7941 (pttt) cc_final: 0.6774 (mmtt) REVERT: C 223 TRP cc_start: 0.7475 (t-100) cc_final: 0.6760 (m100) REVERT: C 289 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7534 (mp0) REVERT: C 331 THR cc_start: 0.8744 (t) cc_final: 0.8497 (m) REVERT: C 352 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: C 353 LYS cc_start: 0.8309 (tptt) cc_final: 0.7905 (tppp) REVERT: C 358 GLU cc_start: 0.8242 (tt0) cc_final: 0.7935 (tt0) REVERT: C 495 GLU cc_start: 0.7725 (pt0) cc_final: 0.7397 (pt0) REVERT: C 549 PHE cc_start: 0.7990 (m-10) cc_final: 0.6651 (t80) REVERT: C 609 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7634 (mm-30) REVERT: C 687 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.7013 (mtm-85) REVERT: C 690 LYS cc_start: 0.7822 (tttt) cc_final: 0.6829 (ttpt) REVERT: D 123 LYS cc_start: 0.6756 (tttt) cc_final: 0.5966 (tptp) REVERT: D 221 LYS cc_start: 0.7933 (pttt) cc_final: 0.6767 (mmtt) REVERT: D 223 TRP cc_start: 0.7486 (t-100) cc_final: 0.6775 (m100) REVERT: D 289 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7531 (mp0) REVERT: D 331 THR cc_start: 0.8747 (t) cc_final: 0.8514 (m) REVERT: D 352 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6829 (pm20) REVERT: D 353 LYS cc_start: 0.8309 (tptt) cc_final: 0.7907 (tppp) REVERT: D 358 GLU cc_start: 0.8236 (tt0) cc_final: 0.7931 (tt0) REVERT: D 495 GLU cc_start: 0.7721 (pt0) cc_final: 0.7353 (pt0) REVERT: D 528 MET cc_start: 0.7376 (mtt) cc_final: 0.7156 (mtp) REVERT: D 549 PHE cc_start: 0.7994 (m-10) cc_final: 0.6652 (t80) REVERT: D 609 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7621 (mm-30) REVERT: D 687 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6935 (mtm-85) REVERT: D 690 LYS cc_start: 0.7827 (tttt) cc_final: 0.6836 (ttpt) outliers start: 35 outliers final: 11 residues processed: 269 average time/residue: 0.6350 time to fit residues: 192.2927 Evaluate side-chains 246 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 131 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.164048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124948 restraints weight = 19358.080| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.57 r_work: 0.3281 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3091 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= 0.103 Angle : 0.422 5.019 27500 Z= 0.226 Chirality : 0.037 0.110 3088 Planarity : 0.004 0.039 3376 Dihedral : 8.651 60.434 2858 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.46 % Allowed : 9.85 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.18), residues: 2394 helix: 2.08 (0.14), residues: 1482 sheet: 0.80 (0.51), residues: 120 loop : 0.92 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.014 0.001 TYR B 525 PHE 0.010 0.001 PHE A 467 TRP 0.013 0.001 TRP D 333 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00230 (20313) covalent geometry : angle 0.42176 (27500) hydrogen bonds : bond 0.03234 ( 1104) hydrogen bonds : angle 3.46487 ( 3168) *********************** 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 280 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.818 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6557 (tttt) cc_final: 0.5795 (tptp) REVERT: A 223 TRP cc_start: 0.7468 (t-100) cc_final: 0.6701 (m100) REVERT: A 289 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7445 (mp0) REVERT: A 331 THR cc_start: 0.8716 (t) cc_final: 0.8457 (m) REVERT: A 352 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6762 (pm20) REVERT: A 353 LYS cc_start: 0.8280 (tptt) cc_final: 0.7872 (tppp) REVERT: A 358 GLU cc_start: 0.8195 (tt0) cc_final: 0.7871 (tt0) REVERT: A 495 GLU cc_start: 0.7642 (pt0) cc_final: 0.7276 (pt0) REVERT: A 549 PHE cc_start: 0.7915 (m-10) cc_final: 0.6507 (t80) REVERT: A 609 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 687 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6802 (mtm-85) REVERT: A 690 LYS cc_start: 0.7793 (tttt) cc_final: 0.6779 (ttpt) REVERT: B 123 LYS cc_start: 0.6559 (tttt) cc_final: 0.5791 (tptp) REVERT: B 221 LYS cc_start: 0.7899 (pttt) cc_final: 0.6688 (mmtt) REVERT: B 223 TRP cc_start: 0.7468 (t-100) cc_final: 0.6712 (m100) REVERT: B 289 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7448 (mp0) REVERT: B 331 THR cc_start: 0.8734 (t) cc_final: 0.8486 (m) REVERT: B 352 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: B 353 LYS cc_start: 0.8301 (tptt) cc_final: 0.7891 (tppp) REVERT: B 358 GLU cc_start: 0.8195 (tt0) cc_final: 0.7870 (tt0) REVERT: B 495 GLU cc_start: 0.7672 (pt0) cc_final: 0.7273 (pt0) REVERT: B 535 ARG cc_start: 0.7585 (tmm160) cc_final: 0.7359 (ttp-170) REVERT: B 549 PHE cc_start: 0.7921 (m-10) cc_final: 0.6518 (t80) REVERT: B 609 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 687 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6853 (mtm-85) REVERT: B 690 LYS cc_start: 0.7715 (tttt) cc_final: 0.6699 (ttpt) REVERT: C 123 LYS cc_start: 0.6552 (tttt) cc_final: 0.5784 (tptp) REVERT: C 221 LYS cc_start: 0.7899 (pttt) cc_final: 0.6689 (mmtt) REVERT: C 223 TRP cc_start: 0.7458 (t-100) cc_final: 0.6715 (m100) REVERT: C 289 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7435 (mp0) REVERT: C 331 THR cc_start: 0.8729 (t) cc_final: 0.8467 (m) REVERT: C 352 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: C 353 LYS cc_start: 0.8291 (tptt) cc_final: 0.7880 (tppp) REVERT: C 358 GLU cc_start: 0.8195 (tt0) cc_final: 0.7870 (tt0) REVERT: C 495 GLU cc_start: 0.7680 (pt0) cc_final: 0.7283 (pt0) REVERT: C 535 ARG cc_start: 0.7593 (tmm160) cc_final: 0.7371 (ttp-170) REVERT: C 549 PHE cc_start: 0.7921 (m-10) cc_final: 0.6512 (t80) REVERT: C 609 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 687 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6872 (mtm-85) REVERT: C 690 LYS cc_start: 0.7717 (tttt) cc_final: 0.6701 (ttpt) REVERT: D 123 LYS cc_start: 0.6570 (tttt) cc_final: 0.5797 (tptp) REVERT: D 221 LYS cc_start: 0.7902 (pttt) cc_final: 0.6691 (mmtt) REVERT: D 223 TRP cc_start: 0.7466 (t-100) cc_final: 0.6719 (m100) REVERT: D 289 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7447 (mp0) REVERT: D 331 THR cc_start: 0.8733 (t) cc_final: 0.8491 (m) REVERT: D 352 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: D 353 LYS cc_start: 0.8290 (tptt) cc_final: 0.7882 (tppp) REVERT: D 358 GLU cc_start: 0.8200 (tt0) cc_final: 0.7877 (tt0) REVERT: D 495 GLU cc_start: 0.7675 (pt0) cc_final: 0.7345 (pt0) REVERT: D 528 MET cc_start: 0.7296 (mtt) cc_final: 0.7092 (mtp) REVERT: D 535 ARG cc_start: 0.7578 (tmm160) cc_final: 0.7354 (ttp-170) REVERT: D 549 PHE cc_start: 0.7922 (m-10) cc_final: 0.6513 (t80) REVERT: D 609 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7573 (mm-30) REVERT: D 640 MET cc_start: 0.8746 (ttp) cc_final: 0.8466 (tmm) REVERT: D 687 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6806 (mtm-85) REVERT: D 690 LYS cc_start: 0.7744 (tttt) cc_final: 0.6744 (ttpt) outliers start: 31 outliers final: 8 residues processed: 272 average time/residue: 0.7281 time to fit residues: 220.9517 Evaluate side-chains 245 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 233 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 B residue 88 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL 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 D residue 88 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 356 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 36 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 294 GLN B 294 GLN C 294 GLN D 165 HIS D 294 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120325 restraints weight = 19366.479| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.56 r_work: 0.3217 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20313 Z= 0.189 Angle : 0.530 7.043 27500 Z= 0.279 Chirality : 0.041 0.135 3088 Planarity : 0.004 0.042 3376 Dihedral : 9.856 83.474 2858 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.56 % Allowed : 10.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.18), residues: 2394 helix: 1.86 (0.13), residues: 1464 sheet: 0.65 (0.49), residues: 120 loop : 0.60 (0.25), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 339 TYR 0.026 0.002 TYR B 525 PHE 0.015 0.002 PHE C 394 TRP 0.013 0.001 TRP D 333 HIS 0.006 0.002 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00446 (20313) covalent geometry : angle 0.53039 (27500) hydrogen bonds : bond 0.04108 ( 1104) hydrogen bonds : angle 3.72115 ( 3168) *********************** 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 302 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 0.573 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6676 (tttt) cc_final: 0.5871 (tptp) REVERT: A 221 LYS cc_start: 0.8305 (ptmt) cc_final: 0.7032 (mmtt) REVERT: A 223 TRP cc_start: 0.7439 (t-100) cc_final: 0.6691 (m100) REVERT: A 289 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7521 (mp0) REVERT: A 331 THR cc_start: 0.8847 (t) cc_final: 0.8502 (m) REVERT: A 352 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: A 353 LYS cc_start: 0.8313 (tptt) cc_final: 0.7904 (tppp) REVERT: A 358 GLU cc_start: 0.8258 (tt0) cc_final: 0.7349 (mt-10) REVERT: A 384 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: A 392 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7362 (ttp-170) REVERT: A 495 GLU cc_start: 0.7815 (pt0) cc_final: 0.7466 (pt0) REVERT: A 549 PHE cc_start: 0.8075 (m-10) cc_final: 0.6649 (t80) REVERT: A 609 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 613 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6767 (mt0) REVERT: A 650 ASN cc_start: 0.7825 (m-40) cc_final: 0.7149 (p0) REVERT: A 690 LYS cc_start: 0.7778 (tttt) cc_final: 0.6845 (ttpp) REVERT: B 123 LYS cc_start: 0.6652 (tttt) cc_final: 0.6231 (tptp) REVERT: B 223 TRP cc_start: 0.7457 (t-100) cc_final: 0.6716 (m100) REVERT: B 289 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7524 (mp0) REVERT: B 331 THR cc_start: 0.8848 (t) cc_final: 0.8501 (m) REVERT: B 352 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: B 353 LYS cc_start: 0.8315 (tptt) cc_final: 0.7906 (tppp) REVERT: B 358 GLU cc_start: 0.8251 (tt0) cc_final: 0.7336 (mt-10) REVERT: B 384 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: B 392 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7363 (ttp-170) REVERT: B 495 GLU cc_start: 0.7803 (pt0) cc_final: 0.7419 (pt0) REVERT: B 549 PHE cc_start: 0.8074 (m-10) cc_final: 0.6643 (t80) REVERT: B 609 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 613 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6788 (mt0) REVERT: B 650 ASN cc_start: 0.7799 (m-40) cc_final: 0.7107 (p0) REVERT: B 690 LYS cc_start: 0.7757 (tttt) cc_final: 0.6823 (ttpp) REVERT: C 123 LYS cc_start: 0.6654 (tttt) cc_final: 0.6234 (tptp) REVERT: C 223 TRP cc_start: 0.7457 (t-100) cc_final: 0.6715 (m100) REVERT: C 289 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7495 (mp0) REVERT: C 331 THR cc_start: 0.8849 (t) cc_final: 0.8509 (m) REVERT: C 352 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: C 353 LYS cc_start: 0.8307 (tptt) cc_final: 0.7901 (tppp) REVERT: C 358 GLU cc_start: 0.8246 (tt0) cc_final: 0.7334 (mt-10) REVERT: C 384 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: C 392 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7361 (ttp-170) REVERT: C 495 GLU cc_start: 0.7808 (pt0) cc_final: 0.7424 (pt0) REVERT: C 549 PHE cc_start: 0.8083 (m-10) cc_final: 0.6654 (t80) REVERT: C 609 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7659 (mm-30) REVERT: C 613 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6795 (mt0) REVERT: C 650 ASN cc_start: 0.7803 (m-40) cc_final: 0.7112 (p0) REVERT: C 690 LYS cc_start: 0.7756 (tttt) cc_final: 0.6823 (ttpp) REVERT: D 123 LYS cc_start: 0.6655 (tttt) cc_final: 0.6231 (tptp) REVERT: D 223 TRP cc_start: 0.7458 (t-100) cc_final: 0.6720 (m100) REVERT: D 289 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7507 (mp0) REVERT: D 331 THR cc_start: 0.8847 (t) cc_final: 0.8520 (m) REVERT: D 352 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: D 353 LYS cc_start: 0.8307 (tptt) cc_final: 0.7902 (tppp) REVERT: D 358 GLU cc_start: 0.8245 (tt0) cc_final: 0.7344 (mt-10) REVERT: D 384 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: D 392 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7353 (ttp-170) REVERT: D 495 GLU cc_start: 0.7788 (pt0) cc_final: 0.7453 (pt0) REVERT: D 549 PHE cc_start: 0.8074 (m-10) cc_final: 0.6644 (t80) REVERT: D 609 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 613 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6808 (mt0) REVERT: D 650 ASN cc_start: 0.7818 (m-40) cc_final: 0.7132 (p0) REVERT: D 690 LYS cc_start: 0.7766 (tttt) cc_final: 0.6837 (ttpp) outliers start: 33 outliers final: 12 residues processed: 293 average time/residue: 0.6517 time to fit residues: 215.0502 Evaluate side-chains 281 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 384 GLU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 613 GLN 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 384 GLU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 613 GLN 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 384 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 613 GLN 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 613 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 188 optimal weight: 0.1980 chunk 135 optimal weight: 0.9980 chunk 216 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124065 restraints weight = 19414.246| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.57 r_work: 0.3260 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20313 Z= 0.104 Angle : 0.433 4.824 27500 Z= 0.230 Chirality : 0.037 0.108 3088 Planarity : 0.004 0.039 3376 Dihedral : 9.031 67.984 2858 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.65 % Allowed : 10.37 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.18), residues: 2394 helix: 2.08 (0.13), residues: 1468 sheet: 0.87 (0.50), residues: 120 loop : 0.90 (0.25), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.023 0.001 TYR C 525 PHE 0.011 0.001 PHE A 547 TRP 0.015 0.001 TRP D 333 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00232 (20313) covalent geometry : angle 0.43261 (27500) hydrogen bonds : bond 0.03250 ( 1104) hydrogen bonds : angle 3.53422 ( 3168) *********************** 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 280 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.657 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.6471 (tttt) cc_final: 0.5726 (tptp) REVERT: A 221 LYS cc_start: 0.8162 (ptmt) cc_final: 0.6938 (mmtt) REVERT: A 223 TRP cc_start: 0.7525 (t-100) cc_final: 0.6723 (m100) REVERT: A 289 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7475 (mp0) REVERT: A 331 THR cc_start: 0.8708 (t) cc_final: 0.8456 (m) REVERT: A 352 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: A 353 LYS cc_start: 0.8296 (tptt) cc_final: 0.7874 (tppp) REVERT: A 358 GLU cc_start: 0.8201 (tt0) cc_final: 0.7263 (mt-10) REVERT: A 384 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: A 392 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7236 (ttp-170) REVERT: A 495 GLU cc_start: 0.7728 (pt0) cc_final: 0.7347 (pt0) REVERT: A 549 PHE cc_start: 0.7906 (m-10) cc_final: 0.6536 (t80) REVERT: A 609 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 613 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6752 (mt0) REVERT: A 640 MET cc_start: 0.8729 (ttp) cc_final: 0.8469 (tmm) REVERT: A 687 ARG cc_start: 0.7324 (mtm-85) cc_final: 0.7008 (mtm-85) REVERT: A 690 LYS cc_start: 0.7757 (tttt) cc_final: 0.6824 (ttpp) REVERT: B 123 LYS cc_start: 0.6464 (tttt) cc_final: 0.5718 (tptp) REVERT: B 221 LYS cc_start: 0.8170 (ptmt) cc_final: 0.6956 (mmtt) REVERT: B 223 TRP cc_start: 0.7381 (t-100) cc_final: 0.6714 (m100) REVERT: B 289 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7466 (mp0) REVERT: B 331 THR cc_start: 0.8723 (t) cc_final: 0.8488 (m) REVERT: B 352 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: B 353 LYS cc_start: 0.8306 (tptt) cc_final: 0.7880 (tppp) REVERT: B 358 GLU cc_start: 0.8196 (tt0) cc_final: 0.7264 (mt-10) REVERT: B 392 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7248 (ttp-170) REVERT: B 495 GLU cc_start: 0.7704 (pt0) cc_final: 0.7308 (pt0) REVERT: B 549 PHE cc_start: 0.7909 (m-10) cc_final: 0.6535 (t80) REVERT: B 609 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 613 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6753 (mt0) REVERT: B 640 MET cc_start: 0.8694 (ttp) cc_final: 0.8437 (tmm) REVERT: B 687 ARG cc_start: 0.7332 (mtm-85) cc_final: 0.7022 (mtm-85) REVERT: B 690 LYS cc_start: 0.7733 (tttt) cc_final: 0.6694 (ttpt) REVERT: C 123 LYS cc_start: 0.6444 (tttt) cc_final: 0.5699 (tptp) REVERT: C 221 LYS cc_start: 0.8177 (ptmt) cc_final: 0.6962 (mmtt) REVERT: C 223 TRP cc_start: 0.7380 (t-100) cc_final: 0.6716 (m100) REVERT: C 289 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7447 (mp0) REVERT: C 331 THR cc_start: 0.8716 (t) cc_final: 0.8475 (m) REVERT: C 352 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: C 353 LYS cc_start: 0.8300 (tptt) cc_final: 0.7873 (tppp) REVERT: C 358 GLU cc_start: 0.8207 (tt0) cc_final: 0.7278 (mt-10) REVERT: C 392 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7243 (ttp-170) REVERT: C 495 GLU cc_start: 0.7712 (pt0) cc_final: 0.7316 (pt0) REVERT: C 549 PHE cc_start: 0.7914 (m-10) cc_final: 0.6544 (t80) REVERT: C 609 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7571 (mm-30) REVERT: C 613 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6760 (mt0) REVERT: C 640 MET cc_start: 0.8705 (ttp) cc_final: 0.8456 (tmm) REVERT: C 687 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7036 (mtm-85) REVERT: C 690 LYS cc_start: 0.7738 (tttt) cc_final: 0.6701 (ttpt) REVERT: D 123 LYS cc_start: 0.6457 (tttt) cc_final: 0.5707 (tptp) REVERT: D 221 LYS cc_start: 0.8168 (ptmt) cc_final: 0.6952 (mmtt) REVERT: D 223 TRP cc_start: 0.7391 (t-100) cc_final: 0.6720 (m100) REVERT: D 289 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7461 (mp0) REVERT: D 331 THR cc_start: 0.8725 (t) cc_final: 0.8499 (m) REVERT: D 352 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: D 353 LYS cc_start: 0.8295 (tptt) cc_final: 0.7871 (tppp) REVERT: D 358 GLU cc_start: 0.8202 (tt0) cc_final: 0.7270 (mt-10) REVERT: D 384 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: D 392 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7240 (ttp-170) REVERT: D 495 GLU cc_start: 0.7703 (pt0) cc_final: 0.7291 (pt0) REVERT: D 528 MET cc_start: 0.7356 (mtt) cc_final: 0.7141 (mtp) REVERT: D 549 PHE cc_start: 0.7914 (m-10) cc_final: 0.6542 (t80) REVERT: D 609 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7578 (mm-30) REVERT: D 613 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6777 (mt0) REVERT: D 687 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.7012 (mtm-85) REVERT: D 690 LYS cc_start: 0.7745 (tttt) cc_final: 0.6712 (ttpt) outliers start: 35 outliers final: 12 residues processed: 268 average time/residue: 0.7120 time to fit residues: 212.0823 Evaluate side-chains 259 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 384 GLU Chi-restraints excluded: chain A residue 613 GLN 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 384 GLU Chi-restraints excluded: chain B residue 613 GLN 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 384 GLU Chi-restraints excluded: chain C residue 613 GLN 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 384 GLU Chi-restraints excluded: chain D residue 613 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 149 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 157 optimal weight: 0.0970 chunk 139 optimal weight: 0.7980 chunk 236 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 229 optimal weight: 0.4980 chunk 216 optimal weight: 0.7980 chunk 193 optimal weight: 0.1980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126667 restraints weight = 19231.116| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.57 r_work: 0.3242 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20313 Z= 0.089 Angle : 0.414 4.478 27500 Z= 0.221 Chirality : 0.036 0.110 3088 Planarity : 0.003 0.038 3376 Dihedral : 8.430 59.055 2858 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.51 % Allowed : 10.65 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.18), residues: 2394 helix: 2.30 (0.14), residues: 1461 sheet: 0.89 (0.50), residues: 120 loop : 0.92 (0.25), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 339 TYR 0.017 0.001 TYR C 525 PHE 0.013 0.001 PHE D 540 TRP 0.014 0.001 TRP C 333 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00191 (20313) covalent geometry : angle 0.41366 (27500) hydrogen bonds : bond 0.03018 ( 1104) hydrogen bonds : angle 3.43242 ( 3168) *********************** 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 293 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.571 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6563 (tttt) cc_final: 0.5837 (tptp) REVERT: A 221 LYS cc_start: 0.8085 (ptmt) cc_final: 0.6938 (mmtm) REVERT: A 223 TRP cc_start: 0.7467 (t-100) cc_final: 0.6866 (m100) REVERT: A 289 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7583 (mp0) REVERT: A 331 THR cc_start: 0.8818 (t) cc_final: 0.8559 (m) REVERT: A 352 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: A 353 LYS cc_start: 0.8356 (tptt) cc_final: 0.7967 (tppp) REVERT: A 358 GLU cc_start: 0.8288 (tt0) cc_final: 0.8007 (tt0) REVERT: A 392 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7395 (ttp-170) REVERT: A 495 GLU cc_start: 0.7776 (pt0) cc_final: 0.7486 (pt0) REVERT: A 549 PHE cc_start: 0.7938 (m-10) cc_final: 0.6708 (t80) REVERT: A 609 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7695 (mm-30) REVERT: A 613 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6781 (mt0) REVERT: A 687 ARG cc_start: 0.7378 (mtm-85) cc_final: 0.6995 (mtm-85) REVERT: A 690 LYS cc_start: 0.7818 (tttt) cc_final: 0.6789 (ttpt) REVERT: B 123 LYS cc_start: 0.6538 (tttt) cc_final: 0.5814 (tptp) REVERT: B 221 LYS cc_start: 0.8143 (ptmt) cc_final: 0.6947 (mmtt) REVERT: B 289 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7574 (mp0) REVERT: B 331 THR cc_start: 0.8806 (t) cc_final: 0.8560 (m) REVERT: B 352 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: B 353 LYS cc_start: 0.8371 (tptt) cc_final: 0.7988 (tppp) REVERT: B 358 GLU cc_start: 0.8289 (tt0) cc_final: 0.7965 (tt0) REVERT: B 392 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7405 (ttp-170) REVERT: B 495 GLU cc_start: 0.7789 (pt0) cc_final: 0.7452 (pt0) REVERT: B 549 PHE cc_start: 0.7930 (m-10) cc_final: 0.6696 (t80) REVERT: B 609 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7767 (mm-30) REVERT: B 613 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6787 (mt0) REVERT: B 687 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7027 (mtm-85) REVERT: B 690 LYS cc_start: 0.7785 (tttt) cc_final: 0.6762 (ttpt) REVERT: C 123 LYS cc_start: 0.6527 (tttt) cc_final: 0.5803 (tptp) REVERT: C 221 LYS cc_start: 0.8147 (ptmt) cc_final: 0.6949 (mmtt) REVERT: C 289 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7557 (mp0) REVERT: C 331 THR cc_start: 0.8807 (t) cc_final: 0.8543 (m) REVERT: C 352 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: C 353 LYS cc_start: 0.8371 (tptt) cc_final: 0.7983 (tppp) REVERT: C 358 GLU cc_start: 0.8299 (tt0) cc_final: 0.7980 (tt0) REVERT: C 392 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7395 (ttp-170) REVERT: C 495 GLU cc_start: 0.7804 (pt0) cc_final: 0.7467 (pt0) REVERT: C 549 PHE cc_start: 0.7943 (m-10) cc_final: 0.6707 (t80) REVERT: C 609 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7723 (mm-30) REVERT: C 613 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6787 (mt0) REVERT: C 687 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7038 (mtm-85) REVERT: C 690 LYS cc_start: 0.7787 (tttt) cc_final: 0.6765 (ttpt) REVERT: D 123 LYS cc_start: 0.6544 (tttt) cc_final: 0.5816 (tptp) REVERT: D 221 LYS cc_start: 0.8142 (ptmt) cc_final: 0.6945 (mmtt) REVERT: D 289 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7580 (mp0) REVERT: D 331 THR cc_start: 0.8809 (t) cc_final: 0.8565 (m) REVERT: D 352 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: D 353 LYS cc_start: 0.8370 (tptt) cc_final: 0.7985 (tppp) REVERT: D 358 GLU cc_start: 0.8300 (tt0) cc_final: 0.8017 (tt0) REVERT: D 392 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7398 (ttp-170) REVERT: D 495 GLU cc_start: 0.7758 (pt0) cc_final: 0.7421 (pt0) REVERT: D 549 PHE cc_start: 0.7947 (m-10) cc_final: 0.6698 (t80) REVERT: D 609 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 613 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6794 (mt0) REVERT: D 687 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.7001 (mtm-85) REVERT: D 690 LYS cc_start: 0.7798 (tttt) cc_final: 0.6777 (ttpt) outliers start: 32 outliers final: 7 residues processed: 277 average time/residue: 0.7109 time to fit residues: 219.0432 Evaluate side-chains 253 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 613 GLN 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 613 GLN 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 613 GLN 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 613 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 106 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 201 optimal weight: 0.0570 chunk 103 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.164618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125423 restraints weight = 19391.355| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.58 r_work: 0.3224 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20313 Z= 0.100 Angle : 0.434 5.052 27500 Z= 0.231 Chirality : 0.037 0.116 3088 Planarity : 0.004 0.039 3376 Dihedral : 8.472 60.071 2858 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.80 % Allowed : 11.22 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.18), residues: 2394 helix: 2.23 (0.13), residues: 1482 sheet: 0.85 (0.50), residues: 120 loop : 0.91 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 388 TYR 0.019 0.001 TYR C 525 PHE 0.011 0.001 PHE A 547 TRP 0.013 0.001 TRP C 333 HIS 0.004 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00223 (20313) covalent geometry : angle 0.43369 (27500) hydrogen bonds : bond 0.03183 ( 1104) hydrogen bonds : angle 3.44802 ( 3168) ********************** 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 269 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 0.746 Fit side-chains TARDY: cannot create tardy model for: "ARG A 694 " (corrupted residue). Skipping it. REVERT: A 123 LYS cc_start: 0.6583 (tttt) cc_final: 0.5850 (tptp) REVERT: A 221 LYS cc_start: 0.8104 (ptmt) cc_final: 0.6940 (mmtm) REVERT: A 289 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7596 (mp0) REVERT: A 331 THR cc_start: 0.8804 (t) cc_final: 0.8566 (m) REVERT: A 352 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6954 (pm20) REVERT: A 353 LYS cc_start: 0.8346 (tptt) cc_final: 0.7961 (tppp) REVERT: A 358 GLU cc_start: 0.8273 (tt0) cc_final: 0.7991 (tt0) REVERT: A 392 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7404 (ttp-170) REVERT: A 495 GLU cc_start: 0.7824 (pt0) cc_final: 0.7534 (pt0) REVERT: A 549 PHE cc_start: 0.7958 (m-10) cc_final: 0.6732 (t80) REVERT: A 609 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 687 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7000 (mtm-85) REVERT: A 690 LYS cc_start: 0.7862 (tttt) cc_final: 0.6837 (ttpt) REVERT: B 123 LYS cc_start: 0.6569 (tttt) cc_final: 0.5840 (tptp) REVERT: B 161 PHE cc_start: 0.7674 (m-80) cc_final: 0.6657 (t80) REVERT: B 221 LYS cc_start: 0.8142 (ptmt) cc_final: 0.6940 (mmtm) REVERT: B 289 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7581 (mp0) REVERT: B 331 THR cc_start: 0.8838 (t) cc_final: 0.8566 (m) REVERT: B 352 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: B 353 LYS cc_start: 0.8365 (tptt) cc_final: 0.7984 (tppp) REVERT: B 358 GLU cc_start: 0.8260 (tt0) cc_final: 0.7981 (tt0) REVERT: B 392 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7413 (ttp-170) REVERT: B 495 GLU cc_start: 0.7785 (pt0) cc_final: 0.7478 (pt0) REVERT: B 535 ARG cc_start: 0.7675 (tmm160) cc_final: 0.7356 (ttp-170) REVERT: B 549 PHE cc_start: 0.7957 (m-10) cc_final: 0.6734 (t80) REVERT: B 609 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7773 (mm-30) REVERT: B 687 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7010 (mtm-85) REVERT: B 690 LYS cc_start: 0.7822 (tttt) cc_final: 0.6785 (ttpt) REVERT: C 123 LYS cc_start: 0.6551 (tttt) cc_final: 0.5821 (tptp) REVERT: C 161 PHE cc_start: 0.7667 (m-80) cc_final: 0.6653 (t80) REVERT: C 221 LYS cc_start: 0.8171 (ptmt) cc_final: 0.6978 (mmtt) REVERT: C 289 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7580 (mp0) REVERT: C 331 THR cc_start: 0.8835 (t) cc_final: 0.8546 (m) REVERT: C 352 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: C 353 LYS cc_start: 0.8373 (tptt) cc_final: 0.7984 (tppp) REVERT: C 358 GLU cc_start: 0.8282 (tt0) cc_final: 0.8000 (tt0) REVERT: C 392 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7409 (ttp-170) REVERT: C 495 GLU cc_start: 0.7796 (pt0) cc_final: 0.7488 (pt0) REVERT: C 535 ARG cc_start: 0.7685 (tmm160) cc_final: 0.7370 (ttp-170) REVERT: C 549 PHE cc_start: 0.7956 (m-10) cc_final: 0.6736 (t80) REVERT: C 609 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7703 (mm-30) REVERT: C 687 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.7019 (mtm-85) REVERT: C 690 LYS cc_start: 0.7835 (tttt) cc_final: 0.6805 (ttpt) REVERT: D 123 LYS cc_start: 0.6567 (tttt) cc_final: 0.5834 (tptp) REVERT: D 161 PHE cc_start: 0.7670 (m-80) cc_final: 0.6644 (t80) REVERT: D 221 LYS cc_start: 0.8144 (ptmt) cc_final: 0.6938 (mmtm) REVERT: D 289 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7587 (mp0) REVERT: D 331 THR cc_start: 0.8818 (t) cc_final: 0.8559 (m) REVERT: D 352 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: D 353 LYS cc_start: 0.8381 (tptt) cc_final: 0.8006 (tppp) REVERT: D 358 GLU cc_start: 0.8281 (tt0) cc_final: 0.8001 (tt0) REVERT: D 392 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7405 (ttp-170) REVERT: D 495 GLU cc_start: 0.7771 (pt0) cc_final: 0.7444 (pt0) REVERT: D 535 ARG cc_start: 0.7674 (tmm160) cc_final: 0.7363 (ttp-170) REVERT: D 549 PHE cc_start: 0.7970 (m-10) cc_final: 0.6733 (t80) REVERT: D 609 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7689 (mm-30) REVERT: D 613 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: D 687 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.7014 (mtm-85) REVERT: D 690 LYS cc_start: 0.7842 (tttt) cc_final: 0.6812 (ttpt) outliers start: 17 outliers final: 11 residues processed: 264 average time/residue: 0.7358 time to fit residues: 215.7791 Evaluate side-chains 256 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 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 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 613 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 209 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 121 optimal weight: 0.0370 chunk 157 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 204 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125309 restraints weight = 19370.526| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.58 r_work: 0.3224 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20313 Z= 0.102 Angle : 0.430 4.624 27500 Z= 0.229 Chirality : 0.037 0.109 3088 Planarity : 0.004 0.039 3376 Dihedral : 8.465 60.531 2858 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.80 % Allowed : 11.22 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.18), residues: 2394 helix: 2.24 (0.13), residues: 1481 sheet: 0.82 (0.50), residues: 120 loop : 0.92 (0.26), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 388 TYR 0.017 0.001 TYR D 525 PHE 0.011 0.001 PHE A 547 TRP 0.013 0.001 TRP C 333 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00226 (20313) covalent geometry : angle 0.42984 (27500) hydrogen bonds : bond 0.03208 ( 1104) hydrogen bonds : angle 3.45663 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8850.01 seconds wall clock time: 151 minutes 0.71 seconds (9060.71 seconds total)