Starting phenix.real_space_refine on Fri Feb 6 00:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hxq_52489/02_2026/9hxq_52489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hxq_52489/02_2026/9hxq_52489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hxq_52489/02_2026/9hxq_52489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hxq_52489/02_2026/9hxq_52489.map" model { file = "/net/cci-nas-00/data/ceres_data/9hxq_52489/02_2026/9hxq_52489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hxq_52489/02_2026/9hxq_52489.cif" } resolution = 2.8 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= 0.001 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 13420 2.51 5 N 3528 2.21 5 O 3648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20740 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5173 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 650} Chain breaks: 3 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 8, 'GLN:plan1': 8, 'TYR:plan': 1, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 214 Chain: "A" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5173 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 650} Chain breaks: 3 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 8, 'GLN:plan1': 8, 'TYR:plan': 1, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 214 Chain: "C" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5173 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 650} Chain breaks: 3 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 8, 'GLN:plan1': 8, 'TYR:plan': 1, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 214 Chain: "D" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5173 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 650} Chain breaks: 3 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 29, 'ARG:plan': 8, 'GLN:plan1': 8, 'TYR:plan': 1, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 214 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'AES': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'AES': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'AES': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'AES': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.82, per 1000 atoms: 0.23 Number of scatterers: 20740 At special positions: 0 Unit cell: (135.75, 87.75, 132.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 3648 8.00 N 3528 7.00 C 13420 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.0 seconds 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5160 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 40 sheets defined 21.7% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 9 through 22 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.851A pdb=" N GLU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.985A pdb=" N VAL B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.615A pdb=" N GLU B 475 " --> pdb=" O PRO B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 544 through 551 removed outlier: 3.509A pdb=" N ILE B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 575 Processing helix chain 'B' and resid 587 through 600 removed outlier: 3.682A pdb=" N TYR B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 620 removed outlier: 3.531A pdb=" N MET B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 634 removed outlier: 4.364A pdb=" N CYS B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET B 630 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 removed outlier: 3.579A pdb=" N LYS B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 Proline residue: B 661 - end of helix Processing helix chain 'B' and resid 680 through 692 removed outlier: 3.564A pdb=" N MET B 684 " --> pdb=" O PHE B 680 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 686 " --> pdb=" O GLN B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 730 Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.523A pdb=" N ARG A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.851A pdb=" N GLU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.984A pdb=" N VAL A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.615A pdb=" N GLU A 475 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 544 through 551 removed outlier: 3.509A pdb=" N ILE A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 575 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 615 through 620 removed outlier: 3.531A pdb=" N MET A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 removed outlier: 4.364A pdb=" N CYS A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET A 630 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.583A pdb=" N LYS A 654 " --> pdb=" O ALA A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 663 Proline residue: A 661 - end of helix Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.564A pdb=" N MET A 684 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 686 " --> pdb=" O GLN A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 730 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.852A pdb=" N GLU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.985A pdb=" N VAL C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 removed outlier: 3.615A pdb=" N GLU C 475 " --> pdb=" O PRO C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.509A pdb=" N ILE C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 575 Processing helix chain 'C' and resid 587 through 600 Processing helix chain 'C' and resid 615 through 620 removed outlier: 3.532A pdb=" N MET C 620 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 634 removed outlier: 4.364A pdb=" N CYS C 629 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET C 630 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 654 removed outlier: 3.563A pdb=" N LYS C 654 " --> pdb=" O ALA C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 Proline residue: C 661 - end of helix Processing helix chain 'C' and resid 680 through 692 removed outlier: 3.564A pdb=" N MET C 684 " --> pdb=" O PHE C 680 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 686 " --> pdb=" O GLN C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 730 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.851A pdb=" N GLU D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 139' Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 443 through 447 removed outlier: 3.985A pdb=" N VAL D 447 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 removed outlier: 3.615A pdb=" N GLU D 475 " --> pdb=" O PRO D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 544 through 551 removed outlier: 3.509A pdb=" N ILE D 548 " --> pdb=" O GLY D 544 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 575 Processing helix chain 'D' and resid 587 through 600 Processing helix chain 'D' and resid 615 through 620 removed outlier: 3.532A pdb=" N MET D 620 " --> pdb=" O ILE D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 634 removed outlier: 4.364A pdb=" N CYS D 629 " --> pdb=" O ILE D 625 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET D 630 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 654 removed outlier: 3.563A pdb=" N LYS D 654 " --> pdb=" O ALA D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 663 Proline residue: D 661 - end of helix Processing helix chain 'D' and resid 680 through 692 removed outlier: 3.564A pdb=" N MET D 684 " --> pdb=" O PHE D 680 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D 686 " --> pdb=" O GLN D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 730 Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 31 removed outlier: 6.794A pdb=" N GLU B 49 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 29 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS B 47 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU B 31 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR B 45 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.990A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 96 removed outlier: 5.954A pdb=" N GLU B 91 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS B 108 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 93 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 131 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 125 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'B' and resid 244 through 251 removed outlier: 4.341A pdb=" N ALA B 249 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 259 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP B 251 " --> pdb=" O GLY B 257 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY B 257 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.686A pdb=" N ALA B 301 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 315 " --> pdb=" O PRO B 305 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU B 307 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG B 313 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 331 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 375 through 382 Processing sheet with id=AA9, first strand: chain 'B' and resid 409 through 416 removed outlier: 6.876A pdb=" N VAL B 421 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 415 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR B 426 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 435 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER B 451 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N PHE B 437 " --> pdb=" O TRP B 449 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TRP B 449 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 461 through 468 removed outlier: 3.550A pdb=" N GLU B 485 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY B 586 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 606 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 25 through 31 removed outlier: 6.799A pdb=" N GLU A 49 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA A 29 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS A 47 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU A 31 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 45 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 42 " --> pdb=" O HIS A 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.989A pdb=" N ARG A 42 " --> pdb=" O HIS A 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 96 removed outlier: 5.954A pdb=" N GLU A 91 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS A 108 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 93 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 131 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 125 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AB6, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AB7, first strand: chain 'A' and resid 244 through 251 removed outlier: 4.341A pdb=" N ALA A 249 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 259 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP A 251 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY A 257 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.686A pdb=" N ALA A 301 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 315 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU A 307 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG A 313 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 331 " --> pdb=" O VAL A 344 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 375 through 382 Processing sheet with id=AC1, first strand: chain 'A' and resid 409 through 416 removed outlier: 6.877A pdb=" N VAL A 421 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 415 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR A 426 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 435 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER A 451 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N PHE A 437 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N TRP A 449 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 461 through 468 removed outlier: 3.547A pdb=" N GLU A 485 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY A 586 " --> pdb=" O PRO A 506 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 606 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 25 through 31 removed outlier: 6.796A pdb=" N GLU C 49 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA C 29 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS C 47 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU C 31 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR C 45 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.989A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 96 removed outlier: 5.954A pdb=" N GLU C 91 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS C 108 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 93 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 131 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU C 125 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AC7, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AC8, first strand: chain 'C' and resid 244 through 251 removed outlier: 4.341A pdb=" N ALA C 249 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 259 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP C 251 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 257 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 301 through 307 removed outlier: 3.686A pdb=" N ALA C 301 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 315 " --> pdb=" O PRO C 305 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU C 307 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG C 313 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 331 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 375 through 382 Processing sheet with id=AD2, first strand: chain 'C' and resid 409 through 416 removed outlier: 6.876A pdb=" N VAL C 421 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C 415 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR C 426 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 435 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER C 451 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N PHE C 437 " --> pdb=" O TRP C 449 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TRP C 449 " --> pdb=" O PHE C 437 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 461 through 468 removed outlier: 3.547A pdb=" N GLU C 485 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY C 586 " --> pdb=" O PRO C 506 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA C 606 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 25 through 31 removed outlier: 6.796A pdb=" N GLU D 49 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA D 29 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS D 47 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU D 31 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR D 45 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.990A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 96 removed outlier: 5.954A pdb=" N GLU D 91 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS D 108 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 93 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 131 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU D 125 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AD8, first strand: chain 'D' and resid 173 through 174 Processing sheet with id=AD9, first strand: chain 'D' and resid 244 through 251 removed outlier: 4.341A pdb=" N ALA D 249 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 259 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP D 251 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY D 257 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 301 through 307 removed outlier: 3.686A pdb=" N ALA D 301 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 315 " --> pdb=" O PRO D 305 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU D 307 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG D 313 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 331 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 375 through 382 Processing sheet with id=AE3, first strand: chain 'D' and resid 409 through 416 removed outlier: 6.876A pdb=" N VAL D 421 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE D 415 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR D 426 " --> pdb=" O PRO D 430 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL D 435 " --> pdb=" O SER D 451 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER D 451 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N PHE D 437 " --> pdb=" O TRP D 449 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TRP D 449 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 461 through 468 removed outlier: 3.546A pdb=" N GLU D 485 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY D 586 " --> pdb=" O PRO D 506 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D 606 " --> pdb=" O VAL D 581 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6612 1.34 - 1.46: 5045 1.46 - 1.58: 9439 1.58 - 1.70: 0 1.70 - 1.81: 212 Bond restraints: 21308 Sorted by residual: bond pdb=" N ILE B 272 " pdb=" CA ILE B 272 " ideal model delta sigma weight residual 1.456 1.496 -0.040 9.50e-03 1.11e+04 1.73e+01 bond pdb=" C1 AES D 801 " pdb=" S AES D 801 " ideal model delta sigma weight residual 1.747 1.814 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 AES C 801 " pdb=" S AES C 801 " ideal model delta sigma weight residual 1.747 1.813 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 AES A 801 " pdb=" S AES A 801 " ideal model delta sigma weight residual 1.747 1.812 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 AES B 801 " pdb=" S AES B 801 " ideal model delta sigma weight residual 1.747 1.812 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 21303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 28854 2.49 - 4.98: 212 4.98 - 7.47: 12 7.47 - 9.96: 6 9.96 - 12.46: 4 Bond angle restraints: 29088 Sorted by residual: angle pdb=" C ARG B 383 " pdb=" CA ARG B 383 " pdb=" CB ARG B 383 " ideal model delta sigma weight residual 116.54 111.00 5.54 1.15e+00 7.56e-01 2.32e+01 angle pdb=" N SER B 384 " pdb=" CA SER B 384 " pdb=" C SER B 384 " ideal model delta sigma weight residual 112.93 118.23 -5.30 1.12e+00 7.97e-01 2.24e+01 angle pdb=" O1S AES B 801 " pdb=" S AES B 801 " pdb=" O2S AES B 801 " ideal model delta sigma weight residual 121.42 108.96 12.46 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C PHE D 274 " pdb=" CA PHE D 274 " pdb=" CB PHE D 274 " ideal model delta sigma weight residual 111.36 118.13 -6.77 1.63e+00 3.76e-01 1.72e+01 angle pdb=" N ILE B 272 " pdb=" CA ILE B 272 " pdb=" C ILE B 272 " ideal model delta sigma weight residual 113.53 109.48 4.05 9.80e-01 1.04e+00 1.71e+01 ... (remaining 29083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 11464 16.30 - 32.60: 753 32.60 - 48.90: 179 48.90 - 65.20: 75 65.20 - 81.50: 21 Dihedral angle restraints: 12492 sinusoidal: 4476 harmonic: 8016 Sorted by residual: dihedral pdb=" CA ASP C 147 " pdb=" CB ASP C 147 " pdb=" CG ASP C 147 " pdb=" OD1 ASP C 147 " ideal model delta sinusoidal sigma weight residual -30.00 -88.70 58.70 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 147 " pdb=" CB ASP B 147 " pdb=" CG ASP B 147 " pdb=" OD1 ASP B 147 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 147 " pdb=" CB ASP A 147 " pdb=" CG ASP A 147 " pdb=" OD1 ASP A 147 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 12489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2315 0.040 - 0.080: 642 0.080 - 0.120: 289 0.120 - 0.160: 32 0.160 - 0.200: 6 Chirality restraints: 3284 Sorted by residual: chirality pdb=" CA ARG D 383 " pdb=" N ARG D 383 " pdb=" C ARG D 383 " pdb=" CB ARG D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA VAL A 560 " pdb=" N VAL A 560 " pdb=" C VAL A 560 " pdb=" CB VAL A 560 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA VAL D 560 " pdb=" N VAL D 560 " pdb=" C VAL D 560 " pdb=" CB VAL D 560 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 3281 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 383 " -0.244 9.50e-02 1.11e+02 1.10e-01 7.36e+00 pdb=" NE ARG C 383 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 383 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 383 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 383 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 273 " 0.146 9.50e-02 1.11e+02 6.52e-02 2.62e+00 pdb=" NE ARG D 273 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG D 273 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG D 273 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 273 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 382 " 0.007 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C GLN D 382 " -0.026 2.00e-02 2.50e+03 pdb=" O GLN D 382 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG D 383 " 0.009 2.00e-02 2.50e+03 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5297 2.81 - 3.33: 16253 3.33 - 3.85: 32083 3.85 - 4.38: 37744 4.38 - 4.90: 69966 Nonbonded interactions: 161343 Sorted by model distance: nonbonded pdb=" OD2 ASP B 559 " pdb=" CD2 LEU B 592 " model vdw 2.282 3.460 nonbonded pdb=" OD2 ASP A 559 " pdb=" CD2 LEU A 592 " model vdw 2.286 3.460 nonbonded pdb=" OG SER D 370 " pdb=" OD1 ASP D 372 " model vdw 2.355 3.040 nonbonded pdb=" OG SER A 370 " pdb=" OD1 ASP A 372 " model vdw 2.355 3.040 nonbonded pdb=" OG SER C 370 " pdb=" OD1 ASP C 372 " model vdw 2.355 3.040 ... (remaining 161338 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.390 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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 : 0.004 0.232 21312 Z= 0.344 Angle : 0.542 12.455 29088 Z= 0.302 Chirality : 0.044 0.200 3284 Planarity : 0.005 0.110 3708 Dihedral : 12.883 81.497 7332 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.88 % Allowed : 7.28 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.13 (0.16), residues: 2756 helix: 1.86 (0.25), residues: 456 sheet: 0.99 (0.18), residues: 912 loop : -1.20 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 65 TYR 0.006 0.001 TYR C 686 PHE 0.011 0.001 PHE D 70 TRP 0.010 0.001 TRP C 155 HIS 0.002 0.001 HIS B 511 Details of bonding type rmsd covalent geometry : bond 0.00276 (21308) covalent geometry : angle 0.54171 (29088) hydrogen bonds : bond 0.12033 ( 827) hydrogen bonds : angle 5.55864 ( 2445) Misc. bond : bond 0.22089 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.823 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.6145 time to fit residues: 75.4396 Evaluate side-chains 106 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.065635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.054250 restraints weight = 40895.721| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 2.55 r_work: 0.2438 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2315 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 21312 Z= 0.291 Angle : 0.627 8.878 29088 Z= 0.320 Chirality : 0.049 0.141 3284 Planarity : 0.005 0.037 3708 Dihedral : 4.834 56.697 2996 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.07 % Allowed : 7.81 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: -0.07 (0.16), residues: 2756 helix: 1.69 (0.25), residues: 460 sheet: 1.05 (0.17), residues: 868 loop : -1.43 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 383 TYR 0.012 0.002 TYR C 283 PHE 0.026 0.002 PHE A 591 TRP 0.013 0.002 TRP C 155 HIS 0.009 0.002 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00747 (21308) covalent geometry : angle 0.62731 (29088) hydrogen bonds : bond 0.05226 ( 827) hydrogen bonds : angle 4.94675 ( 2445) Misc. bond : bond 0.00631 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.798 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 116 average time/residue: 0.5478 time to fit residues: 74.3529 Evaluate side-chains 105 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 62 optimal weight: 0.0010 chunk 55 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.068322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.056859 restraints weight = 40326.408| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 2.55 r_work: 0.2497 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2374 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21312 Z= 0.106 Angle : 0.484 7.247 29088 Z= 0.246 Chirality : 0.044 0.131 3284 Planarity : 0.004 0.036 3708 Dihedral : 4.008 19.377 2980 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.32 % Allowed : 7.86 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.06 (0.16), residues: 2756 helix: 1.76 (0.25), residues: 460 sheet: 1.14 (0.17), residues: 868 loop : -1.32 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 269 TYR 0.006 0.001 TYR C 283 PHE 0.015 0.001 PHE A 591 TRP 0.010 0.001 TRP A 155 HIS 0.003 0.001 HIS D 325 Details of bonding type rmsd covalent geometry : bond 0.00255 (21308) covalent geometry : angle 0.48417 (29088) hydrogen bonds : bond 0.03440 ( 827) hydrogen bonds : angle 4.60304 ( 2445) Misc. bond : bond 0.00015 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.787 Fit side-chains outliers start: 27 outliers final: 10 residues processed: 115 average time/residue: 0.5844 time to fit residues: 77.7706 Evaluate side-chains 106 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 172 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 220 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.066941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.055462 restraints weight = 40675.460| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 2.55 r_work: 0.2468 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2346 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21312 Z= 0.174 Angle : 0.526 8.525 29088 Z= 0.267 Chirality : 0.046 0.130 3284 Planarity : 0.005 0.037 3708 Dihedral : 4.063 18.699 2976 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.46 % Allowed : 8.25 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.01 (0.16), residues: 2756 helix: 1.71 (0.25), residues: 460 sheet: 1.11 (0.17), residues: 860 loop : -1.35 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 383 TYR 0.008 0.001 TYR B 283 PHE 0.020 0.001 PHE C 591 TRP 0.010 0.001 TRP A 155 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00443 (21308) covalent geometry : angle 0.52640 (29088) hydrogen bonds : bond 0.04109 ( 827) hydrogen bonds : angle 4.64834 ( 2445) Misc. bond : bond 0.00073 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.853 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 118 average time/residue: 0.5380 time to fit residues: 74.4027 Evaluate side-chains 112 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 727 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 225 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.068464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.057032 restraints weight = 40223.976| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 2.54 r_work: 0.2497 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21312 Z= 0.104 Angle : 0.476 7.515 29088 Z= 0.241 Chirality : 0.044 0.128 3284 Planarity : 0.004 0.036 3708 Dihedral : 3.842 17.160 2976 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.07 % Allowed : 8.94 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.14 (0.16), residues: 2756 helix: 1.79 (0.25), residues: 460 sheet: 1.24 (0.17), residues: 856 loop : -1.28 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.006 0.001 TYR B 316 PHE 0.015 0.001 PHE A 591 TRP 0.009 0.001 TRP A 155 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00254 (21308) covalent geometry : angle 0.47572 (29088) hydrogen bonds : bond 0.03246 ( 827) hydrogen bonds : angle 4.49209 ( 2445) Misc. bond : bond 0.00006 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.797 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 110 average time/residue: 0.5742 time to fit residues: 73.4246 Evaluate side-chains 107 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 52 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 215 optimal weight: 0.3980 chunk 272 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.067360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.055915 restraints weight = 40469.797| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 2.55 r_work: 0.2473 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21312 Z= 0.165 Angle : 0.516 8.394 29088 Z= 0.261 Chirality : 0.045 0.128 3284 Planarity : 0.004 0.037 3708 Dihedral : 3.916 16.402 2972 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.22 % Allowed : 8.98 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.05 (0.16), residues: 2756 helix: 1.74 (0.25), residues: 460 sheet: 1.12 (0.17), residues: 860 loop : -1.30 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 128 TYR 0.008 0.001 TYR C 283 PHE 0.019 0.001 PHE C 591 TRP 0.009 0.001 TRP A 155 HIS 0.006 0.001 HIS D 557 Details of bonding type rmsd covalent geometry : bond 0.00420 (21308) covalent geometry : angle 0.51614 (29088) hydrogen bonds : bond 0.03924 ( 827) hydrogen bonds : angle 4.56966 ( 2445) Misc. bond : bond 0.00074 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.849 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 113 average time/residue: 0.5189 time to fit residues: 68.3827 Evaluate side-chains 108 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 557 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 193 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.069181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.057772 restraints weight = 40045.809| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 2.54 r_work: 0.2515 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2393 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21312 Z= 0.090 Angle : 0.463 7.047 29088 Z= 0.234 Chirality : 0.043 0.127 3284 Planarity : 0.004 0.036 3708 Dihedral : 3.712 17.140 2972 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.98 % Allowed : 9.28 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.13 (0.16), residues: 2756 helix: 1.80 (0.25), residues: 460 sheet: 1.16 (0.18), residues: 848 loop : -1.21 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 269 TYR 0.005 0.001 TYR B 360 PHE 0.014 0.001 PHE D 591 TRP 0.010 0.001 TRP C 155 HIS 0.006 0.001 HIS D 557 Details of bonding type rmsd covalent geometry : bond 0.00214 (21308) covalent geometry : angle 0.46312 (29088) hydrogen bonds : bond 0.03005 ( 827) hydrogen bonds : angle 4.41980 ( 2445) Misc. bond : bond 0.00016 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.765 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 110 average time/residue: 0.5327 time to fit residues: 68.4539 Evaluate side-chains 105 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 32 optimal weight: 0.0170 chunk 247 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.067264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.055780 restraints weight = 40311.890| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 2.56 r_work: 0.2474 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2352 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21312 Z= 0.171 Angle : 0.527 8.693 29088 Z= 0.266 Chirality : 0.046 0.129 3284 Planarity : 0.004 0.035 3708 Dihedral : 3.918 16.542 2972 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.98 % Allowed : 9.57 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.07 (0.16), residues: 2756 helix: 1.72 (0.25), residues: 460 sheet: 1.12 (0.17), residues: 860 loop : -1.26 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 128 TYR 0.009 0.001 TYR C 283 PHE 0.020 0.001 PHE C 591 TRP 0.008 0.001 TRP C 155 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00434 (21308) covalent geometry : angle 0.52750 (29088) hydrogen bonds : bond 0.04011 ( 827) hydrogen bonds : angle 4.55830 ( 2445) Misc. bond : bond 0.00090 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.848 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 112 average time/residue: 0.5488 time to fit residues: 71.9400 Evaluate side-chains 106 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 216 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.067787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.056296 restraints weight = 40276.253| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 2.55 r_work: 0.2482 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 21312 Z= 0.144 Angle : 0.511 8.429 29088 Z= 0.257 Chirality : 0.045 0.128 3284 Planarity : 0.004 0.036 3708 Dihedral : 3.900 17.017 2972 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.54 % Allowed : 10.30 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.08 (0.16), residues: 2756 helix: 1.71 (0.25), residues: 460 sheet: 1.13 (0.17), residues: 860 loop : -1.26 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 65 TYR 0.007 0.001 TYR C 283 PHE 0.018 0.001 PHE C 591 TRP 0.009 0.001 TRP C 155 HIS 0.006 0.001 HIS C 557 Details of bonding type rmsd covalent geometry : bond 0.00363 (21308) covalent geometry : angle 0.51115 (29088) hydrogen bonds : bond 0.03725 ( 827) hydrogen bonds : angle 4.53113 ( 2445) Misc. bond : bond 0.00053 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.763 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 0.5987 time to fit residues: 71.2982 Evaluate side-chains 105 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 240 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.068338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.056958 restraints weight = 40373.846| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 2.54 r_work: 0.2494 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21312 Z= 0.111 Angle : 0.489 7.916 29088 Z= 0.245 Chirality : 0.044 0.128 3284 Planarity : 0.004 0.036 3708 Dihedral : 3.802 17.105 2972 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.63 % Allowed : 10.01 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.15 (0.16), residues: 2756 helix: 1.75 (0.25), residues: 460 sheet: 1.23 (0.17), residues: 856 loop : -1.23 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 65 TYR 0.006 0.001 TYR B 316 PHE 0.015 0.001 PHE C 591 TRP 0.010 0.001 TRP C 155 HIS 0.006 0.001 HIS D 557 Details of bonding type rmsd covalent geometry : bond 0.00273 (21308) covalent geometry : angle 0.48859 (29088) hydrogen bonds : bond 0.03325 ( 827) hydrogen bonds : angle 4.47088 ( 2445) Misc. bond : bond 0.00017 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.017 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.5869 time to fit residues: 71.6122 Evaluate side-chains 105 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 81 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.067008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.055513 restraints weight = 40526.086| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 2.56 r_work: 0.2469 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 21312 Z= 0.186 Angle : 0.541 8.952 29088 Z= 0.272 Chirality : 0.046 0.131 3284 Planarity : 0.004 0.036 3708 Dihedral : 3.987 16.638 2972 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.59 % Allowed : 10.06 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 are not related in a simple way. whole: 0.04 (0.16), residues: 2756 helix: 1.64 (0.25), residues: 460 sheet: 1.11 (0.17), residues: 856 loop : -1.27 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 128 TYR 0.009 0.001 TYR B 283 PHE 0.020 0.001 PHE C 591 TRP 0.008 0.001 TRP C 155 HIS 0.006 0.001 HIS C 557 Details of bonding type rmsd covalent geometry : bond 0.00473 (21308) covalent geometry : angle 0.54078 (29088) hydrogen bonds : bond 0.04106 ( 827) hydrogen bonds : angle 4.59327 ( 2445) Misc. bond : bond 0.00101 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4655.76 seconds wall clock time: 80 minutes 39.05 seconds (4839.05 seconds total)