Starting phenix.real_space_refine on Wed May 6 02:43:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvq_42627/05_2026/8uvq_42627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvq_42627/05_2026/8uvq_42627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvq_42627/05_2026/8uvq_42627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvq_42627/05_2026/8uvq_42627.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvq_42627/05_2026/8uvq_42627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvq_42627/05_2026/8uvq_42627.cif" } resolution = 3.42 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= 0.015 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 186 5.16 5 C 22302 2.51 5 N 6300 2.21 5 O 6780 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35604 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5836 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5836 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5836 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5836 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5836 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5836 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ADP': 2, 'XO8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ADP': 2, 'XO8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ADP': 2, 'XO8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ADP': 2, 'XO8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ADP': 2, 'XO8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ADP': 2, 'XO8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.26, per 1000 atoms: 0.23 Number of scatterers: 35604 At special positions: 0 Unit cell: (179.92, 165.36, 102.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 186 16.00 P 24 15.00 F 12 9.00 O 6780 8.00 N 6300 7.00 C 22302 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8352 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 24 sheets defined 48.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 removed outlier: 4.652A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 78 removed outlier: 4.022A pdb=" N SER A 78 " --> pdb=" O ASP A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.911A pdb=" N TYR A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 5.438A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.693A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.783A pdb=" N ILE A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.957A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.676A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 333 removed outlier: 4.327A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.854A pdb=" N LEU A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.671A pdb=" N MET A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 445 " --> pdb=" O MET A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.500A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 4.268A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.986A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.547A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.921A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 598 through 611 removed outlier: 4.020A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.721A pdb=" N ILE A 628 " --> pdb=" O ARG A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.725A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 715 Processing helix chain 'A' and resid 732 through 742 Processing helix chain 'A' and resid 748 through 760 removed outlier: 3.606A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 763 No H-bonds generated for 'chain 'A' and resid 761 through 763' Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.652A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 78 removed outlier: 4.019A pdb=" N SER B 78 " --> pdb=" O ASP B 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 75 through 78' Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.914A pdb=" N TYR B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 5.437A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.789A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 231' Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.695A pdb=" N THR B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.777A pdb=" N ILE B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.958A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.678A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 333 removed outlier: 4.325A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.877A pdb=" N LEU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.597A pdb=" N MET B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 445 " --> pdb=" O MET B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.502A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 499 removed outlier: 4.264A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.988A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.538A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.923A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 598 through 611 removed outlier: 4.016A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.723A pdb=" N ILE B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.723A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 715 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 748 through 760 removed outlier: 3.608A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 756 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 763 No H-bonds generated for 'chain 'B' and resid 761 through 763' Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.652A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 removed outlier: 4.022A pdb=" N SER C 78 " --> pdb=" O ASP C 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.916A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.434A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.695A pdb=" N THR C 262 " --> pdb=" O VAL C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.779A pdb=" N ILE C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.958A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.675A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 319 through 333 removed outlier: 4.325A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.855A pdb=" N LEU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.596A pdb=" N MET C 442 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 445 " --> pdb=" O MET C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.787A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 499 removed outlier: 4.263A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.987A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.539A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.922A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 Processing helix chain 'C' and resid 598 through 611 removed outlier: 4.010A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.719A pdb=" N ILE C 628 " --> pdb=" O ARG C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.725A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 715 Processing helix chain 'C' and resid 732 through 742 Processing helix chain 'C' and resid 748 through 760 removed outlier: 3.609A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 763 No H-bonds generated for 'chain 'C' and resid 761 through 763' Processing helix chain 'D' and resid 42 through 50 removed outlier: 4.652A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 removed outlier: 4.023A pdb=" N SER D 78 " --> pdb=" O ASP D 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 78' Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.911A pdb=" N TYR D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.441A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.693A pdb=" N THR D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 removed outlier: 3.781A pdb=" N ILE D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.958A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.676A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 333 removed outlier: 4.326A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.856A pdb=" N LEU D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.671A pdb=" N MET D 442 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 445 " --> pdb=" O MET D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.767A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 499 removed outlier: 4.269A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.984A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.526A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.922A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 585 Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.501A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 614 No H-bonds generated for 'chain 'D' and resid 612 through 614' Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.721A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.721A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 715 Processing helix chain 'D' and resid 732 through 742 Processing helix chain 'D' and resid 748 through 760 removed outlier: 3.605A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 756 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 763 No H-bonds generated for 'chain 'D' and resid 761 through 763' Processing helix chain 'E' and resid 42 through 50 removed outlier: 4.651A pdb=" N GLU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 78 removed outlier: 4.022A pdb=" N SER E 78 " --> pdb=" O ASP E 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 75 through 78' Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 129 through 134 removed outlier: 3.908A pdb=" N TYR E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.468A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.793A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 226 through 231' Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.694A pdb=" N THR E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.776A pdb=" N ILE E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.957A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.676A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 333 removed outlier: 4.321A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 removed outlier: 3.877A pdb=" N LEU E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.597A pdb=" N MET E 442 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 445 " --> pdb=" O MET E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.503A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 499 removed outlier: 4.266A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.987A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.534A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 568 removed outlier: 3.923A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 585 Processing helix chain 'E' and resid 598 through 611 removed outlier: 4.019A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 614 No H-bonds generated for 'chain 'E' and resid 612 through 614' Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.725A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.722A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 715 Processing helix chain 'E' and resid 732 through 742 Processing helix chain 'E' and resid 748 through 760 removed outlier: 3.609A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU E 756 " --> pdb=" O ILE E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 763 No H-bonds generated for 'chain 'E' and resid 761 through 763' Processing helix chain 'F' and resid 42 through 50 removed outlier: 4.650A pdb=" N GLU F 48 " --> pdb=" O PRO F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 78 removed outlier: 4.023A pdb=" N SER F 78 " --> pdb=" O ASP F 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 75 through 78' Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 129 through 134 removed outlier: 3.913A pdb=" N TYR F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 5.432A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.694A pdb=" N THR F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 276 removed outlier: 3.781A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.958A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.675A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 333 removed outlier: 4.324A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 removed outlier: 3.872A pdb=" N LEU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.599A pdb=" N MET F 442 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU F 445 " --> pdb=" O MET F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.802A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 499 removed outlier: 4.268A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.988A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.531A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 568 removed outlier: 3.923A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 585 Processing helix chain 'F' and resid 598 through 611 removed outlier: 4.008A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.719A pdb=" N ILE F 628 " --> pdb=" O ARG F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.724A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 715 Processing helix chain 'F' and resid 732 through 742 Processing helix chain 'F' and resid 748 through 760 removed outlier: 3.608A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU F 756 " --> pdb=" O ILE F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 763 No H-bonds generated for 'chain 'F' and resid 761 through 763' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.654A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.899A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 150 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.503A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 removed outlier: 6.465A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.650A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.901A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.501A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR B 347 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 243 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 575 through 576 removed outlier: 6.461A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.652A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 118 removed outlier: 6.898A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP C 150 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 240 through 244 removed outlier: 6.496A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR C 347 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 243 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 575 through 576 removed outlier: 6.480A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.655A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 115 through 118 removed outlier: 6.900A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 150 " --> pdb=" O VAL D 165 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.499A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 575 through 576 removed outlier: 6.465A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 66 through 67 removed outlier: 3.655A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 115 through 118 removed outlier: 6.902A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP E 150 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 240 through 244 removed outlier: 6.505A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 575 through 576 removed outlier: 6.480A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.653A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.900A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP F 150 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 240 through 244 removed outlier: 6.497A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 575 through 576 removed outlier: 6.490A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) 1312 hydrogen bonds defined for protein. 3678 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: 8.32 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 12380 1.37 - 1.51: 9138 1.51 - 1.66: 14422 1.66 - 1.80: 166 1.80 - 1.94: 134 Bond restraints: 36240 Sorted by residual: bond pdb=" C29 XO8 F 903 " pdb=" S28 XO8 F 903 " ideal model delta sigma weight residual 1.868 1.944 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C29 XO8 C 903 " pdb=" S28 XO8 C 903 " ideal model delta sigma weight residual 1.868 1.944 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C29 XO8 A 903 " pdb=" S28 XO8 A 903 " ideal model delta sigma weight residual 1.868 1.944 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C29 XO8 B 903 " pdb=" S28 XO8 B 903 " ideal model delta sigma weight residual 1.868 1.943 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C29 XO8 D 903 " pdb=" S28 XO8 D 903 " ideal model delta sigma weight residual 1.868 1.943 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 36235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 48415 2.91 - 5.83: 569 5.83 - 8.74: 24 8.74 - 11.65: 12 11.65 - 14.57: 6 Bond angle restraints: 49026 Sorted by residual: angle pdb=" C27 XO8 E 903 " pdb=" S28 XO8 E 903 " pdb=" C29 XO8 E 903 " ideal model delta sigma weight residual 102.73 117.30 -14.57 3.00e+00 1.11e-01 2.36e+01 angle pdb=" C27 XO8 B 903 " pdb=" S28 XO8 B 903 " pdb=" C29 XO8 B 903 " ideal model delta sigma weight residual 102.73 117.28 -14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C27 XO8 C 903 " pdb=" S28 XO8 C 903 " pdb=" C29 XO8 C 903 " ideal model delta sigma weight residual 102.73 117.20 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C27 XO8 F 903 " pdb=" S28 XO8 F 903 " pdb=" C29 XO8 F 903 " ideal model delta sigma weight residual 102.73 117.20 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C27 XO8 A 903 " pdb=" S28 XO8 A 903 " pdb=" C29 XO8 A 903 " ideal model delta sigma weight residual 102.73 117.19 -14.46 3.00e+00 1.11e-01 2.32e+01 ... (remaining 49021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.57: 21892 30.57 - 61.15: 428 61.15 - 91.72: 54 91.72 - 122.30: 54 122.30 - 152.87: 18 Dihedral angle restraints: 22446 sinusoidal: 9564 harmonic: 12882 Sorted by residual: dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 92.87 -152.87 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" C5' ADP D 902 " pdb=" O5' ADP D 902 " pdb=" PA ADP D 902 " pdb=" O2A ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 92.87 -152.87 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 92.60 -152.60 1 2.00e+01 2.50e-03 4.53e+01 ... (remaining 22443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4621 0.057 - 0.114: 725 0.114 - 0.171: 114 0.171 - 0.228: 0 0.228 - 0.285: 6 Chirality restraints: 5466 Sorted by residual: chirality pdb=" CA ASP A 169 " pdb=" N ASP A 169 " pdb=" C ASP A 169 " pdb=" CB ASP A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASP D 169 " pdb=" N ASP D 169 " pdb=" C ASP D 169 " pdb=" CB ASP D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASP C 169 " pdb=" N ASP C 169 " pdb=" C ASP C 169 " pdb=" CB ASP C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 5463 not shown) Planarity restraints: 6432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 169 " -0.059 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO E 170 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO E 170 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 170 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 169 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO D 170 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO D 170 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 170 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 169 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO C 170 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " 0.048 5.00e-02 4.00e+02 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 843 2.65 - 3.22: 37143 3.22 - 3.78: 55411 3.78 - 4.34: 77238 4.34 - 4.90: 124542 Nonbonded interactions: 295177 Sorted by model distance: nonbonded pdb=" O GLU B 124 " pdb=" NZ LYS C 231 " model vdw 2.092 3.120 nonbonded pdb=" O GLU E 124 " pdb=" NZ LYS F 231 " model vdw 2.095 3.120 nonbonded pdb=" NZ LYS A 231 " pdb=" O GLU F 124 " model vdw 2.096 3.120 nonbonded pdb=" O GLU C 124 " pdb=" NZ LYS D 231 " model vdw 2.096 3.120 nonbonded pdb=" O GLU A 124 " pdb=" NZ LYS B 231 " model vdw 2.116 3.120 ... (remaining 295172 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.430 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 0.076 36240 Z= 0.180 Angle : 0.747 14.566 49026 Z= 0.358 Chirality : 0.043 0.285 5466 Planarity : 0.005 0.088 6432 Dihedral : 15.390 152.870 14094 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -1.21 (0.13), residues: 4452 helix: 0.04 (0.13), residues: 1656 sheet: -1.69 (0.22), residues: 528 loop : -1.17 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 83 TYR 0.011 0.001 TYR E 244 PHE 0.013 0.001 PHE D 230 TRP 0.012 0.001 TRP F 454 HIS 0.006 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00370 (36240) covalent geometry : angle 0.74660 (49026) hydrogen bonds : bond 0.20290 ( 1312) hydrogen bonds : angle 7.26800 ( 3678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 702 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7270 (mtm) cc_final: 0.6953 (mtt) REVERT: A 85 ASN cc_start: 0.6980 (p0) cc_final: 0.6604 (p0) REVERT: A 152 PHE cc_start: 0.8023 (p90) cc_final: 0.7463 (p90) REVERT: A 162 GLU cc_start: 0.6331 (pt0) cc_final: 0.5996 (pt0) REVERT: A 317 HIS cc_start: 0.4220 (t-90) cc_final: 0.3843 (t-90) REVERT: A 464 LEU cc_start: 0.8334 (tp) cc_final: 0.8119 (pt) REVERT: A 488 GLU cc_start: 0.7548 (tt0) cc_final: 0.7314 (tm-30) REVERT: A 624 ASN cc_start: 0.7792 (m-40) cc_final: 0.7498 (m-40) REVERT: A 734 ASP cc_start: 0.7604 (p0) cc_final: 0.7284 (t0) REVERT: C 84 MET cc_start: 0.6896 (mtm) cc_final: 0.6458 (mtt) REVERT: C 85 ASN cc_start: 0.7360 (p0) cc_final: 0.7008 (p0) REVERT: C 162 GLU cc_start: 0.7010 (pt0) cc_final: 0.6607 (pt0) REVERT: D 84 MET cc_start: 0.7331 (mtm) cc_final: 0.6975 (mtt) REVERT: D 85 ASN cc_start: 0.6885 (p0) cc_final: 0.6521 (p0) REVERT: D 152 PHE cc_start: 0.7990 (p90) cc_final: 0.7408 (p90) REVERT: D 162 GLU cc_start: 0.6429 (pt0) cc_final: 0.6078 (pt0) REVERT: D 317 HIS cc_start: 0.4240 (t-90) cc_final: 0.3740 (t-90) REVERT: D 488 GLU cc_start: 0.7550 (tt0) cc_final: 0.7328 (tm-30) REVERT: D 624 ASN cc_start: 0.7823 (m-40) cc_final: 0.7551 (m-40) REVERT: D 734 ASP cc_start: 0.7574 (p0) cc_final: 0.7217 (t0) REVERT: F 84 MET cc_start: 0.6852 (mtm) cc_final: 0.6419 (mtt) REVERT: F 85 ASN cc_start: 0.7484 (p0) cc_final: 0.7126 (p0) REVERT: F 162 GLU cc_start: 0.6887 (pt0) cc_final: 0.6487 (pt0) outliers start: 0 outliers final: 0 residues processed: 702 average time/residue: 0.2631 time to fit residues: 285.6473 Evaluate side-chains 297 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 6.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 155 HIS A 387 ASN A 538 ASN B 115 HIS B 155 HIS ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 155 HIS ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 155 HIS D 387 ASN D 538 ASN E 115 HIS E 155 HIS ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 155 HIS ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.196018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.157774 restraints weight = 47053.990| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 3.26 r_work: 0.3719 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36240 Z= 0.167 Angle : 0.779 9.018 49026 Z= 0.378 Chirality : 0.048 0.160 5466 Planarity : 0.006 0.075 6432 Dihedral : 15.423 163.520 5190 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.40 % Allowed : 9.10 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.05 (0.13), residues: 4452 helix: 0.08 (0.12), residues: 1758 sheet: -1.38 (0.23), residues: 546 loop : -1.10 (0.15), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 83 TYR 0.025 0.002 TYR D 755 PHE 0.022 0.002 PHE C 360 TRP 0.014 0.002 TRP C 454 HIS 0.010 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00385 (36240) covalent geometry : angle 0.77860 (49026) hydrogen bonds : bond 0.04502 ( 1312) hydrogen bonds : angle 5.02686 ( 3678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 330 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7740 (mtm) cc_final: 0.7427 (mtt) REVERT: A 152 PHE cc_start: 0.7739 (p90) cc_final: 0.7232 (p90) REVERT: A 162 GLU cc_start: 0.6731 (pt0) cc_final: 0.6411 (pt0) REVERT: A 449 MET cc_start: 0.7961 (tpp) cc_final: 0.7736 (tpp) REVERT: A 689 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7586 (tt0) REVERT: B 162 GLU cc_start: 0.6575 (pt0) cc_final: 0.6344 (pt0) REVERT: B 388 MET cc_start: 0.7621 (mtt) cc_final: 0.7242 (mtt) REVERT: B 677 LYS cc_start: 0.8905 (pptt) cc_final: 0.8698 (pptt) REVERT: B 689 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7467 (tt0) REVERT: C 84 MET cc_start: 0.7818 (mtm) cc_final: 0.7106 (mtm) REVERT: C 162 GLU cc_start: 0.6968 (pt0) cc_final: 0.6470 (pt0) REVERT: C 449 MET cc_start: 0.7848 (tpp) cc_final: 0.7581 (tpp) REVERT: C 689 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7696 (tt0) REVERT: D 84 MET cc_start: 0.7738 (mtm) cc_final: 0.7331 (mtt) REVERT: D 152 PHE cc_start: 0.7722 (p90) cc_final: 0.7225 (p90) REVERT: D 162 GLU cc_start: 0.6825 (pt0) cc_final: 0.6481 (pt0) REVERT: D 317 HIS cc_start: 0.4714 (t-90) cc_final: 0.4223 (t-90) REVERT: D 689 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7560 (tt0) REVERT: E 388 MET cc_start: 0.7661 (mtt) cc_final: 0.7291 (mtt) REVERT: E 689 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7470 (tt0) REVERT: F 84 MET cc_start: 0.7792 (mtm) cc_final: 0.7273 (mtt) REVERT: F 85 ASN cc_start: 0.6866 (p0) cc_final: 0.6547 (p0) REVERT: F 162 GLU cc_start: 0.6943 (pt0) cc_final: 0.6443 (pt0) REVERT: F 564 ASP cc_start: 0.8165 (t70) cc_final: 0.7950 (t0) REVERT: F 689 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7706 (tt0) outliers start: 53 outliers final: 26 residues processed: 360 average time/residue: 0.2216 time to fit residues: 132.7452 Evaluate side-chains 278 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 360 PHE Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 750 ASN Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 531 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 442 optimal weight: 6.9990 chunk 379 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 372 optimal weight: 30.0000 chunk 417 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 436 optimal weight: 3.9990 chunk 328 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN B 538 ASN ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS E 387 ASN E 538 ASN ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS F 538 ASN ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.192207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.156204 restraints weight = 47524.846| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 3.25 r_work: 0.3678 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36240 Z= 0.182 Angle : 0.731 9.221 49026 Z= 0.353 Chirality : 0.047 0.151 5466 Planarity : 0.005 0.066 6432 Dihedral : 14.764 166.850 5190 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 2.82 % Allowed : 10.31 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.07 (0.13), residues: 4452 helix: 0.19 (0.13), residues: 1722 sheet: -1.30 (0.24), residues: 510 loop : -1.24 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 83 TYR 0.024 0.002 TYR D 755 PHE 0.017 0.002 PHE F 516 TRP 0.008 0.001 TRP D 454 HIS 0.006 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00432 (36240) covalent geometry : angle 0.73102 (49026) hydrogen bonds : bond 0.03796 ( 1312) hydrogen bonds : angle 4.80880 ( 3678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 313 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7771 (mtm) cc_final: 0.7197 (mtm) REVERT: A 96 LEU cc_start: 0.8505 (tt) cc_final: 0.8289 (tp) REVERT: A 152 PHE cc_start: 0.7731 (p90) cc_final: 0.7307 (p90) REVERT: A 162 GLU cc_start: 0.6599 (pt0) cc_final: 0.6311 (pt0) REVERT: A 321 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6552 (mt-10) REVERT: A 332 MET cc_start: 0.8136 (tpp) cc_final: 0.7827 (tpp) REVERT: A 492 LEU cc_start: 0.7909 (mp) cc_final: 0.7677 (mt) REVERT: A 494 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6515 (tm-30) REVERT: B 134 TYR cc_start: 0.5415 (m-80) cc_final: 0.5106 (m-80) REVERT: B 315 LYS cc_start: 0.7483 (mmtt) cc_final: 0.7275 (ttmt) REVERT: C 84 MET cc_start: 0.7817 (mtm) cc_final: 0.7127 (mtm) REVERT: C 162 GLU cc_start: 0.6839 (pt0) cc_final: 0.6419 (pt0) REVERT: C 494 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6408 (tm-30) REVERT: D 84 MET cc_start: 0.7770 (mtm) cc_final: 0.7283 (mtm) REVERT: D 96 LEU cc_start: 0.8509 (tt) cc_final: 0.8278 (tp) REVERT: D 152 PHE cc_start: 0.7724 (p90) cc_final: 0.7294 (p90) REVERT: D 162 GLU cc_start: 0.6626 (pt0) cc_final: 0.6337 (pt0) REVERT: D 321 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6576 (mt-10) REVERT: D 332 MET cc_start: 0.8144 (tpp) cc_final: 0.7844 (tpp) REVERT: D 494 GLN cc_start: 0.7096 (tm-30) cc_final: 0.6519 (tm-30) REVERT: E 134 TYR cc_start: 0.5318 (m-80) cc_final: 0.5112 (m-80) REVERT: E 315 LYS cc_start: 0.7544 (mmtt) cc_final: 0.7227 (ttmt) REVERT: F 84 MET cc_start: 0.7806 (mtm) cc_final: 0.7139 (mtm) REVERT: F 162 GLU cc_start: 0.6738 (pt0) cc_final: 0.6333 (pt0) REVERT: F 494 GLN cc_start: 0.6959 (tm-30) cc_final: 0.6405 (tm-30) outliers start: 107 outliers final: 67 residues processed: 396 average time/residue: 0.2172 time to fit residues: 143.3939 Evaluate side-chains 311 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 244 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 64 optimal weight: 9.9990 chunk 319 optimal weight: 2.9990 chunk 441 optimal weight: 7.9990 chunk 12 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 405 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 217 optimal weight: 0.4980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS ** B 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.190255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.152638 restraints weight = 49714.433| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.57 r_work: 0.3640 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 36240 Z= 0.165 Angle : 0.712 9.842 49026 Z= 0.344 Chirality : 0.047 0.185 5466 Planarity : 0.005 0.051 6432 Dihedral : 14.272 167.450 5190 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.14 % Allowed : 12.18 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.97 (0.13), residues: 4452 helix: 0.26 (0.13), residues: 1746 sheet: -1.37 (0.22), residues: 558 loop : -1.14 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 322 TYR 0.024 0.002 TYR D 755 PHE 0.022 0.002 PHE F 360 TRP 0.006 0.001 TRP D 454 HIS 0.008 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00390 (36240) covalent geometry : angle 0.71170 (49026) hydrogen bonds : bond 0.03516 ( 1312) hydrogen bonds : angle 4.63051 ( 3678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 270 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7874 (mtm) cc_final: 0.7360 (mtm) REVERT: A 162 GLU cc_start: 0.6701 (pt0) cc_final: 0.6384 (pt0) REVERT: A 321 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6723 (mt-10) REVERT: A 332 MET cc_start: 0.8314 (tpp) cc_final: 0.8055 (tpp) REVERT: A 449 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7477 (tpp) REVERT: A 492 LEU cc_start: 0.7890 (mp) cc_final: 0.7599 (mt) REVERT: B 90 ASN cc_start: 0.7578 (m-40) cc_final: 0.7010 (p0) REVERT: C 84 MET cc_start: 0.7935 (mtm) cc_final: 0.7233 (mtm) REVERT: C 162 GLU cc_start: 0.6862 (pt0) cc_final: 0.6427 (pt0) REVERT: C 494 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6722 (tm-30) REVERT: D 84 MET cc_start: 0.7883 (mtm) cc_final: 0.7360 (mtm) REVERT: D 162 GLU cc_start: 0.6721 (pt0) cc_final: 0.6395 (pt0) REVERT: D 332 MET cc_start: 0.8315 (tpp) cc_final: 0.8059 (tpp) REVERT: E 321 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6486 (mt-10) REVERT: F 84 MET cc_start: 0.7854 (mtm) cc_final: 0.7181 (mtm) REVERT: F 162 GLU cc_start: 0.6837 (pt0) cc_final: 0.6419 (pt0) REVERT: F 244 TYR cc_start: 0.7905 (p90) cc_final: 0.7627 (p90) REVERT: F 321 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6883 (mt-10) REVERT: F 494 GLN cc_start: 0.7037 (tm-30) cc_final: 0.6715 (tm-30) outliers start: 119 outliers final: 71 residues processed: 362 average time/residue: 0.2028 time to fit residues: 125.4184 Evaluate side-chains 301 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 229 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 198 optimal weight: 4.9990 chunk 207 optimal weight: 0.0980 chunk 416 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 345 optimal weight: 0.0370 chunk 82 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 151 optimal weight: 30.0000 chunk 291 optimal weight: 6.9990 chunk 406 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 overall best weight: 2.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS A 533 ASN B 660 ASN C 660 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS E 384 HIS E 660 ASN F 660 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.191455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.156873 restraints weight = 47199.022| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.42 r_work: 0.3619 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36240 Z= 0.175 Angle : 0.706 7.835 49026 Z= 0.341 Chirality : 0.047 0.193 5466 Planarity : 0.005 0.049 6432 Dihedral : 13.871 159.536 5190 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 3.11 % Allowed : 12.68 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.92 (0.13), residues: 4452 helix: 0.30 (0.13), residues: 1746 sheet: -1.25 (0.23), residues: 552 loop : -1.14 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG E 83 TYR 0.023 0.002 TYR D 244 PHE 0.022 0.002 PHE A 360 TRP 0.005 0.001 TRP D 454 HIS 0.008 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00420 (36240) covalent geometry : angle 0.70561 (49026) hydrogen bonds : bond 0.03433 ( 1312) hydrogen bonds : angle 4.55169 ( 3678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 256 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.5072 (ttm) cc_final: 0.4659 (tmm) REVERT: A 84 MET cc_start: 0.7903 (mtm) cc_final: 0.7388 (mtm) REVERT: A 162 GLU cc_start: 0.6784 (pt0) cc_final: 0.6449 (pt0) REVERT: A 321 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 332 MET cc_start: 0.8274 (tpp) cc_final: 0.8030 (tpp) REVERT: A 449 MET cc_start: 0.7981 (tpp) cc_final: 0.7579 (tpp) REVERT: A 492 LEU cc_start: 0.7874 (mp) cc_final: 0.7593 (mt) REVERT: B 317 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.6336 (t-90) REVERT: C 84 MET cc_start: 0.7873 (mtm) cc_final: 0.7222 (mtm) REVERT: C 162 GLU cc_start: 0.6863 (pt0) cc_final: 0.6461 (pt0) REVERT: C 244 TYR cc_start: 0.7990 (p90) cc_final: 0.7688 (p90) REVERT: C 494 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6786 (tm-30) REVERT: D 46 MET cc_start: 0.5064 (ttm) cc_final: 0.4659 (tmm) REVERT: D 84 MET cc_start: 0.7900 (mtm) cc_final: 0.7378 (mtm) REVERT: D 162 GLU cc_start: 0.6824 (pt0) cc_final: 0.6480 (pt0) REVERT: D 332 MET cc_start: 0.8272 (tpp) cc_final: 0.8035 (tpp) REVERT: F 84 MET cc_start: 0.7922 (mtm) cc_final: 0.7242 (mtm) REVERT: F 162 GLU cc_start: 0.6775 (pt0) cc_final: 0.6362 (pt0) REVERT: F 321 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6904 (mt-10) REVERT: F 494 GLN cc_start: 0.7146 (tm-30) cc_final: 0.6457 (tm-30) REVERT: F 564 ASP cc_start: 0.8111 (t70) cc_final: 0.7752 (t0) outliers start: 118 outliers final: 92 residues processed: 347 average time/residue: 0.2006 time to fit residues: 117.6937 Evaluate side-chains 324 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 231 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 384 HIS Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 687 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 427 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 362 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 390 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 418 optimal weight: 4.9990 chunk 346 optimal weight: 0.4980 chunk 176 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 304 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS A 533 ASN B 384 HIS B 533 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.190472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.151136 restraints weight = 48649.942| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 3.74 r_work: 0.3634 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36240 Z= 0.140 Angle : 0.684 7.548 49026 Z= 0.330 Chirality : 0.046 0.180 5466 Planarity : 0.005 0.049 6432 Dihedral : 13.412 150.027 5190 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.01 % Allowed : 13.45 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.83 (0.13), residues: 4452 helix: 0.42 (0.13), residues: 1746 sheet: -1.28 (0.23), residues: 546 loop : -1.12 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 322 TYR 0.032 0.002 TYR F 244 PHE 0.016 0.001 PHE D 152 TRP 0.004 0.001 TRP D 454 HIS 0.007 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00325 (36240) covalent geometry : angle 0.68446 (49026) hydrogen bonds : bond 0.03232 ( 1312) hydrogen bonds : angle 4.43610 ( 3678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 245 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.4849 (ttm) cc_final: 0.4399 (tmm) REVERT: A 84 MET cc_start: 0.7996 (mtm) cc_final: 0.7595 (mtt) REVERT: A 162 GLU cc_start: 0.6666 (pt0) cc_final: 0.6335 (pt0) REVERT: A 449 MET cc_start: 0.8049 (tpp) cc_final: 0.7700 (tpp) REVERT: A 605 LEU cc_start: 0.8413 (tt) cc_final: 0.7894 (mp) REVERT: B 134 TYR cc_start: 0.5571 (m-80) cc_final: 0.5368 (m-80) REVERT: B 317 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6241 (t-90) REVERT: B 388 MET cc_start: 0.7480 (mtt) cc_final: 0.7108 (mtm) REVERT: C 84 MET cc_start: 0.7979 (mtm) cc_final: 0.7255 (mtm) REVERT: C 162 GLU cc_start: 0.6912 (pt0) cc_final: 0.6490 (pt0) REVERT: C 244 TYR cc_start: 0.8045 (p90) cc_final: 0.7718 (p90) REVERT: C 360 PHE cc_start: 0.8096 (m-80) cc_final: 0.7831 (m-80) REVERT: C 494 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6320 (tm-30) REVERT: C 605 LEU cc_start: 0.8383 (tt) cc_final: 0.7973 (mp) REVERT: D 46 MET cc_start: 0.4842 (ttm) cc_final: 0.4394 (tmm) REVERT: D 84 MET cc_start: 0.7991 (mtm) cc_final: 0.7582 (mtt) REVERT: D 162 GLU cc_start: 0.6675 (pt0) cc_final: 0.6340 (pt0) REVERT: D 492 LEU cc_start: 0.7724 (mp) cc_final: 0.7516 (mt) REVERT: E 384 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7329 (m170) REVERT: E 388 MET cc_start: 0.7412 (mtt) cc_final: 0.7048 (mtm) REVERT: F 84 MET cc_start: 0.7934 (mtm) cc_final: 0.7241 (mtm) REVERT: F 162 GLU cc_start: 0.6863 (pt0) cc_final: 0.6431 (pt0) REVERT: F 321 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6898 (mt-10) REVERT: F 494 GLN cc_start: 0.7088 (tm-30) cc_final: 0.6353 (tm-30) REVERT: F 564 ASP cc_start: 0.8171 (t70) cc_final: 0.7824 (t0) REVERT: F 605 LEU cc_start: 0.8416 (tt) cc_final: 0.7965 (mp) outliers start: 114 outliers final: 87 residues processed: 329 average time/residue: 0.1957 time to fit residues: 111.2235 Evaluate side-chains 319 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 230 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 384 HIS Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 384 HIS Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 23 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 416 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 439 optimal weight: 4.9990 chunk 328 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 209 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 533 ASN C 533 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS E 533 ASN F 533 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.190925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.151396 restraints weight = 48728.835| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.71 r_work: 0.3581 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36240 Z= 0.178 Angle : 0.696 7.350 49026 Z= 0.336 Chirality : 0.047 0.179 5466 Planarity : 0.005 0.049 6432 Dihedral : 13.146 147.502 5190 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.22 % Allowed : 14.11 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.86 (0.13), residues: 4452 helix: 0.42 (0.13), residues: 1740 sheet: -1.42 (0.23), residues: 540 loop : -1.12 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.033 0.002 TYR E 134 PHE 0.021 0.002 PHE D 360 TRP 0.005 0.001 TRP D 551 HIS 0.011 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00427 (36240) covalent geometry : angle 0.69590 (49026) hydrogen bonds : bond 0.03276 ( 1312) hydrogen bonds : angle 4.42474 ( 3678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 242 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.4916 (ttm) cc_final: 0.4458 (tmm) REVERT: A 84 MET cc_start: 0.8054 (mtm) cc_final: 0.7650 (mtt) REVERT: A 162 GLU cc_start: 0.6716 (pt0) cc_final: 0.6382 (pt0) REVERT: A 332 MET cc_start: 0.8305 (tpp) cc_final: 0.8070 (tpt) REVERT: A 449 MET cc_start: 0.8072 (tpp) cc_final: 0.7774 (tpp) REVERT: B 317 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6309 (t-90) REVERT: B 384 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.7356 (m-70) REVERT: B 388 MET cc_start: 0.7464 (mtt) cc_final: 0.7081 (mtm) REVERT: B 449 MET cc_start: 0.7994 (tpp) cc_final: 0.7724 (tpp) REVERT: C 84 MET cc_start: 0.8021 (mtm) cc_final: 0.7289 (mtm) REVERT: C 162 GLU cc_start: 0.6972 (pt0) cc_final: 0.6549 (pt0) REVERT: C 244 TYR cc_start: 0.8128 (p90) cc_final: 0.7852 (p90) REVERT: C 494 GLN cc_start: 0.7170 (tm-30) cc_final: 0.6461 (tm-30) REVERT: D 46 MET cc_start: 0.4917 (ttm) cc_final: 0.4467 (tmm) REVERT: D 84 MET cc_start: 0.8005 (mtm) cc_final: 0.7458 (mtm) REVERT: D 162 GLU cc_start: 0.6756 (pt0) cc_final: 0.6416 (pt0) REVERT: D 332 MET cc_start: 0.8300 (tpp) cc_final: 0.8055 (tpt) REVERT: E 46 MET cc_start: 0.5320 (tpp) cc_final: 0.5077 (tpp) REVERT: E 384 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7302 (m-70) REVERT: E 388 MET cc_start: 0.7465 (mtt) cc_final: 0.7052 (mtm) REVERT: F 84 MET cc_start: 0.7878 (mtm) cc_final: 0.7165 (mtm) REVERT: F 162 GLU cc_start: 0.6904 (pt0) cc_final: 0.6488 (pt0) REVERT: F 494 GLN cc_start: 0.7222 (tm-30) cc_final: 0.6497 (tm-30) REVERT: F 564 ASP cc_start: 0.8148 (t70) cc_final: 0.7789 (t0) outliers start: 122 outliers final: 94 residues processed: 331 average time/residue: 0.2008 time to fit residues: 114.8019 Evaluate side-chains 327 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 230 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 736 PHE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 384 HIS Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 736 PHE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 687 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 159 optimal weight: 20.0000 chunk 242 optimal weight: 0.7980 chunk 349 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 chunk 138 optimal weight: 0.2980 chunk 368 optimal weight: 0.5980 chunk 409 optimal weight: 4.9990 chunk 363 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 533 ASN C 533 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS E 533 ASN F 533 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.193260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.156456 restraints weight = 49303.956| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.50 r_work: 0.3661 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36240 Z= 0.121 Angle : 0.671 7.938 49026 Z= 0.321 Chirality : 0.045 0.208 5466 Planarity : 0.004 0.047 6432 Dihedral : 12.595 145.487 5190 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.85 % Allowed : 14.85 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.68 (0.13), residues: 4452 helix: 0.63 (0.13), residues: 1740 sheet: -1.30 (0.23), residues: 546 loop : -1.08 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 322 TYR 0.039 0.002 TYR B 134 PHE 0.015 0.001 PHE D 360 TRP 0.007 0.001 TRP A 551 HIS 0.015 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00268 (36240) covalent geometry : angle 0.67076 (49026) hydrogen bonds : bond 0.03024 ( 1312) hydrogen bonds : angle 4.27913 ( 3678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 254 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.4926 (ttm) cc_final: 0.4515 (tmm) REVERT: A 84 MET cc_start: 0.7861 (mtm) cc_final: 0.7540 (mtt) REVERT: A 162 GLU cc_start: 0.6598 (pt0) cc_final: 0.6303 (pt0) REVERT: A 332 MET cc_start: 0.8147 (tpp) cc_final: 0.7943 (tpt) REVERT: A 449 MET cc_start: 0.8037 (tpp) cc_final: 0.7564 (tpp) REVERT: B 317 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.6311 (t-90) REVERT: B 384 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.7186 (m170) REVERT: C 84 MET cc_start: 0.7818 (mtm) cc_final: 0.7154 (mtm) REVERT: C 162 GLU cc_start: 0.6852 (pt0) cc_final: 0.6451 (pt0) REVERT: C 244 TYR cc_start: 0.7951 (p90) cc_final: 0.7563 (p90) REVERT: C 410 ASP cc_start: 0.7911 (m-30) cc_final: 0.7547 (m-30) REVERT: C 494 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6406 (tm-30) REVERT: C 605 LEU cc_start: 0.8299 (tt) cc_final: 0.7964 (mp) REVERT: D 46 MET cc_start: 0.4928 (ttm) cc_final: 0.4526 (tmm) REVERT: D 84 MET cc_start: 0.7807 (mtm) cc_final: 0.7379 (mtm) REVERT: D 162 GLU cc_start: 0.6615 (pt0) cc_final: 0.6315 (pt0) REVERT: D 244 TYR cc_start: 0.7733 (p90) cc_final: 0.7463 (p90) REVERT: D 332 MET cc_start: 0.8123 (tpp) cc_final: 0.7918 (tpt) REVERT: D 492 LEU cc_start: 0.7595 (mp) cc_final: 0.7386 (mt) REVERT: E 384 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.7196 (m170) REVERT: E 449 MET cc_start: 0.7990 (tpp) cc_final: 0.7781 (tpp) REVERT: F 84 MET cc_start: 0.7738 (mtm) cc_final: 0.7134 (mtm) REVERT: F 162 GLU cc_start: 0.6820 (pt0) cc_final: 0.6408 (pt0) REVERT: F 494 GLN cc_start: 0.7035 (tm-30) cc_final: 0.6372 (tm-30) REVERT: F 564 ASP cc_start: 0.7986 (t70) cc_final: 0.7588 (t0) REVERT: F 605 LEU cc_start: 0.8342 (tt) cc_final: 0.7961 (mp) outliers start: 108 outliers final: 80 residues processed: 333 average time/residue: 0.1998 time to fit residues: 114.3776 Evaluate side-chains 303 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 220 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 736 PHE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 384 HIS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 384 HIS Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 736 PHE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 278 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 254 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 533 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS E 533 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.192832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.155838 restraints weight = 49326.138| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.56 r_work: 0.3664 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36240 Z= 0.127 Angle : 0.666 7.912 49026 Z= 0.319 Chirality : 0.045 0.221 5466 Planarity : 0.005 0.047 6432 Dihedral : 12.236 144.838 5190 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.64 % Allowed : 15.32 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.81 (0.13), residues: 4452 helix: 0.47 (0.13), residues: 1818 sheet: -1.25 (0.24), residues: 540 loop : -1.19 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 322 TYR 0.023 0.001 TYR F 244 PHE 0.017 0.001 PHE B 360 TRP 0.003 0.001 TRP D 476 HIS 0.006 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00292 (36240) covalent geometry : angle 0.66571 (49026) hydrogen bonds : bond 0.02977 ( 1312) hydrogen bonds : angle 4.25523 ( 3678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 244 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.4927 (ttm) cc_final: 0.4562 (tmm) REVERT: A 84 MET cc_start: 0.7780 (mtm) cc_final: 0.7258 (mtm) REVERT: A 162 GLU cc_start: 0.6541 (pt0) cc_final: 0.6264 (pt0) REVERT: A 449 MET cc_start: 0.7990 (tpp) cc_final: 0.7529 (tpp) REVERT: B 46 MET cc_start: 0.5317 (tpp) cc_final: 0.5069 (tpp) REVERT: B 317 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6335 (t-90) REVERT: B 384 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.7198 (m170) REVERT: C 84 MET cc_start: 0.7750 (mtm) cc_final: 0.7137 (mtm) REVERT: C 162 GLU cc_start: 0.6788 (pt0) cc_final: 0.6405 (pt0) REVERT: C 244 TYR cc_start: 0.7933 (p90) cc_final: 0.7614 (p90) REVERT: C 410 ASP cc_start: 0.7871 (m-30) cc_final: 0.7479 (m-30) REVERT: C 494 GLN cc_start: 0.7011 (tm-30) cc_final: 0.6338 (tm-30) REVERT: C 605 LEU cc_start: 0.8334 (tt) cc_final: 0.7991 (mp) REVERT: D 46 MET cc_start: 0.4937 (ttm) cc_final: 0.4576 (tmm) REVERT: D 84 MET cc_start: 0.7728 (mtm) cc_final: 0.7321 (mtm) REVERT: D 162 GLU cc_start: 0.6568 (pt0) cc_final: 0.6296 (pt0) REVERT: E 46 MET cc_start: 0.5584 (tpp) cc_final: 0.5297 (tpp) REVERT: E 384 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7180 (m170) REVERT: F 84 MET cc_start: 0.7670 (mtm) cc_final: 0.7108 (mtm) REVERT: F 162 GLU cc_start: 0.6774 (pt0) cc_final: 0.6379 (pt0) REVERT: F 494 GLN cc_start: 0.7033 (tm-30) cc_final: 0.6358 (tm-30) REVERT: F 564 ASP cc_start: 0.7943 (t70) cc_final: 0.7547 (t0) REVERT: F 605 LEU cc_start: 0.8359 (tt) cc_final: 0.7990 (mp) outliers start: 100 outliers final: 82 residues processed: 316 average time/residue: 0.1909 time to fit residues: 104.7625 Evaluate side-chains 309 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 224 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 736 PHE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 384 HIS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 384 HIS Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 384 HIS Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 736 PHE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 34 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 304 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 275 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 263 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 533 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 533 ASN E 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.191166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.151937 restraints weight = 49042.375| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 3.76 r_work: 0.3645 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36240 Z= 0.131 Angle : 0.673 9.187 49026 Z= 0.324 Chirality : 0.046 0.356 5466 Planarity : 0.004 0.049 6432 Dihedral : 11.999 144.504 5190 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.43 % Allowed : 15.64 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.76 (0.13), residues: 4452 helix: 0.49 (0.13), residues: 1812 sheet: -1.20 (0.24), residues: 546 loop : -1.14 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 349 TYR 0.023 0.001 TYR F 244 PHE 0.016 0.001 PHE D 360 TRP 0.004 0.001 TRP A 476 HIS 0.005 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00303 (36240) covalent geometry : angle 0.67277 (49026) hydrogen bonds : bond 0.02978 ( 1312) hydrogen bonds : angle 4.25124 ( 3678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 241 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.4876 (ttm) cc_final: 0.4461 (tmm) REVERT: A 84 MET cc_start: 0.7918 (mtm) cc_final: 0.7435 (mtm) REVERT: A 162 GLU cc_start: 0.6598 (pt0) cc_final: 0.6289 (pt0) REVERT: A 244 TYR cc_start: 0.7808 (p90) cc_final: 0.7591 (p90) REVERT: A 449 MET cc_start: 0.7948 (tpp) cc_final: 0.7728 (tpp) REVERT: B 46 MET cc_start: 0.4991 (tpp) cc_final: 0.4721 (tpp) REVERT: B 317 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.6421 (t-90) REVERT: B 384 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7069 (m170) REVERT: C 84 MET cc_start: 0.7820 (mtm) cc_final: 0.7139 (mtm) REVERT: C 162 GLU cc_start: 0.6826 (pt0) cc_final: 0.6398 (pt0) REVERT: C 244 TYR cc_start: 0.7973 (p90) cc_final: 0.7661 (p90) REVERT: C 410 ASP cc_start: 0.7882 (m-30) cc_final: 0.7472 (m-30) REVERT: C 494 GLN cc_start: 0.7104 (tm-30) cc_final: 0.6356 (tm-30) REVERT: C 564 ASP cc_start: 0.8007 (m-30) cc_final: 0.7770 (m-30) REVERT: C 605 LEU cc_start: 0.8354 (tt) cc_final: 0.8000 (mp) REVERT: C 757 MET cc_start: 0.8113 (tmm) cc_final: 0.7841 (tmm) REVERT: D 46 MET cc_start: 0.4962 (ttm) cc_final: 0.4534 (tmm) REVERT: D 84 MET cc_start: 0.7888 (mtm) cc_final: 0.7423 (mtm) REVERT: D 162 GLU cc_start: 0.6620 (pt0) cc_final: 0.6313 (pt0) REVERT: E 384 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.7021 (m170) REVERT: E 449 MET cc_start: 0.7962 (tpp) cc_final: 0.7752 (tpp) REVERT: F 84 MET cc_start: 0.7807 (mtm) cc_final: 0.7167 (mtm) REVERT: F 162 GLU cc_start: 0.6845 (pt0) cc_final: 0.6415 (pt0) REVERT: F 494 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6339 (tm-30) REVERT: F 564 ASP cc_start: 0.8035 (t70) cc_final: 0.7717 (t0) REVERT: F 605 LEU cc_start: 0.8342 (tt) cc_final: 0.7977 (mp) REVERT: F 757 MET cc_start: 0.8112 (tmm) cc_final: 0.7841 (tmm) outliers start: 92 outliers final: 78 residues processed: 310 average time/residue: 0.1987 time to fit residues: 107.7519 Evaluate side-chains 317 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 236 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 384 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 736 PHE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 384 HIS Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 697 LEU Chi-restraints excluded: chain E residue 736 PHE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 634 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 379 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 376 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 429 optimal weight: 0.6980 chunk 409 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 533 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN E 533 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.203198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.156760 restraints weight = 51391.279| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.19 r_work: 0.4091 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 36240 Z= 0.244 Angle : 0.746 8.537 49026 Z= 0.364 Chirality : 0.050 0.246 5466 Planarity : 0.005 0.053 6432 Dihedral : 12.268 148.516 5190 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 2.48 % Allowed : 15.69 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.05 (0.13), residues: 4452 helix: 0.26 (0.13), residues: 1770 sheet: -1.51 (0.23), residues: 540 loop : -1.25 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 349 TYR 0.030 0.002 TYR D 755 PHE 0.025 0.002 PHE A 539 TRP 0.010 0.002 TRP D 551 HIS 0.010 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00593 (36240) covalent geometry : angle 0.74579 (49026) hydrogen bonds : bond 0.03447 ( 1312) hydrogen bonds : angle 4.52179 ( 3678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7958.36 seconds wall clock time: 137 minutes 20.85 seconds (8240.85 seconds total)