Starting phenix.real_space_refine on Sat Mar 7 08:03:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vh5_31986/03_2026/7vh5_31986_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vh5_31986/03_2026/7vh5_31986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vh5_31986/03_2026/7vh5_31986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vh5_31986/03_2026/7vh5_31986.map" model { file = "/net/cci-nas-00/data/ceres_data/7vh5_31986/03_2026/7vh5_31986_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vh5_31986/03_2026/7vh5_31986_neut.cif" } resolution = 3.2 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 186 5.16 5 C 26016 2.51 5 N 6172 2.21 5 O 7190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 256 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39615 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "B" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "C" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "D" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "E" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "F" Number of atoms: 6157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6157 Classifications: {'peptide': 804} Link IDs: {'PTRANS': 30, 'TRANS': 773} Chain breaks: 2 Chain: "A" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 416 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 489 Unusual residues: {'POV': 9, 'SPH': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 9.14, per 1000 atoms: 0.23 Number of scatterers: 39615 At special positions: 0 Unit cell: (175.959, 167.727, 182.133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 186 16.00 P 51 15.00 O 7190 8.00 N 6172 7.00 C 26016 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8808 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 24 sheets defined 59.7% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 110 through 121 removed outlier: 3.519A pdb=" N LYS A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 Processing helix chain 'A' and resid 140 through 174 removed outlier: 3.570A pdb=" N VAL A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.548A pdb=" N ILE A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.500A pdb=" N ILE A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.944A pdb=" N GLU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.978A pdb=" N MET A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 420 through 428 removed outlier: 3.768A pdb=" N LYS A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 490 through 508 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.591A pdb=" N GLU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.568A pdb=" N GLY A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 585' Processing helix chain 'A' and resid 593 through 604 Processing helix chain 'A' and resid 611 through 625 removed outlier: 3.517A pdb=" N TYR A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 617 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 670 through 714 removed outlier: 3.720A pdb=" N ILE A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 737 removed outlier: 3.695A pdb=" N PHE A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 732 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 734 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 737 " --> pdb=" O THR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 777 Processing helix chain 'A' and resid 790 through 805 Processing helix chain 'A' and resid 805 through 811 removed outlier: 3.702A pdb=" N ILE A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 843 Processing helix chain 'A' and resid 851 through 878 Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 896 through 917 removed outlier: 3.647A pdb=" N GLU A 915 " --> pdb=" O SER A 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.519A pdb=" N LYS B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 Processing helix chain 'B' and resid 140 through 174 removed outlier: 3.570A pdb=" N VAL B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 267 through 280 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.548A pdb=" N ILE B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 337 through 356 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.944A pdb=" N GLU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 removed outlier: 3.979A pdb=" N MET B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 420 through 428 removed outlier: 3.768A pdb=" N LYS B 428 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 490 through 508 Processing helix chain 'B' and resid 539 through 550 Processing helix chain 'B' and resid 561 through 573 removed outlier: 3.591A pdb=" N GLU B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.568A pdb=" N GLY B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 585' Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 611 through 625 removed outlier: 3.518A pdb=" N TYR B 616 " --> pdb=" O PRO B 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 617 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 670 through 714 removed outlier: 3.719A pdb=" N ILE B 674 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 699 " --> pdb=" O ARG B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 737 removed outlier: 3.695A pdb=" N PHE B 724 " --> pdb=" O ASP B 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 732 " --> pdb=" O PHE B 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B 733 " --> pdb=" O ALA B 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 735 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 737 " --> pdb=" O THR B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 777 Processing helix chain 'B' and resid 790 through 805 Processing helix chain 'B' and resid 805 through 811 removed outlier: 3.702A pdb=" N ILE B 809 " --> pdb=" O TRP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 843 Processing helix chain 'B' and resid 851 through 878 Processing helix chain 'B' and resid 879 through 888 Processing helix chain 'B' and resid 896 through 917 removed outlier: 3.647A pdb=" N GLU B 915 " --> pdb=" O SER B 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 121 removed outlier: 3.518A pdb=" N LYS C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 138 Processing helix chain 'C' and resid 140 through 174 removed outlier: 3.570A pdb=" N VAL C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 267 through 280 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.548A pdb=" N ILE C 295 " --> pdb=" O ASN C 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 337 through 356 Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.944A pdb=" N GLU C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 411 removed outlier: 3.979A pdb=" N MET C 405 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 420 through 428 removed outlier: 3.768A pdb=" N LYS C 428 " --> pdb=" O LYS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'C' and resid 539 through 550 Processing helix chain 'C' and resid 561 through 573 removed outlier: 3.591A pdb=" N GLU C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 removed outlier: 3.569A pdb=" N GLY C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 581 through 585' Processing helix chain 'C' and resid 593 through 604 Processing helix chain 'C' and resid 611 through 625 removed outlier: 3.517A pdb=" N TYR C 616 " --> pdb=" O PRO C 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG C 617 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 645 Processing helix chain 'C' and resid 655 through 662 Processing helix chain 'C' and resid 670 through 714 removed outlier: 3.721A pdb=" N ILE C 674 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 699 " --> pdb=" O ARG C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 737 removed outlier: 3.695A pdb=" N PHE C 724 " --> pdb=" O ASP C 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C 732 " --> pdb=" O PHE C 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 734 " --> pdb=" O ASP C 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 735 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 737 " --> pdb=" O THR C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 777 Processing helix chain 'C' and resid 790 through 805 Processing helix chain 'C' and resid 805 through 811 removed outlier: 3.702A pdb=" N ILE C 809 " --> pdb=" O TRP C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 843 Processing helix chain 'C' and resid 851 through 878 Processing helix chain 'C' and resid 879 through 888 Processing helix chain 'C' and resid 896 through 917 removed outlier: 3.647A pdb=" N GLU C 915 " --> pdb=" O SER C 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.518A pdb=" N LYS D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 Processing helix chain 'D' and resid 140 through 174 removed outlier: 3.570A pdb=" N VAL D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 267 through 280 Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.548A pdb=" N ILE D 295 " --> pdb=" O ASN D 291 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS D 312 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 Processing helix chain 'D' and resid 337 through 356 Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.944A pdb=" N GLU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 411 removed outlier: 3.978A pdb=" N MET D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 406 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 420 through 428 removed outlier: 3.767A pdb=" N LYS D 428 " --> pdb=" O LYS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 482 Processing helix chain 'D' and resid 490 through 508 Processing helix chain 'D' and resid 539 through 550 Processing helix chain 'D' and resid 561 through 573 removed outlier: 3.591A pdb=" N GLU D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 removed outlier: 3.568A pdb=" N GLY D 585 " --> pdb=" O ALA D 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 585' Processing helix chain 'D' and resid 593 through 604 Processing helix chain 'D' and resid 611 through 625 removed outlier: 3.517A pdb=" N TYR D 616 " --> pdb=" O PRO D 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 617 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 645 Processing helix chain 'D' and resid 655 through 662 Processing helix chain 'D' and resid 670 through 714 removed outlier: 3.720A pdb=" N ILE D 674 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER D 699 " --> pdb=" O ARG D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 737 removed outlier: 3.695A pdb=" N PHE D 724 " --> pdb=" O ASP D 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 732 " --> pdb=" O PHE D 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR D 733 " --> pdb=" O ALA D 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 734 " --> pdb=" O ASP D 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 735 " --> pdb=" O VAL D 731 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA D 737 " --> pdb=" O THR D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 777 Processing helix chain 'D' and resid 790 through 805 Processing helix chain 'D' and resid 805 through 811 removed outlier: 3.703A pdb=" N ILE D 809 " --> pdb=" O TRP D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 843 Processing helix chain 'D' and resid 851 through 878 Processing helix chain 'D' and resid 879 through 888 Processing helix chain 'D' and resid 896 through 917 removed outlier: 3.647A pdb=" N GLU D 915 " --> pdb=" O SER D 911 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.519A pdb=" N LYS E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 138 Processing helix chain 'E' and resid 140 through 174 removed outlier: 3.571A pdb=" N VAL E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 267 through 280 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.549A pdb=" N ILE E 295 " --> pdb=" O ASN E 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 337 through 356 Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.944A pdb=" N GLU E 367 " --> pdb=" O LEU E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 411 removed outlier: 3.979A pdb=" N MET E 405 " --> pdb=" O PRO E 401 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'E' and resid 420 through 428 removed outlier: 3.768A pdb=" N LYS E 428 " --> pdb=" O LYS E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 482 Processing helix chain 'E' and resid 490 through 508 Processing helix chain 'E' and resid 539 through 550 Processing helix chain 'E' and resid 561 through 573 removed outlier: 3.591A pdb=" N GLU E 567 " --> pdb=" O GLY E 563 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 568 " --> pdb=" O ILE E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.568A pdb=" N GLY E 585 " --> pdb=" O ALA E 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 581 through 585' Processing helix chain 'E' and resid 593 through 604 Processing helix chain 'E' and resid 611 through 625 removed outlier: 3.517A pdb=" N TYR E 616 " --> pdb=" O PRO E 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG E 617 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 645 Processing helix chain 'E' and resid 655 through 662 Processing helix chain 'E' and resid 670 through 714 removed outlier: 3.720A pdb=" N ILE E 674 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 699 " --> pdb=" O ARG E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 737 removed outlier: 3.694A pdb=" N PHE E 724 " --> pdb=" O ASP E 720 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA E 732 " --> pdb=" O PHE E 728 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR E 733 " --> pdb=" O ALA E 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 734 " --> pdb=" O ASP E 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA E 735 " --> pdb=" O VAL E 731 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 737 " --> pdb=" O THR E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 777 Processing helix chain 'E' and resid 790 through 805 Processing helix chain 'E' and resid 805 through 811 removed outlier: 3.702A pdb=" N ILE E 809 " --> pdb=" O TRP E 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 843 Processing helix chain 'E' and resid 851 through 878 Processing helix chain 'E' and resid 879 through 888 Processing helix chain 'E' and resid 896 through 917 removed outlier: 3.647A pdb=" N GLU E 915 " --> pdb=" O SER E 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 121 removed outlier: 3.519A pdb=" N LYS F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 138 Processing helix chain 'F' and resid 140 through 174 removed outlier: 3.570A pdb=" N VAL F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 267 through 280 Processing helix chain 'F' and resid 284 through 315 removed outlier: 3.548A pdb=" N ILE F 295 " --> pdb=" O ASN F 291 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS F 312 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.500A pdb=" N ILE F 332 " --> pdb=" O GLY F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 356 Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.945A pdb=" N GLU F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 411 removed outlier: 3.979A pdb=" N MET F 405 " --> pdb=" O PRO F 401 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU F 406 " --> pdb=" O ASP F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 Processing helix chain 'F' and resid 420 through 428 removed outlier: 3.768A pdb=" N LYS F 428 " --> pdb=" O LYS F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 482 Processing helix chain 'F' and resid 490 through 508 Processing helix chain 'F' and resid 539 through 550 Processing helix chain 'F' and resid 561 through 573 removed outlier: 3.590A pdb=" N GLU F 567 " --> pdb=" O GLY F 563 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR F 568 " --> pdb=" O ILE F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.568A pdb=" N GLY F 585 " --> pdb=" O ALA F 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 581 through 585' Processing helix chain 'F' and resid 593 through 604 Processing helix chain 'F' and resid 611 through 625 removed outlier: 3.517A pdb=" N TYR F 616 " --> pdb=" O PRO F 612 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG F 617 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 645 Processing helix chain 'F' and resid 655 through 662 Processing helix chain 'F' and resid 670 through 714 removed outlier: 3.720A pdb=" N ILE F 674 " --> pdb=" O GLY F 670 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER F 699 " --> pdb=" O ARG F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 737 removed outlier: 3.695A pdb=" N PHE F 724 " --> pdb=" O ASP F 720 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA F 732 " --> pdb=" O PHE F 728 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR F 733 " --> pdb=" O ALA F 729 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 734 " --> pdb=" O ASP F 730 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 735 " --> pdb=" O VAL F 731 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA F 737 " --> pdb=" O THR F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 777 Processing helix chain 'F' and resid 790 through 805 Processing helix chain 'F' and resid 805 through 811 removed outlier: 3.702A pdb=" N ILE F 809 " --> pdb=" O TRP F 805 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 843 Processing helix chain 'F' and resid 851 through 878 Processing helix chain 'F' and resid 879 through 888 Processing helix chain 'F' and resid 896 through 917 removed outlier: 3.647A pdb=" N GLU F 915 " --> pdb=" O SER F 911 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192 removed outlier: 4.385A pdb=" N VAL A 181 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A 183 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 201 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP A 200 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.613A pdb=" N ARG A 253 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP A 226 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL A 251 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 360 removed outlier: 6.148A pdb=" N GLY A 648 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE A 666 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 650 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 374 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR A 632 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N CYS A 376 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE A 607 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET A 556 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR A 579 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 390 removed outlier: 5.117A pdb=" N ILE A 526 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 517 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 516 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 459 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 447 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU A 463 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 445 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.384A pdb=" N VAL B 181 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE B 183 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 201 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP B 200 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.612A pdb=" N ARG B 253 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 251 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 358 through 360 removed outlier: 6.148A pdb=" N GLY B 648 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE B 666 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 650 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 374 " --> pdb=" O ALA B 630 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR B 632 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N CYS B 376 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE B 607 " --> pdb=" O VAL B 554 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET B 556 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR B 579 " --> pdb=" O ALA B 608 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 389 through 390 removed outlier: 5.118A pdb=" N ILE B 526 " --> pdb=" O ARG B 517 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG B 517 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 516 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 459 " --> pdb=" O HIS B 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 447 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B 463 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 445 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 187 through 192 removed outlier: 4.384A pdb=" N VAL C 181 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE C 183 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 201 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP C 200 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.612A pdb=" N ARG C 253 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP C 226 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL C 251 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 358 through 360 removed outlier: 6.148A pdb=" N GLY C 648 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE C 666 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 650 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 374 " --> pdb=" O ALA C 630 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR C 632 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N CYS C 376 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE C 607 " --> pdb=" O VAL C 554 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET C 556 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR C 579 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 389 through 390 removed outlier: 5.118A pdb=" N ILE C 526 " --> pdb=" O ARG C 517 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG C 517 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 516 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C 459 " --> pdb=" O HIS C 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 447 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU C 463 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL C 445 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 187 through 192 removed outlier: 4.385A pdb=" N VAL D 181 " --> pdb=" O GLN D 203 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE D 183 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 201 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP D 200 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.612A pdb=" N ARG D 253 " --> pdb=" O GLN D 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP D 226 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL D 251 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 358 through 360 removed outlier: 6.148A pdb=" N GLY D 648 " --> pdb=" O ILE D 664 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE D 666 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA D 650 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE D 374 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR D 632 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N CYS D 376 " --> pdb=" O THR D 632 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE D 607 " --> pdb=" O VAL D 554 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET D 556 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR D 579 " --> pdb=" O ALA D 608 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 389 through 390 removed outlier: 5.117A pdb=" N ILE D 526 " --> pdb=" O ARG D 517 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG D 517 " --> pdb=" O ILE D 526 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 516 " --> pdb=" O VAL D 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 459 " --> pdb=" O HIS D 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 447 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU D 463 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL D 445 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 187 through 192 removed outlier: 4.384A pdb=" N VAL E 181 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE E 183 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE E 201 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP E 200 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.613A pdb=" N ARG E 253 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP E 226 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL E 251 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 358 through 360 removed outlier: 6.148A pdb=" N GLY E 648 " --> pdb=" O ILE E 664 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE E 666 " --> pdb=" O GLY E 648 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA E 650 " --> pdb=" O PHE E 666 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE E 374 " --> pdb=" O ALA E 630 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR E 632 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N CYS E 376 " --> pdb=" O THR E 632 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE E 607 " --> pdb=" O VAL E 554 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET E 556 " --> pdb=" O PHE E 607 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR E 579 " --> pdb=" O ALA E 608 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 389 through 390 removed outlier: 5.118A pdb=" N ILE E 526 " --> pdb=" O ARG E 517 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG E 517 " --> pdb=" O ILE E 526 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 516 " --> pdb=" O VAL E 473 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 459 " --> pdb=" O HIS E 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU E 447 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU E 463 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL E 445 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 187 through 192 removed outlier: 4.385A pdb=" N VAL F 181 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE F 183 " --> pdb=" O ILE F 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE F 201 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP F 200 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 237 through 239 removed outlier: 3.613A pdb=" N ARG F 253 " --> pdb=" O GLN F 224 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP F 226 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL F 251 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 358 through 360 removed outlier: 6.149A pdb=" N GLY F 648 " --> pdb=" O ILE F 664 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE F 666 " --> pdb=" O GLY F 648 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA F 650 " --> pdb=" O PHE F 666 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE F 374 " --> pdb=" O ALA F 630 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR F 632 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N CYS F 376 " --> pdb=" O THR F 632 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE F 607 " --> pdb=" O VAL F 554 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET F 556 " --> pdb=" O PHE F 607 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR F 579 " --> pdb=" O ALA F 608 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 389 through 390 removed outlier: 5.117A pdb=" N ILE F 526 " --> pdb=" O ARG F 517 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG F 517 " --> pdb=" O ILE F 526 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA F 516 " --> pdb=" O VAL F 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR F 459 " --> pdb=" O HIS F 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU F 447 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU F 463 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL F 445 " --> pdb=" O GLU F 463 " (cutoff:3.500A) 2315 hydrogen bonds defined for protein. 6765 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: 9.67 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6231 1.31 - 1.43: 9858 1.43 - 1.56: 23217 1.56 - 1.68: 638 1.68 - 1.81: 369 Bond restraints: 40313 Sorted by residual: bond pdb=" C4 SPH F1010 " pdb=" C5 SPH F1010 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C31 POV D1003 " pdb=" O31 POV D1003 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C31 POV E1007 " pdb=" O31 POV E1007 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C31 POV C1003 " pdb=" O31 POV C1003 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C31 POV B1003 " pdb=" O31 POV B1003 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.24e+01 ... (remaining 40308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 50083 2.49 - 4.98: 3015 4.98 - 7.47: 734 7.47 - 9.97: 275 9.97 - 12.46: 109 Bond angle restraints: 54216 Sorted by residual: angle pdb=" N VAL E 399 " pdb=" CA VAL E 399 " pdb=" C VAL E 399 " ideal model delta sigma weight residual 110.62 116.54 -5.92 1.02e+00 9.61e-01 3.36e+01 angle pdb=" N VAL B 399 " pdb=" CA VAL B 399 " pdb=" C VAL B 399 " ideal model delta sigma weight residual 110.62 116.50 -5.88 1.02e+00 9.61e-01 3.33e+01 angle pdb=" N VAL D 399 " pdb=" CA VAL D 399 " pdb=" C VAL D 399 " ideal model delta sigma weight residual 110.62 116.48 -5.86 1.02e+00 9.61e-01 3.31e+01 angle pdb=" N VAL A 399 " pdb=" CA VAL A 399 " pdb=" C VAL A 399 " ideal model delta sigma weight residual 110.62 116.48 -5.86 1.02e+00 9.61e-01 3.30e+01 angle pdb=" N VAL F 399 " pdb=" CA VAL F 399 " pdb=" C VAL F 399 " ideal model delta sigma weight residual 110.62 116.47 -5.85 1.02e+00 9.61e-01 3.29e+01 ... (remaining 54211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.14: 21380 19.14 - 38.28: 2180 38.28 - 57.43: 617 57.43 - 76.57: 152 76.57 - 95.71: 162 Dihedral angle restraints: 24491 sinusoidal: 10769 harmonic: 13722 Sorted by residual: dihedral pdb=" CA LYS D 379 " pdb=" C LYS D 379 " pdb=" N THR D 380 " pdb=" CA THR D 380 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LYS B 379 " pdb=" C LYS B 379 " pdb=" N THR B 380 " pdb=" CA THR B 380 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LYS A 379 " pdb=" C LYS A 379 " pdb=" N THR A 380 " pdb=" CA THR A 380 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 24488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5165 0.088 - 0.176: 806 0.176 - 0.264: 71 0.264 - 0.353: 11 0.353 - 0.441: 6 Chirality restraints: 6059 Sorted by residual: chirality pdb=" CG LEU B 698 " pdb=" CB LEU B 698 " pdb=" CD1 LEU B 698 " pdb=" CD2 LEU B 698 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CG LEU F 698 " pdb=" CB LEU F 698 " pdb=" CD1 LEU F 698 " pdb=" CD2 LEU F 698 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CG LEU A 698 " pdb=" CB LEU A 698 " pdb=" CD1 LEU A 698 " pdb=" CD2 LEU A 698 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 6056 not shown) Planarity restraints: 6604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH F1010 " 0.104 2.00e-02 2.50e+03 1.79e-01 3.20e+02 pdb=" C4 SPH F1010 " -0.232 2.00e-02 2.50e+03 pdb=" C5 SPH F1010 " 0.230 2.00e-02 2.50e+03 pdb=" C6 SPH F1010 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 397 " -0.025 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C GLU C 397 " 0.086 2.00e-02 2.50e+03 pdb=" O GLU C 397 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY C 398 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 397 " -0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C GLU A 397 " 0.086 2.00e-02 2.50e+03 pdb=" O GLU A 397 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY A 398 " -0.029 2.00e-02 2.50e+03 ... (remaining 6601 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 16 1.99 - 2.71: 2924 2.71 - 3.44: 54474 3.44 - 4.17: 95902 4.17 - 4.90: 176412 Nonbonded interactions: 329728 Sorted by model distance: nonbonded pdb=" OE2 GLU A 893 " pdb=" CG2 THR B 897 " model vdw 1.257 3.460 nonbonded pdb=" CG2 THR A 897 " pdb=" OE2 GLU F 893 " model vdw 1.258 3.460 nonbonded pdb=" OE2 GLU C 893 " pdb=" CG2 THR D 897 " model vdw 1.260 3.460 nonbonded pdb=" OE2 GLU E 893 " pdb=" CG2 THR F 897 " model vdw 1.266 3.460 nonbonded pdb=" OE2 GLU B 893 " pdb=" CG2 THR C 897 " model vdw 1.349 3.460 ... (remaining 329723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 110 through 1008) selection = chain 'D' selection = (chain 'E' and resid 110 through 1008) selection = (chain 'F' and resid 110 through 1008) } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 38.650 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.018 0.400 40325 Z= 0.889 Angle : 1.533 12.457 54216 Z= 0.677 Chirality : 0.066 0.441 6059 Planarity : 0.007 0.179 6604 Dihedral : 18.878 95.711 15683 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.31 % Allowed : 1.07 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.75 (0.10), residues: 4788 helix: -2.29 (0.08), residues: 2688 sheet: -0.02 (0.19), residues: 612 loop : -1.22 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 324 TYR 0.023 0.003 TYR E 694 PHE 0.032 0.003 PHE B 816 TRP 0.025 0.004 TRP B 309 HIS 0.013 0.002 HIS D 701 Details of bonding type rmsd covalent geometry : bond 0.01681 (40313) covalent geometry : angle 1.53293 (54216) hydrogen bonds : bond 0.26375 ( 2315) hydrogen bonds : angle 10.43629 ( 6765) Misc. bond : bond 0.28824 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 447 time to evaluate : 1.210 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: A 152 MET cc_start: 0.7582 (mmt) cc_final: 0.7366 (mmt) REVERT: A 171 GLU cc_start: 0.6150 (tm-30) cc_final: 0.5584 (tm-30) REVERT: A 405 MET cc_start: 0.1965 (ptt) cc_final: 0.0520 (mtt) REVERT: A 433 TYR cc_start: -0.0535 (OUTLIER) cc_final: -0.1770 (m-80) REVERT: A 548 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.7736 (mtm-85) REVERT: B 546 GLU cc_start: 0.7768 (tt0) cc_final: 0.7547 (tt0) REVERT: B 736 ILE cc_start: 0.8110 (tp) cc_final: 0.7867 (tp) REVERT: B 896 SER cc_start: 0.8190 (m) cc_final: 0.7979 (t) REVERT: B 899 SER cc_start: 0.8927 (t) cc_final: 0.8712 (p) REVERT: C 118 MET cc_start: 0.4175 (mtm) cc_final: 0.2655 (tpt) REVERT: C 583 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8251 (ttt180) REVERT: C 823 TRP cc_start: 0.7668 (p-90) cc_final: 0.7287 (p-90) REVERT: C 824 GLN cc_start: 0.8036 (mp10) cc_final: 0.7791 (mp-120) REVERT: C 891 MET cc_start: 0.0438 (mtm) cc_final: 0.0083 (mtp) REVERT: C 904 MET cc_start: 0.7533 (mmp) cc_final: 0.7202 (ttm) REVERT: C 917 GLU cc_start: 0.5809 (pt0) cc_final: 0.4794 (pt0) REVERT: D 143 ASP cc_start: 0.4248 (m-30) cc_final: 0.4007 (m-30) REVERT: D 288 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6567 (tt0) REVERT: D 571 GLN cc_start: 0.8168 (mt0) cc_final: 0.7830 (mt0) REVERT: D 582 GLU cc_start: 0.8084 (tp30) cc_final: 0.7837 (tp30) REVERT: D 775 THR cc_start: 0.8670 (m) cc_final: 0.8274 (p) REVERT: E 288 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6888 (tt0) REVERT: E 656 ASP cc_start: 0.7336 (t0) cc_final: 0.7074 (t0) REVERT: E 889 LYS cc_start: 0.7750 (mttm) cc_final: 0.7244 (pttt) REVERT: E 891 MET cc_start: 0.1600 (mtm) cc_final: 0.1010 (tmm) REVERT: F 152 MET cc_start: 0.5365 (mmt) cc_final: 0.4119 (tmm) REVERT: F 791 MET cc_start: 0.8535 (ttm) cc_final: 0.8259 (ttp) REVERT: F 875 GLU cc_start: 0.6263 (mp0) cc_final: 0.5763 (mp0) REVERT: F 891 MET cc_start: 0.3834 (mtm) cc_final: 0.1812 (mtm) outliers start: 12 outliers final: 1 residues processed: 459 average time/residue: 0.2570 time to fit residues: 188.6922 Evaluate side-chains 321 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain E residue 435 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 HIS A 614 HIS C 164 GLN D 391 HIS D 542 GLN D 908 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.232615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.225086 restraints weight = 36201.495| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 0.53 r_work: 0.4385 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.4251 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40325 Z= 0.144 Angle : 0.601 9.010 54216 Z= 0.307 Chirality : 0.042 0.145 6059 Planarity : 0.005 0.038 6604 Dihedral : 17.438 88.992 7313 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.59 % Allowed : 5.80 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.11), residues: 4788 helix: 0.12 (0.09), residues: 2748 sheet: -0.40 (0.19), residues: 582 loop : -1.10 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 324 TYR 0.019 0.001 TYR D 352 PHE 0.019 0.001 PHE B 119 TRP 0.011 0.001 TRP E 756 HIS 0.009 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00321 (40313) covalent geometry : angle 0.60110 (54216) hydrogen bonds : bond 0.04432 ( 2315) hydrogen bonds : angle 5.13493 ( 6765) Misc. bond : bond 0.00024 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 361 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.2478 (ptt) cc_final: 0.1399 (mtm) REVERT: A 433 TYR cc_start: 0.0251 (OUTLIER) cc_final: -0.2172 (m-80) REVERT: A 646 ASP cc_start: 0.7567 (m-30) cc_final: 0.7347 (m-30) REVERT: B 646 ASP cc_start: 0.7932 (m-30) cc_final: 0.7597 (m-30) REVERT: B 736 ILE cc_start: 0.7945 (tp) cc_final: 0.7723 (tp) REVERT: B 761 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8582 (mp) REVERT: B 886 MET cc_start: 0.8138 (mmp) cc_final: 0.7891 (mmt) REVERT: B 917 GLU cc_start: 0.5949 (tp30) cc_final: 0.5465 (tt0) REVERT: C 118 MET cc_start: 0.4056 (mtm) cc_final: 0.3453 (tpt) REVERT: C 703 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7353 (mt-10) REVERT: C 823 TRP cc_start: 0.7733 (p-90) cc_final: 0.7261 (p-90) REVERT: D 582 GLU cc_start: 0.8158 (tp30) cc_final: 0.7941 (tp30) REVERT: D 647 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8799 (t) REVERT: D 777 MET cc_start: 0.8341 (mtp) cc_final: 0.7935 (mtp) REVERT: E 405 MET cc_start: 0.2655 (ptm) cc_final: 0.2367 (mtp) REVERT: E 891 MET cc_start: 0.2107 (mtm) cc_final: 0.1848 (tmm) REVERT: F 676 ASP cc_start: 0.7474 (m-30) cc_final: 0.7268 (m-30) REVERT: F 891 MET cc_start: 0.4111 (mtm) cc_final: 0.2403 (mtm) outliers start: 23 outliers final: 7 residues processed: 374 average time/residue: 0.2408 time to fit residues: 150.1480 Evaluate side-chains 294 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 284 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain C residue 777 MET Chi-restraints excluded: chain D residue 647 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 299 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 394 optimal weight: 0.6980 chunk 469 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 chunk 173 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 421 optimal weight: 0.7980 chunk 470 optimal weight: 0.1980 chunk 300 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 GLN C 203 GLN C 614 HIS D 542 GLN D 908 GLN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 787 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.231518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.184347 restraints weight = 36118.483| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 4.02 r_work: 0.3895 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40325 Z= 0.133 Angle : 0.531 7.654 54216 Z= 0.270 Chirality : 0.041 0.171 6059 Planarity : 0.004 0.040 6604 Dihedral : 15.968 89.808 7309 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.09 % Allowed : 7.40 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.12), residues: 4788 helix: 1.08 (0.10), residues: 2772 sheet: -0.58 (0.19), residues: 588 loop : -1.04 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 682 TYR 0.014 0.001 TYR D 352 PHE 0.014 0.001 PHE E 510 TRP 0.012 0.001 TRP C 756 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00303 (40313) covalent geometry : angle 0.53087 (54216) hydrogen bonds : bond 0.03855 ( 2315) hydrogen bonds : angle 4.59510 ( 6765) Misc. bond : bond 0.00063 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.2333 (ptt) cc_final: 0.1209 (mtm) REVERT: A 433 TYR cc_start: 0.0191 (OUTLIER) cc_final: -0.1801 (m-80) REVERT: A 646 ASP cc_start: 0.7715 (m-30) cc_final: 0.7513 (m-30) REVERT: B 646 ASP cc_start: 0.8127 (m-30) cc_final: 0.7745 (m-30) REVERT: B 672 SER cc_start: 0.8468 (t) cc_final: 0.8130 (p) REVERT: B 736 ILE cc_start: 0.8203 (tp) cc_final: 0.7975 (tp) REVERT: B 761 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8781 (mp) REVERT: B 886 MET cc_start: 0.8339 (mmp) cc_final: 0.8002 (mmt) REVERT: D 582 GLU cc_start: 0.8296 (tp30) cc_final: 0.8056 (tp30) REVERT: D 777 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7992 (mtp) REVERT: E 405 MET cc_start: 0.2942 (ptm) cc_final: 0.2202 (mtp) REVERT: E 891 MET cc_start: 0.2253 (mtm) cc_final: 0.1507 (tmm) REVERT: F 405 MET cc_start: 0.4359 (pmm) cc_final: 0.4029 (pmm) REVERT: F 676 ASP cc_start: 0.7500 (m-30) cc_final: 0.7258 (m-30) REVERT: F 792 ASN cc_start: 0.8690 (m-40) cc_final: 0.8486 (m-40) REVERT: F 891 MET cc_start: 0.3770 (mtm) cc_final: 0.2037 (mtm) outliers start: 43 outliers final: 13 residues processed: 356 average time/residue: 0.2337 time to fit residues: 140.4022 Evaluate side-chains 300 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 549 HIS Chi-restraints excluded: chain C residue 688 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain F residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 270 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 280 optimal weight: 0.0970 chunk 228 optimal weight: 0.5980 chunk 404 optimal weight: 7.9990 chunk 414 optimal weight: 0.0870 chunk 400 optimal weight: 20.0000 chunk 424 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 ASN D 542 GLN D 908 GLN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 787 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.225761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.176596 restraints weight = 36047.450| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 4.04 r_work: 0.3801 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 40325 Z= 0.228 Angle : 0.600 9.056 54216 Z= 0.300 Chirality : 0.043 0.214 6059 Planarity : 0.004 0.049 6604 Dihedral : 16.386 90.539 7309 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.15 % Allowed : 9.52 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.12), residues: 4788 helix: 1.22 (0.10), residues: 2772 sheet: -0.56 (0.19), residues: 588 loop : -0.93 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 682 TYR 0.015 0.001 TYR A 691 PHE 0.015 0.002 PHE B 119 TRP 0.015 0.001 TRP C 756 HIS 0.007 0.001 HIS C 701 Details of bonding type rmsd covalent geometry : bond 0.00541 (40313) covalent geometry : angle 0.59984 (54216) hydrogen bonds : bond 0.04077 ( 2315) hydrogen bonds : angle 4.57606 ( 6765) Misc. bond : bond 0.00107 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 308 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.2415 (ptt) cc_final: 0.1313 (mtm) REVERT: A 777 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8436 (mtp) REVERT: B 646 ASP cc_start: 0.8151 (m-30) cc_final: 0.7881 (m-30) REVERT: B 672 SER cc_start: 0.8445 (t) cc_final: 0.8095 (p) REVERT: B 736 ILE cc_start: 0.8219 (tp) cc_final: 0.7998 (tt) REVERT: B 761 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 777 MET cc_start: 0.8502 (mtp) cc_final: 0.8165 (mtm) REVERT: B 886 MET cc_start: 0.8348 (mmp) cc_final: 0.8089 (mmt) REVERT: C 777 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8256 (mtp) REVERT: D 582 GLU cc_start: 0.8344 (tp30) cc_final: 0.8119 (tp30) REVERT: D 647 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8745 (t) REVERT: D 777 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: E 405 MET cc_start: 0.3084 (ptm) cc_final: 0.2385 (mtp) REVERT: E 891 MET cc_start: 0.2120 (mtm) cc_final: 0.1182 (tmm) REVERT: F 552 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8670 (pt) REVERT: F 676 ASP cc_start: 0.7478 (m-30) cc_final: 0.7226 (m-30) REVERT: F 891 MET cc_start: 0.3601 (mtm) cc_final: 0.1764 (mtm) REVERT: F 917 GLU cc_start: 0.6227 (tp30) cc_final: 0.5379 (tt0) outliers start: 45 outliers final: 24 residues processed: 336 average time/residue: 0.2263 time to fit residues: 128.3600 Evaluate side-chains 310 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 777 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 899 SER Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain F residue 820 ILE Chi-restraints excluded: chain F residue 876 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 388 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 321 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 256 optimal weight: 0.2980 chunk 358 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 308 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 247 optimal weight: 0.0010 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 792 ASN D 203 GLN D 542 GLN D 908 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.232709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.184033 restraints weight = 35879.571| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 4.24 r_work: 0.3893 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 40325 Z= 0.104 Angle : 0.493 7.076 54216 Z= 0.250 Chirality : 0.040 0.204 6059 Planarity : 0.003 0.052 6604 Dihedral : 14.680 89.692 7307 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.07 % Allowed : 11.02 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.12), residues: 4788 helix: 1.66 (0.10), residues: 2820 sheet: -0.56 (0.19), residues: 582 loop : -0.84 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 414 TYR 0.012 0.001 TYR C 691 PHE 0.014 0.001 PHE E 510 TRP 0.011 0.001 TRP C 750 HIS 0.002 0.000 HIS D 686 Details of bonding type rmsd covalent geometry : bond 0.00227 (40313) covalent geometry : angle 0.49290 (54216) hydrogen bonds : bond 0.03320 ( 2315) hydrogen bonds : angle 4.20573 ( 6765) Misc. bond : bond 0.00036 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 336 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.2292 (ptt) cc_final: 0.1246 (mtm) REVERT: A 433 TYR cc_start: -0.0034 (OUTLIER) cc_final: -0.1976 (m-80) REVERT: B 646 ASP cc_start: 0.8021 (m-30) cc_final: 0.7635 (m-30) REVERT: B 672 SER cc_start: 0.8398 (t) cc_final: 0.8045 (p) REVERT: B 761 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8722 (mp) REVERT: B 777 MET cc_start: 0.8383 (mtp) cc_final: 0.8072 (mtm) REVERT: B 907 MET cc_start: 0.8826 (mtp) cc_final: 0.8583 (mtp) REVERT: C 118 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.2883 (tpt) REVERT: C 405 MET cc_start: 0.5109 (ppp) cc_final: 0.4539 (ppp) REVERT: D 552 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8532 (pt) REVERT: D 647 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8586 (t) REVERT: D 777 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7975 (mtp) REVERT: D 903 PHE cc_start: 0.8511 (t80) cc_final: 0.8310 (t80) REVERT: F 387 LYS cc_start: 0.7196 (mtmm) cc_final: 0.6972 (mmtt) REVERT: F 676 ASP cc_start: 0.7391 (m-30) cc_final: 0.7131 (m-30) REVERT: F 891 MET cc_start: 0.3687 (mtm) cc_final: 0.1920 (mtm) outliers start: 42 outliers final: 17 residues processed: 359 average time/residue: 0.2270 time to fit residues: 137.8277 Evaluate side-chains 323 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 300 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 777 MET Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain F residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 300 optimal weight: 1.9990 chunk 420 optimal weight: 0.3980 chunk 235 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 50 optimal weight: 0.0570 chunk 439 optimal weight: 0.9990 chunk 415 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 305 optimal weight: 0.9990 chunk 384 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 887 ASN D 542 GLN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.230874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.181773 restraints weight = 35953.383| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 4.21 r_work: 0.3877 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40325 Z= 0.117 Angle : 0.506 8.325 54216 Z= 0.253 Chirality : 0.040 0.259 6059 Planarity : 0.003 0.055 6604 Dihedral : 14.305 89.163 7307 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.30 % Allowed : 11.91 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.12), residues: 4788 helix: 1.84 (0.10), residues: 2820 sheet: -0.54 (0.19), residues: 582 loop : -0.76 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 414 TYR 0.013 0.001 TYR C 691 PHE 0.020 0.001 PHE A 510 TRP 0.012 0.001 TRP F 756 HIS 0.003 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00268 (40313) covalent geometry : angle 0.50580 (54216) hydrogen bonds : bond 0.03387 ( 2315) hydrogen bonds : angle 4.14007 ( 6765) Misc. bond : bond 0.00045 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.2528 (ptt) cc_final: 0.1272 (mtm) REVERT: A 803 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7569 (mt-10) REVERT: A 875 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6653 (mt-10) REVERT: B 646 ASP cc_start: 0.8089 (m-30) cc_final: 0.7675 (m-30) REVERT: B 761 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8823 (mp) REVERT: C 118 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.2814 (tpt) REVERT: C 405 MET cc_start: 0.4750 (ppp) cc_final: 0.4454 (ppp) REVERT: C 908 GLN cc_start: 0.8262 (tt0) cc_final: 0.7960 (tm-30) REVERT: D 582 GLU cc_start: 0.8423 (tp30) cc_final: 0.8197 (tp30) REVERT: D 647 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8581 (t) REVERT: E 380 THR cc_start: 0.8665 (t) cc_final: 0.8436 (m) REVERT: E 405 MET cc_start: 0.3002 (ptm) cc_final: 0.2099 (mtp) REVERT: F 676 ASP cc_start: 0.7677 (m-30) cc_final: 0.7409 (m-30) REVERT: F 891 MET cc_start: 0.3826 (mtm) cc_final: 0.1915 (mtm) outliers start: 51 outliers final: 29 residues processed: 342 average time/residue: 0.2241 time to fit residues: 130.5721 Evaluate side-chains 323 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 291 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 701 HIS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 899 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 362 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 476 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 chunk 451 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 381 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.227403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.177877 restraints weight = 35935.870| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 4.16 r_work: 0.3833 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40325 Z= 0.169 Angle : 0.547 9.278 54216 Z= 0.271 Chirality : 0.042 0.240 6059 Planarity : 0.003 0.060 6604 Dihedral : 14.744 88.420 7307 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.25 % Allowed : 12.39 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.13 (0.12), residues: 4788 helix: 1.79 (0.10), residues: 2802 sheet: -0.53 (0.19), residues: 588 loop : -0.76 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 682 TYR 0.016 0.001 TYR C 691 PHE 0.017 0.001 PHE A 510 TRP 0.015 0.001 TRP B 309 HIS 0.005 0.001 HIS C 701 Details of bonding type rmsd covalent geometry : bond 0.00399 (40313) covalent geometry : angle 0.54746 (54216) hydrogen bonds : bond 0.03632 ( 2315) hydrogen bonds : angle 4.23284 ( 6765) Misc. bond : bond 0.00084 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 646 ASP cc_start: 0.8303 (m-30) cc_final: 0.7936 (m-30) REVERT: B 672 SER cc_start: 0.8460 (t) cc_final: 0.8227 (p) REVERT: B 761 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8792 (mp) REVERT: C 118 MET cc_start: 0.5135 (OUTLIER) cc_final: 0.2904 (tpt) REVERT: C 405 MET cc_start: 0.4735 (ppp) cc_final: 0.3156 (tpt) REVERT: C 908 GLN cc_start: 0.8300 (tt0) cc_final: 0.8007 (tm-30) REVERT: D 647 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8642 (t) REVERT: D 903 PHE cc_start: 0.8679 (t80) cc_final: 0.8456 (t80) REVERT: E 380 THR cc_start: 0.8715 (t) cc_final: 0.8449 (m) REVERT: E 405 MET cc_start: 0.2931 (ptm) cc_final: 0.2032 (mtp) REVERT: E 894 LYS cc_start: 0.6025 (tttm) cc_final: 0.5307 (ptpp) REVERT: E 917 GLU cc_start: 0.6163 (tm-30) cc_final: 0.5463 (tt0) REVERT: F 676 ASP cc_start: 0.7750 (m-30) cc_final: 0.7477 (m-30) REVERT: F 875 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6001 (mt-10) REVERT: F 891 MET cc_start: 0.3541 (mtm) cc_final: 0.1728 (mtm) outliers start: 49 outliers final: 30 residues processed: 338 average time/residue: 0.2217 time to fit residues: 128.5579 Evaluate side-chains 321 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 191 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 231 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 376 optimal weight: 0.7980 chunk 266 optimal weight: 4.9990 chunk 299 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 542 GLN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.230398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.181107 restraints weight = 35768.720| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 4.25 r_work: 0.3863 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40325 Z= 0.121 Angle : 0.511 8.761 54216 Z= 0.254 Chirality : 0.041 0.212 6059 Planarity : 0.003 0.062 6604 Dihedral : 14.040 89.588 7307 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.15 % Allowed : 12.82 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.12), residues: 4788 helix: 1.91 (0.10), residues: 2784 sheet: -0.52 (0.19), residues: 588 loop : -0.78 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 414 TYR 0.014 0.001 TYR C 691 PHE 0.017 0.001 PHE A 510 TRP 0.012 0.001 TRP B 309 HIS 0.005 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00279 (40313) covalent geometry : angle 0.51101 (54216) hydrogen bonds : bond 0.03365 ( 2315) hydrogen bonds : angle 4.12347 ( 6765) Misc. bond : bond 0.00054 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 310 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 433 TYR cc_start: 0.0182 (OUTLIER) cc_final: -0.1855 (m-80) REVERT: A 875 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6500 (mt-10) REVERT: B 646 ASP cc_start: 0.8082 (m-30) cc_final: 0.7739 (m-30) REVERT: B 672 SER cc_start: 0.8397 (t) cc_final: 0.8158 (p) REVERT: B 761 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8736 (mp) REVERT: B 886 MET cc_start: 0.8205 (mmt) cc_final: 0.7810 (mmp) REVERT: C 118 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.2926 (tpt) REVERT: C 405 MET cc_start: 0.4684 (ppp) cc_final: 0.3159 (tpt) REVERT: D 647 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8544 (t) REVERT: D 903 PHE cc_start: 0.8516 (t80) cc_final: 0.8262 (t80) REVERT: E 380 THR cc_start: 0.8648 (t) cc_final: 0.8357 (m) REVERT: E 405 MET cc_start: 0.2821 (ptm) cc_final: 0.2088 (mtp) REVERT: E 631 MET cc_start: 0.8402 (tpp) cc_final: 0.7686 (tpp) REVERT: E 894 LYS cc_start: 0.5874 (tttm) cc_final: 0.5277 (ptpp) REVERT: F 676 ASP cc_start: 0.7566 (m-30) cc_final: 0.7289 (m-30) REVERT: F 891 MET cc_start: 0.3492 (mtm) cc_final: 0.1657 (mtm) outliers start: 45 outliers final: 28 residues processed: 340 average time/residue: 0.2184 time to fit residues: 127.7428 Evaluate side-chains 320 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 750 TRP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 57 optimal weight: 0.6980 chunk 421 optimal weight: 1.9990 chunk 445 optimal weight: 0.1980 chunk 231 optimal weight: 4.9990 chunk 474 optimal weight: 0.6980 chunk 233 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 ASN ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN ** D 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.229623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.179737 restraints weight = 35916.844| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 4.27 r_work: 0.3851 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40325 Z= 0.133 Angle : 0.532 9.369 54216 Z= 0.262 Chirality : 0.041 0.231 6059 Planarity : 0.003 0.064 6604 Dihedral : 13.938 89.815 7307 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.97 % Allowed : 13.05 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.12), residues: 4788 helix: 1.90 (0.10), residues: 2802 sheet: -0.52 (0.19), residues: 588 loop : -0.76 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 414 TYR 0.014 0.001 TYR C 691 PHE 0.017 0.001 PHE A 510 TRP 0.015 0.001 TRP B 309 HIS 0.005 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00310 (40313) covalent geometry : angle 0.53154 (54216) hydrogen bonds : bond 0.03409 ( 2315) hydrogen bonds : angle 4.11545 ( 6765) Misc. bond : bond 0.00061 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 302 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 TYR cc_start: 0.0266 (OUTLIER) cc_final: -0.1807 (m-80) REVERT: B 646 ASP cc_start: 0.8054 (m-30) cc_final: 0.7739 (m-30) REVERT: B 672 SER cc_start: 0.8420 (t) cc_final: 0.8160 (p) REVERT: B 761 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8766 (mp) REVERT: B 886 MET cc_start: 0.8202 (mmt) cc_final: 0.7823 (mmp) REVERT: C 118 MET cc_start: 0.5088 (OUTLIER) cc_final: 0.2944 (tpt) REVERT: C 405 MET cc_start: 0.4635 (ppp) cc_final: 0.3124 (tpt) REVERT: D 647 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8531 (t) REVERT: D 903 PHE cc_start: 0.8559 (t80) cc_final: 0.8327 (t80) REVERT: E 380 THR cc_start: 0.8649 (t) cc_final: 0.8387 (m) REVERT: E 405 MET cc_start: 0.2938 (ptm) cc_final: 0.2057 (mtp) REVERT: E 894 LYS cc_start: 0.5934 (tttm) cc_final: 0.5328 (ptpp) REVERT: E 917 GLU cc_start: 0.6228 (tm-30) cc_final: 0.5644 (tt0) REVERT: F 676 ASP cc_start: 0.7559 (m-30) cc_final: 0.7280 (m-30) REVERT: F 891 MET cc_start: 0.3330 (mtm) cc_final: 0.1529 (mtm) outliers start: 38 outliers final: 29 residues processed: 327 average time/residue: 0.2150 time to fit residues: 121.6486 Evaluate side-chains 327 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 750 TRP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 701 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 36 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 454 optimal weight: 9.9990 chunk 91 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 466 optimal weight: 1.9990 chunk 435 optimal weight: 10.0000 chunk 318 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 342 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 ASN ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN ** D 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.232042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.183293 restraints weight = 35632.121| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 4.28 r_work: 0.3872 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40325 Z= 0.110 Angle : 0.518 13.332 54216 Z= 0.255 Chirality : 0.041 0.269 6059 Planarity : 0.003 0.064 6604 Dihedral : 13.345 89.120 7307 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.87 % Allowed : 13.13 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.12), residues: 4788 helix: 1.99 (0.10), residues: 2802 sheet: -0.39 (0.20), residues: 558 loop : -0.75 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 414 TYR 0.016 0.001 TYR B 579 PHE 0.023 0.001 PHE E 510 TRP 0.019 0.001 TRP B 750 HIS 0.004 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00251 (40313) covalent geometry : angle 0.51757 (54216) hydrogen bonds : bond 0.03263 ( 2315) hydrogen bonds : angle 4.03777 ( 6765) Misc. bond : bond 0.00048 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 319 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLN cc_start: 0.7237 (tp40) cc_final: 0.6759 (mm-40) REVERT: A 433 TYR cc_start: 0.0186 (OUTLIER) cc_final: -0.1988 (m-80) REVERT: B 646 ASP cc_start: 0.8000 (m-30) cc_final: 0.7645 (m-30) REVERT: B 761 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8745 (mp) REVERT: B 886 MET cc_start: 0.8239 (mmt) cc_final: 0.7888 (mmp) REVERT: C 118 MET cc_start: 0.5079 (OUTLIER) cc_final: 0.2945 (tpt) REVERT: C 405 MET cc_start: 0.4659 (ppp) cc_final: 0.3052 (tpt) REVERT: D 647 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8462 (t) REVERT: E 405 MET cc_start: 0.3141 (ptm) cc_final: 0.2292 (mtp) REVERT: E 631 MET cc_start: 0.8248 (tpp) cc_final: 0.7952 (tpp) REVERT: E 894 LYS cc_start: 0.5939 (tttm) cc_final: 0.5317 (ptpp) REVERT: E 917 GLU cc_start: 0.6184 (tm-30) cc_final: 0.5605 (tt0) REVERT: F 258 MET cc_start: -0.1789 (ptm) cc_final: -0.2090 (ptm) REVERT: F 676 ASP cc_start: 0.7560 (m-30) cc_final: 0.7278 (m-30) REVERT: F 891 MET cc_start: 0.3287 (mtm) cc_final: 0.1447 (mtm) outliers start: 34 outliers final: 23 residues processed: 343 average time/residue: 0.2210 time to fit residues: 130.1116 Evaluate side-chains 331 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 433 TYR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 701 HIS Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 820 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 223 optimal weight: 0.6980 chunk 423 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 379 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 ASN ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN D 542 GLN ** D 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 614 HIS ** 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 = 0.4474 r_free = 0.4474 target = 0.227432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.176950 restraints weight = 35879.617| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 4.23 r_work: 0.3820 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40325 Z= 0.177 Angle : 0.576 12.667 54216 Z= 0.282 Chirality : 0.043 0.273 6059 Planarity : 0.003 0.065 6604 Dihedral : 14.109 89.574 7307 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.99 % Allowed : 13.05 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.12), residues: 4788 helix: 1.85 (0.10), residues: 2790 sheet: -0.51 (0.19), residues: 588 loop : -0.69 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.015 0.001 TYR C 691 PHE 0.023 0.001 PHE D 903 TRP 0.020 0.001 TRP B 309 HIS 0.006 0.001 HIS B 701 Details of bonding type rmsd covalent geometry : bond 0.00422 (40313) covalent geometry : angle 0.57621 (54216) hydrogen bonds : bond 0.03631 ( 2315) hydrogen bonds : angle 4.17828 ( 6765) Misc. bond : bond 0.00087 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9466.73 seconds wall clock time: 163 minutes 23.48 seconds (9803.48 seconds total)