Starting phenix.real_space_refine on Sun Aug 9 14:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uv2_42603/08_2026/8uv2_42603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uv2_42603/08_2026/8uv2_42603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uv2_42603/08_2026/8uv2_42603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uv2_42603/08_2026/8uv2_42603.map" model { file = "/net/cci-nas-00/data/ceres_data/8uv2_42603/08_2026/8uv2_42603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uv2_42603/08_2026/8uv2_42603.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 186 5.16 5 C 22302 2.51 5 N 6306 2.21 5 O 6750 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.09s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35580 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5834 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Chain breaks: 1 Chain: "B" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5834 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Chain breaks: 1 Chain: "C" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5834 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Chain breaks: 1 Chain: "D" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5834 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Chain breaks: 1 Chain: "E" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5834 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Chain breaks: 1 Chain: "F" Number of atoms: 5834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5834 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 701} Chain breaks: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ADP': 2, 'XKM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ADP': 2, 'XKM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ADP': 2, 'XKM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ADP': 2, 'XKM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ADP': 2, 'XKM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ADP': 2, 'XKM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.72, per 1000 atoms: 0.25 Number of scatterers: 35580 At special positions: 0 Unit cell: (173.68, 171.6, 96.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 186 16.00 P 24 15.00 F 12 9.00 O 6750 8.00 N 6306 7.00 C 22302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8316 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 30 sheets defined 50.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 4.007A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 120 through 124 removed outlier: 4.051A pdb=" N VAL A 123 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.556A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.924A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.592A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.826A pdb=" N ASN A 270 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 6.181A pdb=" N LEU A 278 " --> pdb=" O MET A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.894A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 334 removed outlier: 4.136A pdb=" N THR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 removed outlier: 3.650A pdb=" N ARG A 338 " --> pdb=" O LEU A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.584A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 408 through 424 removed outlier: 3.529A pdb=" N ALA A 419 " --> pdb=" O CYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 removed outlier: 3.607A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.509A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.736A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.577A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.630A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 714 removed outlier: 3.839A pdb=" N SER A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.733A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 748 through 764 removed outlier: 3.515A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.990A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 120 through 124 removed outlier: 4.069A pdb=" N VAL B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.544A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.539A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.885A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 250 through 260 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.811A pdb=" N ASN B 270 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 6.186A pdb=" N LEU B 278 " --> pdb=" O MET B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 294 removed outlier: 3.890A pdb=" N GLU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 removed outlier: 4.142A pdb=" N THR B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 removed outlier: 3.644A pdb=" N ARG B 338 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.571A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.582A pdb=" N ALA B 419 " --> pdb=" O CYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.594A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.537A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.534A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 570 removed outlier: 3.729A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 598 through 612 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.591A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 663 removed outlier: 4.517A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.620A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.891A pdb=" N SER B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.706A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 764 removed outlier: 4.097A pdb=" N GLN B 764 " --> pdb=" O GLN B 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 4.006A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 120 through 124 removed outlier: 4.061A pdb=" N VAL C 123 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.536A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 141 Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.520A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.842A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.752A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.824A pdb=" N ASN C 270 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 6.180A pdb=" N LEU C 278 " --> pdb=" O MET C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.903A pdb=" N GLU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 327 through 334 removed outlier: 3.596A pdb=" N LEU C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 338 removed outlier: 3.684A pdb=" N ARG C 338 " --> pdb=" O LEU C 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 335 through 338' Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.572A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 408 through 424 removed outlier: 3.596A pdb=" N ALA C 419 " --> pdb=" O CYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 removed outlier: 3.597A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.549A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.570A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 570 removed outlier: 3.720A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.516A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.542A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.646A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 714 removed outlier: 3.874A pdb=" N SER C 705 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.718A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'D' and resid 42 through 49 removed outlier: 4.008A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.062A pdb=" N VAL D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.505A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.917A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 250 through 260 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.826A pdb=" N ASN D 270 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 removed outlier: 6.178A pdb=" N LEU D 278 " --> pdb=" O MET D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 294 removed outlier: 3.893A pdb=" N GLU D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 318 through 334 removed outlier: 4.138A pdb=" N THR D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 removed outlier: 3.653A pdb=" N ARG D 338 " --> pdb=" O LEU D 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.586A pdb=" N SER D 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 408 through 424 removed outlier: 3.540A pdb=" N ALA D 419 " --> pdb=" O CYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 removed outlier: 3.607A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.508A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 570 removed outlier: 3.741A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 585 Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.578A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.620A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 714 removed outlier: 3.837A pdb=" N SER D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.733A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU D 738 " --> pdb=" O ASP D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 748 through 762 removed outlier: 3.514A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.988A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 120 through 124 removed outlier: 4.076A pdb=" N VAL E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 removed outlier: 3.555A pdb=" N VAL E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.557A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.896A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.684A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 260 Processing helix chain 'E' and resid 266 through 270 removed outlier: 3.811A pdb=" N ASN E 270 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 278 removed outlier: 6.186A pdb=" N LEU E 278 " --> pdb=" O MET E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 294 removed outlier: 3.886A pdb=" N GLU E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU E 294 " --> pdb=" O PHE E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 334 removed outlier: 4.139A pdb=" N THR E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 331 " --> pdb=" O GLN E 327 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 338 removed outlier: 3.685A pdb=" N ARG E 338 " --> pdb=" O LEU E 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 335 through 338' Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.567A pdb=" N SER E 352 " --> pdb=" O ARG E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 408 through 424 removed outlier: 3.588A pdb=" N ALA E 419 " --> pdb=" O CYS E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 444 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 removed outlier: 3.587A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.537A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.533A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 570 removed outlier: 3.729A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 585 Processing helix chain 'E' and resid 598 through 612 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.593A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 663 removed outlier: 4.519A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.630A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 removed outlier: 3.891A pdb=" N SER E 705 " --> pdb=" O GLU E 701 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.714A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU E 738 " --> pdb=" O ASP E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 764 removed outlier: 4.102A pdb=" N GLN E 764 " --> pdb=" O GLN E 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 4.004A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU F 48 " --> pdb=" O PRO F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 120 through 124 removed outlier: 4.064A pdb=" N VAL F 123 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 134 removed outlier: 3.536A pdb=" N VAL F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.876A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 250 through 260 Processing helix chain 'F' and resid 266 through 270 removed outlier: 3.825A pdb=" N ASN F 270 " --> pdb=" O PHE F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 278 removed outlier: 6.182A pdb=" N LEU F 278 " --> pdb=" O MET F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 294 removed outlier: 3.906A pdb=" N GLU F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 327 Processing helix chain 'F' and resid 327 through 334 removed outlier: 3.595A pdb=" N LEU F 331 " --> pdb=" O GLN F 327 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 338 removed outlier: 3.678A pdb=" N ARG F 338 " --> pdb=" O LEU F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 335 through 338' Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.571A pdb=" N SER F 352 " --> pdb=" O ARG F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 386 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 408 through 424 removed outlier: 3.598A pdb=" N ALA F 419 " --> pdb=" O CYS F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 494 removed outlier: 3.591A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.550A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.543A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 570 removed outlier: 3.719A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 585 Processing helix chain 'F' and resid 598 through 612 removed outlier: 3.512A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.545A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.626A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 714 removed outlier: 3.874A pdb=" N SER F 705 " --> pdb=" O GLU F 701 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 3.722A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU F 738 " --> pdb=" O ASP F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 8.011A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 40 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.089A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 117 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 164 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 300 removed outlier: 6.497A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 541 removed outlier: 5.978A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 29 removed outlier: 8.012A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 40 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 117 removed outlier: 6.054A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 117 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 164 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA9, first strand: chain 'B' and resid 299 through 300 removed outlier: 6.484A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR B 347 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 243 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 541 removed outlier: 5.956A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 29 removed outlier: 7.962A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 40 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 115 through 117 removed outlier: 6.063A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 117 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 164 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AB5, first strand: chain 'C' and resid 299 through 300 removed outlier: 6.460A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR C 347 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU C 243 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 541 removed outlier: 6.821A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 29 removed outlier: 8.010A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 40 " --> pdb=" O ARG D 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 115 through 117 removed outlier: 6.088A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 117 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 164 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AC1, first strand: chain 'D' and resid 299 through 300 removed outlier: 6.491A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 541 removed outlier: 5.979A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 29 removed outlier: 8.013A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 40 " --> pdb=" O ARG E 83 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 115 through 117 removed outlier: 6.055A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 117 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 164 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AC6, first strand: chain 'E' and resid 299 through 300 removed outlier: 6.516A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 541 removed outlier: 5.955A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.961A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 40 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 115 through 117 removed outlier: 6.062A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU F 117 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS F 164 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=AD2, first strand: chain 'F' and resid 299 through 300 removed outlier: 6.454A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 541 removed outlier: 6.836A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1379 hydrogen bonds defined for protein. 3846 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: 10.44 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 11575 1.33 - 1.45: 3824 1.45 - 1.57: 20456 1.57 - 1.69: 55 1.69 - 1.81: 300 Bond restraints: 36210 Sorted by residual: bond pdb=" C31 XKM B 903 " pdb=" C32 XKM B 903 " ideal model delta sigma weight residual 1.366 1.718 -0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" C31 XKM E 903 " pdb=" C32 XKM E 903 " ideal model delta sigma weight residual 1.366 1.717 -0.351 2.00e-02 2.50e+03 3.08e+02 bond pdb=" C31 XKM F 903 " pdb=" C32 XKM F 903 " ideal model delta sigma weight residual 1.366 1.716 -0.350 2.00e-02 2.50e+03 3.06e+02 bond pdb=" C31 XKM C 903 " pdb=" C32 XKM C 903 " ideal model delta sigma weight residual 1.366 1.716 -0.350 2.00e-02 2.50e+03 3.05e+02 bond pdb=" C31 XKM A 903 " pdb=" C32 XKM A 903 " ideal model delta sigma weight residual 1.366 1.714 -0.348 2.00e-02 2.50e+03 3.04e+02 ... (remaining 36205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 48330 3.41 - 6.83: 503 6.83 - 10.24: 61 10.24 - 13.65: 30 13.65 - 17.07: 18 Bond angle restraints: 48942 Sorted by residual: angle pdb=" C40 XKM E 903 " pdb=" C19 XKM E 903 " pdb=" O20 XKM E 903 " ideal model delta sigma weight residual 112.40 129.47 -17.07 3.00e+00 1.11e-01 3.24e+01 angle pdb=" C40 XKM B 903 " pdb=" C19 XKM B 903 " pdb=" O20 XKM B 903 " ideal model delta sigma weight residual 112.40 129.43 -17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C40 XKM D 903 " pdb=" C19 XKM D 903 " pdb=" O20 XKM D 903 " ideal model delta sigma weight residual 112.40 129.39 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" C40 XKM C 903 " pdb=" C19 XKM C 903 " pdb=" O20 XKM C 903 " ideal model delta sigma weight residual 112.40 129.38 -16.98 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C40 XKM A 903 " pdb=" C19 XKM A 903 " pdb=" O20 XKM A 903 " ideal model delta sigma weight residual 112.40 129.37 -16.97 3.00e+00 1.11e-01 3.20e+01 ... (remaining 48937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.85: 21522 30.85 - 61.70: 802 61.70 - 92.54: 121 92.54 - 123.39: 20 123.39 - 154.24: 11 Dihedral angle restraints: 22476 sinusoidal: 9648 harmonic: 12828 Sorted by residual: dihedral pdb=" CA ARG B 744 " pdb=" C ARG B 744 " pdb=" N ARG B 745 " pdb=" CA ARG B 745 " ideal model delta harmonic sigma weight residual 180.00 143.66 36.34 0 5.00e+00 4.00e-02 5.28e+01 dihedral pdb=" CA ARG A 744 " pdb=" C ARG A 744 " pdb=" N ARG A 745 " pdb=" CA ARG A 745 " ideal model delta harmonic sigma weight residual 180.00 144.25 35.75 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" CA ARG E 744 " pdb=" C ARG E 744 " pdb=" N ARG E 745 " pdb=" CA ARG E 745 " ideal model delta harmonic sigma weight residual 180.00 144.78 35.22 0 5.00e+00 4.00e-02 4.96e+01 ... (remaining 22473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 5155 0.097 - 0.194: 269 0.194 - 0.291: 0 0.291 - 0.388: 5 0.388 - 0.485: 7 Chirality restraints: 5436 Sorted by residual: chirality pdb=" C27 XKM C 903 " pdb=" C28 XKM C 903 " pdb=" C32 XKM C 903 " pdb=" S26 XKM C 903 " both_signs ideal model delta sigma weight residual False 3.62 3.13 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" C27 XKM F 903 " pdb=" C28 XKM F 903 " pdb=" C32 XKM F 903 " pdb=" S26 XKM F 903 " both_signs ideal model delta sigma weight residual False 3.62 3.13 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C27 XKM E 903 " pdb=" C28 XKM E 903 " pdb=" C32 XKM E 903 " pdb=" S26 XKM E 903 " both_signs ideal model delta sigma weight residual False 3.62 3.14 0.48 2.00e-01 2.50e+01 5.72e+00 ... (remaining 5433 not shown) Planarity restraints: 6420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 766 " 0.309 9.50e-02 1.11e+02 1.38e-01 1.18e+01 pdb=" NE ARG F 766 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG F 766 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG F 766 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG F 766 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 766 " 0.228 9.50e-02 1.11e+02 1.02e-01 6.42e+00 pdb=" NE ARG C 766 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 766 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 766 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 766 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 435 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" CD GLU A 435 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU A 435 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 435 " -0.015 2.00e-02 2.50e+03 ... (remaining 6417 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 382 2.56 - 3.15: 32162 3.15 - 3.73: 55914 3.73 - 4.32: 81188 4.32 - 4.90: 132926 Nonbonded interactions: 302572 Sorted by model distance: nonbonded pdb=" OH TYR A 495 " pdb=" OE2 GLU F 704 " model vdw 1.975 3.040 nonbonded pdb=" OE2 GLU B 704 " pdb=" OH TYR C 495 " model vdw 1.979 3.040 nonbonded pdb=" OE2 GLU C 704 " pdb=" OH TYR D 495 " model vdw 1.980 3.040 nonbonded pdb=" OE2 GLU E 704 " pdb=" OH TYR F 495 " model vdw 1.980 3.040 nonbonded pdb=" OE2 GLU A 704 " pdb=" OH TYR B 495 " model vdw 1.984 3.040 ... (remaining 302567 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 39.150 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.008 0.352 36210 Z= 0.395 Angle : 0.971 17.068 48942 Z= 0.486 Chirality : 0.049 0.485 5436 Planarity : 0.006 0.138 6420 Dihedral : 16.949 154.240 14160 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.29 % Allowed : 12.27 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.66 (0.12), residues: 4434 helix: -1.35 (0.11), residues: 1806 sheet: -2.70 (0.18), residues: 708 loop : -1.60 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 766 TYR 0.019 0.002 TYR D 173 PHE 0.022 0.002 PHE A 230 TRP 0.012 0.002 TRP D 551 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.40 (36210) covalent geometry : angle 0.97114 / 0.49 (48942) hydrogen bonds : bond 0.19616 / 13.07 ( 1379) hydrogen bonds : angle 8.50535 / 5.95 ( 3846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 979 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8050 (mp) cc_final: 0.7848 (mt) REVERT: A 134 TYR cc_start: 0.6853 (m-80) cc_final: 0.6513 (m-10) REVERT: A 183 HIS cc_start: 0.7095 (t70) cc_final: 0.6890 (t-90) REVERT: A 219 MET cc_start: 0.7665 (ttm) cc_final: 0.7413 (ttm) REVERT: A 307 ASP cc_start: 0.8003 (t0) cc_final: 0.7590 (t0) REVERT: A 363 PHE cc_start: 0.8044 (m-80) cc_final: 0.7745 (m-10) REVERT: A 382 GLN cc_start: 0.7524 (mt0) cc_final: 0.7306 (tp-100) REVERT: A 477 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6885 (mt-10) REVERT: A 608 MET cc_start: 0.7799 (mtt) cc_final: 0.7572 (mtp) REVERT: A 625 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7584 (mmm-85) REVERT: A 628 ILE cc_start: 0.7171 (mm) cc_final: 0.6877 (mm) REVERT: A 645 ILE cc_start: 0.8992 (mm) cc_final: 0.8733 (mm) REVERT: A 757 MET cc_start: 0.6562 (ttm) cc_final: 0.6362 (mtp) REVERT: B 102 ILE cc_start: 0.7998 (mp) cc_final: 0.7214 (tt) REVERT: B 167 GLU cc_start: 0.7099 (tp30) cc_final: 0.5862 (mt-10) REVERT: B 216 ILE cc_start: 0.8323 (mm) cc_final: 0.8112 (mt) REVERT: B 307 ASP cc_start: 0.7786 (t0) cc_final: 0.7375 (t0) REVERT: B 381 LEU cc_start: 0.8411 (mt) cc_final: 0.8106 (mt) REVERT: B 477 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6857 (mt-10) REVERT: B 578 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7374 (mt-10) REVERT: B 607 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7271 (mm-30) REVERT: B 625 ARG cc_start: 0.7679 (mmt180) cc_final: 0.7426 (mmm-85) REVERT: B 628 ILE cc_start: 0.7428 (mm) cc_final: 0.7118 (mm) REVERT: C 154 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7751 (t) REVERT: C 307 ASP cc_start: 0.7794 (t0) cc_final: 0.7493 (t0) REVERT: C 378 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7950 (tp) REVERT: C 488 GLU cc_start: 0.7318 (tt0) cc_final: 0.7106 (mt-10) REVERT: C 624 ASN cc_start: 0.7490 (p0) cc_final: 0.6656 (p0) REVERT: C 628 ILE cc_start: 0.7008 (mm) cc_final: 0.6751 (mm) REVERT: C 642 LEU cc_start: 0.8210 (mp) cc_final: 0.8010 (mp) REVERT: C 757 MET cc_start: 0.6478 (ttm) cc_final: 0.6257 (mtp) REVERT: D 102 ILE cc_start: 0.8011 (mp) cc_final: 0.7796 (mt) REVERT: D 134 TYR cc_start: 0.6821 (m-80) cc_final: 0.6583 (m-10) REVERT: D 219 MET cc_start: 0.7807 (ttm) cc_final: 0.7564 (ttm) REVERT: D 307 ASP cc_start: 0.7864 (t0) cc_final: 0.7455 (t0) REVERT: D 363 PHE cc_start: 0.7958 (m-80) cc_final: 0.7646 (m-10) REVERT: D 477 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6857 (mt-10) REVERT: D 578 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7180 (mt-10) REVERT: D 608 MET cc_start: 0.7544 (mtt) cc_final: 0.7331 (mtp) REVERT: D 625 ARG cc_start: 0.7732 (mmt180) cc_final: 0.7499 (mmm-85) REVERT: D 628 ILE cc_start: 0.7103 (mm) cc_final: 0.6684 (mm) REVERT: D 645 ILE cc_start: 0.8853 (mm) cc_final: 0.8595 (mm) REVERT: E 102 ILE cc_start: 0.7999 (mp) cc_final: 0.7200 (tt) REVERT: E 167 GLU cc_start: 0.7005 (tp30) cc_final: 0.5853 (mt-10) REVERT: E 216 ILE cc_start: 0.8236 (mm) cc_final: 0.8026 (mt) REVERT: E 307 ASP cc_start: 0.7791 (t0) cc_final: 0.7373 (t0) REVERT: E 381 LEU cc_start: 0.8385 (mt) cc_final: 0.8127 (mt) REVERT: E 477 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6871 (mt-10) REVERT: E 578 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7350 (mt-10) REVERT: E 607 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7288 (mm-30) REVERT: E 625 ARG cc_start: 0.7657 (mmt180) cc_final: 0.7440 (mmm-85) REVERT: E 628 ILE cc_start: 0.7405 (mm) cc_final: 0.7035 (mm) REVERT: F 307 ASP cc_start: 0.7791 (t0) cc_final: 0.7489 (t0) REVERT: F 488 GLU cc_start: 0.7221 (tt0) cc_final: 0.7011 (mt-10) REVERT: F 624 ASN cc_start: 0.7443 (p0) cc_final: 0.6516 (p0) REVERT: F 628 ILE cc_start: 0.7031 (mm) cc_final: 0.6769 (mm) REVERT: F 642 LEU cc_start: 0.8140 (mp) cc_final: 0.7925 (mp) REVERT: F 757 MET cc_start: 0.6422 (ttm) cc_final: 0.6183 (mtp) outliers start: 11 outliers final: 7 residues processed: 990 average time/residue: 0.2693 time to fit residues: 407.0790 Evaluate side-chains 664 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 655 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain F residue 173 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 406 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN B 90 ASN B 285 ASN B 382 GLN B 406 HIS B 764 GLN C 90 ASN C 226 HIS C 406 HIS C 458 GLN C 616 ASN ** C 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN D 406 HIS ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN E 382 GLN E 406 HIS F 90 ASN F 285 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS F 458 GLN F 616 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.228219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.189849 restraints weight = 39675.561| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.50 r_work: 0.4010 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36210 Z= 0.179 Angle : 0.793 10.384 48942 Z= 0.386 Chirality : 0.048 0.178 5436 Planarity : 0.006 0.053 6420 Dihedral : 13.393 157.943 5224 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.98 % Allowed : 16.30 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.99 (0.13), residues: 4434 helix: -0.63 (0.12), residues: 1860 sheet: -2.36 (0.18), residues: 738 loop : -1.41 (0.16), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 322 TYR 0.016 0.002 TYR C 134 PHE 0.025 0.002 PHE C 363 TRP 0.009 0.002 TRP A 476 HIS 0.007 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (36210) covalent geometry : angle 0.79276 / 0.39 (48942) hydrogen bonds : bond 0.05018 / 3.28 ( 1379) hydrogen bonds : angle 5.84888 / 4.15 ( 3846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 711 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8115 (p90) cc_final: 0.7855 (p90) REVERT: A 167 GLU cc_start: 0.7218 (tp30) cc_final: 0.5590 (mt-10) REVERT: A 183 HIS cc_start: 0.6763 (t70) cc_final: 0.5750 (m90) REVERT: A 236 LYS cc_start: 0.8565 (mttp) cc_final: 0.8048 (mmmt) REVERT: A 238 PRO cc_start: 0.8257 (Cg_exo) cc_final: 0.8045 (Cg_endo) REVERT: A 307 ASP cc_start: 0.7876 (t0) cc_final: 0.7386 (t0) REVERT: A 402 GLU cc_start: 0.7670 (tt0) cc_final: 0.7238 (tt0) REVERT: A 453 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7107 (mmm-85) REVERT: A 608 MET cc_start: 0.7697 (mtt) cc_final: 0.7433 (mtp) REVERT: A 624 ASN cc_start: 0.7458 (p0) cc_final: 0.7097 (p0) REVERT: A 625 ARG cc_start: 0.7656 (mmt180) cc_final: 0.7348 (mmm-85) REVERT: A 628 ILE cc_start: 0.7118 (mm) cc_final: 0.6748 (mm) REVERT: A 645 ILE cc_start: 0.8802 (mm) cc_final: 0.8533 (mm) REVERT: A 701 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 708 ARG cc_start: 0.7062 (ttp80) cc_final: 0.6768 (mtm110) REVERT: A 757 MET cc_start: 0.6782 (ttm) cc_final: 0.6334 (mtp) REVERT: B 60 LYS cc_start: 0.6749 (tptp) cc_final: 0.6205 (ttmt) REVERT: B 134 TYR cc_start: 0.6921 (m-80) cc_final: 0.6304 (m-10) REVERT: B 146 ILE cc_start: 0.7722 (mm) cc_final: 0.7202 (pt) REVERT: B 167 GLU cc_start: 0.7218 (tp30) cc_final: 0.5872 (mt-10) REVERT: B 206 ILE cc_start: 0.8403 (mt) cc_final: 0.8157 (mt) REVERT: B 210 ARG cc_start: 0.6837 (mmt180) cc_final: 0.6218 (mmp-170) REVERT: B 216 ILE cc_start: 0.7771 (mm) cc_final: 0.7485 (mt) REVERT: B 307 ASP cc_start: 0.7994 (t0) cc_final: 0.7616 (t0) REVERT: B 383 ILE cc_start: 0.7532 (mm) cc_final: 0.7313 (mp) REVERT: B 477 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7487 (mt-10) REVERT: B 503 PHE cc_start: 0.7532 (m-80) cc_final: 0.6926 (m-80) REVERT: B 578 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 740 MET cc_start: 0.7129 (tpt) cc_final: 0.6728 (tpt) REVERT: C 167 GLU cc_start: 0.7137 (tp30) cc_final: 0.5695 (mt-10) REVERT: C 183 HIS cc_start: 0.6478 (t-90) cc_final: 0.5282 (m90) REVERT: C 210 ARG cc_start: 0.6859 (mmt180) cc_final: 0.6183 (mmp-170) REVERT: C 236 LYS cc_start: 0.8479 (mttm) cc_final: 0.8053 (mmmt) REVERT: C 488 GLU cc_start: 0.7327 (tt0) cc_final: 0.7072 (mt-10) REVERT: C 503 PHE cc_start: 0.7736 (m-80) cc_final: 0.7031 (m-80) REVERT: C 578 GLU cc_start: 0.7745 (tp30) cc_final: 0.7530 (mm-30) REVERT: C 625 ARG cc_start: 0.7563 (mmt180) cc_final: 0.7333 (mmm-85) REVERT: C 628 ILE cc_start: 0.6906 (mm) cc_final: 0.6617 (mm) REVERT: C 642 LEU cc_start: 0.8278 (mp) cc_final: 0.8032 (mp) REVERT: C 650 GLU cc_start: 0.7119 (tt0) cc_final: 0.6917 (tm-30) REVERT: C 753 ARG cc_start: 0.7367 (mtp180) cc_final: 0.7149 (mtp180) REVERT: C 757 MET cc_start: 0.6592 (ttm) cc_final: 0.6273 (mtp) REVERT: D 152 PHE cc_start: 0.8095 (p90) cc_final: 0.7841 (p90) REVERT: D 167 GLU cc_start: 0.7158 (tp30) cc_final: 0.5542 (mt-10) REVERT: D 183 HIS cc_start: 0.6111 (t-90) cc_final: 0.5250 (m-70) REVERT: D 236 LYS cc_start: 0.8563 (mttp) cc_final: 0.8047 (mmmt) REVERT: D 238 PRO cc_start: 0.8240 (Cg_exo) cc_final: 0.8024 (Cg_endo) REVERT: D 307 ASP cc_start: 0.7869 (t0) cc_final: 0.7385 (t0) REVERT: D 402 GLU cc_start: 0.7746 (tt0) cc_final: 0.7331 (tt0) REVERT: D 445 LEU cc_start: 0.8298 (mt) cc_final: 0.8064 (mp) REVERT: D 453 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7124 (mmm-85) REVERT: D 503 PHE cc_start: 0.7555 (m-80) cc_final: 0.6986 (m-80) REVERT: D 578 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7574 (mt-10) REVERT: D 584 LYS cc_start: 0.8430 (ttpp) cc_final: 0.8139 (ttpp) REVERT: D 608 MET cc_start: 0.7703 (mtt) cc_final: 0.7438 (mtp) REVERT: D 625 ARG cc_start: 0.7590 (mmt180) cc_final: 0.7307 (mmm-85) REVERT: D 628 ILE cc_start: 0.6986 (mm) cc_final: 0.6719 (mm) REVERT: D 645 ILE cc_start: 0.8790 (mm) cc_final: 0.8518 (mm) REVERT: D 701 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6953 (tm-30) REVERT: D 708 ARG cc_start: 0.7083 (ttp80) cc_final: 0.6788 (mtm110) REVERT: E 60 LYS cc_start: 0.6718 (tptp) cc_final: 0.6158 (ttmt) REVERT: E 134 TYR cc_start: 0.6890 (m-80) cc_final: 0.6197 (m-10) REVERT: E 146 ILE cc_start: 0.7733 (mm) cc_final: 0.7212 (pt) REVERT: E 167 GLU cc_start: 0.7179 (tp30) cc_final: 0.5853 (mt-10) REVERT: E 206 ILE cc_start: 0.8416 (mt) cc_final: 0.8131 (mt) REVERT: E 210 ARG cc_start: 0.6930 (mmt180) cc_final: 0.6357 (mmp-170) REVERT: E 216 ILE cc_start: 0.7820 (mm) cc_final: 0.7532 (mt) REVERT: E 229 LEU cc_start: 0.6957 (tt) cc_final: 0.6599 (mp) REVERT: E 236 LYS cc_start: 0.8784 (mttp) cc_final: 0.8197 (mmmt) REVERT: E 307 ASP cc_start: 0.7940 (t0) cc_final: 0.7598 (t0) REVERT: E 383 ILE cc_start: 0.7533 (mm) cc_final: 0.7321 (mp) REVERT: E 445 LEU cc_start: 0.8276 (mp) cc_final: 0.7358 (pp) REVERT: E 477 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7563 (mt-10) REVERT: E 503 PHE cc_start: 0.7513 (m-80) cc_final: 0.6930 (m-80) REVERT: E 526 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7463 (mm) REVERT: E 578 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7545 (mt-10) REVERT: E 740 MET cc_start: 0.7054 (tpt) cc_final: 0.6813 (tpt) REVERT: F 84 MET cc_start: 0.6128 (mtm) cc_final: 0.5915 (mtp) REVERT: F 167 GLU cc_start: 0.7096 (tp30) cc_final: 0.5642 (mt-10) REVERT: F 183 HIS cc_start: 0.6502 (t-90) cc_final: 0.5263 (m90) REVERT: F 210 ARG cc_start: 0.6863 (mmt180) cc_final: 0.6208 (mmp-170) REVERT: F 236 LYS cc_start: 0.8592 (mttm) cc_final: 0.8119 (mmmt) REVERT: F 360 PHE cc_start: 0.7305 (t80) cc_final: 0.7102 (t80) REVERT: F 386 LYS cc_start: 0.7537 (pttm) cc_final: 0.6868 (mmmt) REVERT: F 488 GLU cc_start: 0.7335 (tt0) cc_final: 0.7075 (mt-10) REVERT: F 503 PHE cc_start: 0.7750 (m-80) cc_final: 0.7061 (m-80) REVERT: F 578 GLU cc_start: 0.7739 (tp30) cc_final: 0.7520 (mm-30) REVERT: F 607 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7633 (mm-30) REVERT: F 625 ARG cc_start: 0.7627 (mmt180) cc_final: 0.7411 (mmm-85) REVERT: F 628 ILE cc_start: 0.6960 (mm) cc_final: 0.6676 (mm) REVERT: F 642 LEU cc_start: 0.8261 (mp) cc_final: 0.8020 (mp) REVERT: F 753 ARG cc_start: 0.7360 (mtp180) cc_final: 0.7148 (mtp180) REVERT: F 757 MET cc_start: 0.6545 (ttm) cc_final: 0.6221 (mtp) outliers start: 113 outliers final: 59 residues processed: 797 average time/residue: 0.2339 time to fit residues: 296.3424 Evaluate side-chains 677 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 617 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 771 PHE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 458 GLN Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 771 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 263 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 362 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 348 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 0.0870 chunk 149 optimal weight: 8.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 90 ASN A 285 ASN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 90 ASN B 285 ASN B 404 HIS ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 764 GLN D 85 ASN D 90 ASN D 285 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 90 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 GLN F 85 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.231999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.199481 restraints weight = 40211.748| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.10 r_work: 0.4080 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36210 Z= 0.154 Angle : 0.727 9.356 48942 Z= 0.353 Chirality : 0.047 0.175 5436 Planarity : 0.005 0.055 6420 Dihedral : 12.734 156.563 5221 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.13 % Allowed : 15.82 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.78 (0.13), residues: 4434 helix: -0.47 (0.12), residues: 1842 sheet: -2.26 (0.18), residues: 744 loop : -1.27 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 287 TYR 0.019 0.002 TYR E 138 PHE 0.028 0.002 PHE F 674 TRP 0.009 0.002 TRP E 551 HIS 0.006 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (36210) covalent geometry : angle 0.72717 / 0.35 (48942) hydrogen bonds : bond 0.04257 / 2.79 ( 1379) hydrogen bonds : angle 5.46767 / 3.89 ( 3846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 674 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.6837 (tptp) cc_final: 0.6366 (tppt) REVERT: A 152 PHE cc_start: 0.8031 (p90) cc_final: 0.7635 (p90) REVERT: A 158 MET cc_start: 0.7135 (ttp) cc_final: 0.6592 (ttt) REVERT: A 167 GLU cc_start: 0.7251 (tp30) cc_final: 0.5705 (mt-10) REVERT: A 181 VAL cc_start: 0.5472 (OUTLIER) cc_final: 0.4792 (p) REVERT: A 183 HIS cc_start: 0.6774 (t70) cc_final: 0.5961 (m90) REVERT: A 236 LYS cc_start: 0.8453 (mttp) cc_final: 0.8075 (mmmt) REVERT: A 624 ASN cc_start: 0.7167 (p0) cc_final: 0.6888 (p0) REVERT: A 625 ARG cc_start: 0.7701 (mmt180) cc_final: 0.7451 (mmm-85) REVERT: A 628 ILE cc_start: 0.7234 (mm) cc_final: 0.6853 (mm) REVERT: A 645 ILE cc_start: 0.8720 (mm) cc_final: 0.8448 (mm) REVERT: A 701 GLU cc_start: 0.7256 (tm-30) cc_final: 0.7048 (tm-30) REVERT: A 708 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6758 (mtm110) REVERT: A 752 ILE cc_start: 0.8085 (mt) cc_final: 0.7796 (mm) REVERT: A 757 MET cc_start: 0.6900 (ttm) cc_final: 0.6553 (mtp) REVERT: B 60 LYS cc_start: 0.6792 (tptp) cc_final: 0.6259 (ttmt) REVERT: B 134 TYR cc_start: 0.6798 (m-80) cc_final: 0.6213 (m-10) REVERT: B 146 ILE cc_start: 0.7626 (mm) cc_final: 0.7192 (pt) REVERT: B 158 MET cc_start: 0.7311 (mtm) cc_final: 0.7080 (ttt) REVERT: B 167 GLU cc_start: 0.7255 (tp30) cc_final: 0.5973 (mt-10) REVERT: B 181 VAL cc_start: 0.5271 (OUTLIER) cc_final: 0.4995 (p) REVERT: B 182 ILE cc_start: 0.6836 (mm) cc_final: 0.6615 (mm) REVERT: B 216 ILE cc_start: 0.8082 (mm) cc_final: 0.7793 (mt) REVERT: B 283 GLU cc_start: 0.5349 (mm-30) cc_final: 0.4564 (mt-10) REVERT: B 307 ASP cc_start: 0.7856 (t0) cc_final: 0.7544 (t0) REVERT: B 477 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 494 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6648 (mt0) REVERT: B 578 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7451 (mt-10) REVERT: B 625 ARG cc_start: 0.7640 (mmt180) cc_final: 0.7434 (mmm-85) REVERT: C 60 LYS cc_start: 0.6975 (tptp) cc_final: 0.6186 (tppt) REVERT: C 167 GLU cc_start: 0.7281 (tp30) cc_final: 0.5527 (mt-10) REVERT: C 183 HIS cc_start: 0.6446 (t-90) cc_final: 0.5352 (m90) REVERT: C 206 ILE cc_start: 0.8150 (mt) cc_final: 0.7890 (mt) REVERT: C 210 ARG cc_start: 0.6677 (mmt180) cc_final: 0.6306 (mmp-170) REVERT: C 236 LYS cc_start: 0.8413 (mttm) cc_final: 0.8176 (mmmt) REVERT: C 307 ASP cc_start: 0.7477 (t0) cc_final: 0.7189 (t0) REVERT: C 321 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5916 (tt0) REVERT: C 386 LYS cc_start: 0.7437 (pttm) cc_final: 0.6903 (mmmt) REVERT: C 394 VAL cc_start: 0.8358 (m) cc_final: 0.8098 (p) REVERT: C 488 GLU cc_start: 0.7198 (tt0) cc_final: 0.6986 (mt-10) REVERT: C 624 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7517 (p0) REVERT: C 628 ILE cc_start: 0.7000 (mm) cc_final: 0.6778 (mm) REVERT: C 633 ILE cc_start: 0.8396 (tt) cc_final: 0.8195 (tp) REVERT: C 642 LEU cc_start: 0.8137 (mp) cc_final: 0.7868 (mp) REVERT: C 701 GLU cc_start: 0.6956 (tp30) cc_final: 0.6566 (tm-30) REVERT: C 704 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: C 757 MET cc_start: 0.6695 (ttm) cc_final: 0.6456 (mtp) REVERT: D 60 LYS cc_start: 0.6821 (tptp) cc_final: 0.6318 (tppt) REVERT: D 152 PHE cc_start: 0.8023 (p90) cc_final: 0.7628 (p90) REVERT: D 167 GLU cc_start: 0.7244 (tp30) cc_final: 0.5693 (mt-10) REVERT: D 181 VAL cc_start: 0.5500 (OUTLIER) cc_final: 0.4405 (p) REVERT: D 183 HIS cc_start: 0.6283 (t-90) cc_final: 0.5504 (m90) REVERT: D 236 LYS cc_start: 0.8455 (mttp) cc_final: 0.8098 (mmmt) REVERT: D 578 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7398 (mt-10) REVERT: D 584 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8233 (ttpp) REVERT: D 624 ASN cc_start: 0.7171 (p0) cc_final: 0.6889 (p0) REVERT: D 625 ARG cc_start: 0.7623 (mmt180) cc_final: 0.7391 (mmm-85) REVERT: D 628 ILE cc_start: 0.7246 (mm) cc_final: 0.6888 (mm) REVERT: D 645 ILE cc_start: 0.8731 (mm) cc_final: 0.8458 (mm) REVERT: D 701 GLU cc_start: 0.7256 (tm-30) cc_final: 0.7044 (tm-30) REVERT: D 708 ARG cc_start: 0.6963 (ttp80) cc_final: 0.6754 (mtm110) REVERT: D 772 ARG cc_start: 0.6392 (ptm160) cc_final: 0.6051 (tpt170) REVERT: E 60 LYS cc_start: 0.6783 (tptp) cc_final: 0.6255 (ttmt) REVERT: E 134 TYR cc_start: 0.6834 (m-80) cc_final: 0.6291 (m-10) REVERT: E 146 ILE cc_start: 0.7600 (mm) cc_final: 0.7147 (pt) REVERT: E 154 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7402 (t) REVERT: E 158 MET cc_start: 0.7376 (mtm) cc_final: 0.7043 (ttt) REVERT: E 167 GLU cc_start: 0.7205 (tp30) cc_final: 0.5894 (mt-10) REVERT: E 206 ILE cc_start: 0.8267 (mt) cc_final: 0.7794 (mt) REVERT: E 210 ARG cc_start: 0.6914 (mmt180) cc_final: 0.6406 (mmp-170) REVERT: E 216 ILE cc_start: 0.8088 (mm) cc_final: 0.7800 (mt) REVERT: E 229 LEU cc_start: 0.6874 (tt) cc_final: 0.6538 (mp) REVERT: E 236 LYS cc_start: 0.8722 (mttp) cc_final: 0.8234 (mmmt) REVERT: E 283 GLU cc_start: 0.5340 (mm-30) cc_final: 0.4610 (mt-10) REVERT: E 307 ASP cc_start: 0.7869 (t0) cc_final: 0.7564 (t0) REVERT: E 477 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7629 (mt-10) REVERT: E 494 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6644 (mt0) REVERT: E 578 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7437 (mt-10) REVERT: E 625 ARG cc_start: 0.7658 (mmt180) cc_final: 0.7445 (mmm-85) REVERT: E 740 MET cc_start: 0.7046 (tpt) cc_final: 0.6736 (tpt) REVERT: F 60 LYS cc_start: 0.6972 (tptp) cc_final: 0.6217 (tppt) REVERT: F 167 GLU cc_start: 0.7257 (tp30) cc_final: 0.5507 (mt-10) REVERT: F 183 HIS cc_start: 0.6438 (t-90) cc_final: 0.5332 (m90) REVERT: F 210 ARG cc_start: 0.6719 (mmt180) cc_final: 0.6348 (mmp-170) REVERT: F 236 LYS cc_start: 0.8380 (mttm) cc_final: 0.8126 (mmmt) REVERT: F 321 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5845 (tt0) REVERT: F 360 PHE cc_start: 0.7267 (t80) cc_final: 0.7067 (t80) REVERT: F 386 LYS cc_start: 0.7479 (pttm) cc_final: 0.6890 (mmmt) REVERT: F 394 VAL cc_start: 0.8311 (m) cc_final: 0.8070 (p) REVERT: F 488 GLU cc_start: 0.7216 (tt0) cc_final: 0.6998 (mt-10) REVERT: F 624 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7084 (p0) REVERT: F 628 ILE cc_start: 0.7061 (mm) cc_final: 0.6848 (mm) REVERT: F 642 LEU cc_start: 0.8117 (mp) cc_final: 0.7844 (mp) REVERT: F 701 GLU cc_start: 0.6920 (tp30) cc_final: 0.6562 (tm-30) REVERT: F 704 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: F 757 MET cc_start: 0.6667 (ttm) cc_final: 0.6397 (mtp) outliers start: 195 outliers final: 93 residues processed: 812 average time/residue: 0.2404 time to fit residues: 308.7863 Evaluate side-chains 704 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 599 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 771 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 522 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 771 PHE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 771 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 175 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 408 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 232 optimal weight: 0.0270 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 404 HIS C 85 ASN C 226 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 GLN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN E 348 ASN E 404 HIS ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 624 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.231099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.198881 restraints weight = 40102.818| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.08 r_work: 0.4072 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36210 Z= 0.150 Angle : 0.710 8.484 48942 Z= 0.343 Chirality : 0.046 0.203 5436 Planarity : 0.005 0.048 6420 Dihedral : 12.220 156.273 5221 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.63 % Allowed : 16.77 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.66 (0.13), residues: 4434 helix: -0.33 (0.12), residues: 1842 sheet: -2.20 (0.18), residues: 750 loop : -1.24 (0.16), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 287 TYR 0.013 0.002 TYR D 134 PHE 0.022 0.002 PHE B 674 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (36210) covalent geometry : angle 0.71002 / 0.34 (48942) hydrogen bonds : bond 0.03935 / 2.58 ( 1379) hydrogen bonds : angle 5.33123 / 3.79 ( 3846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 635 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5954 (tp) REVERT: A 60 LYS cc_start: 0.6773 (tptp) cc_final: 0.6320 (tppt) REVERT: A 89 ARG cc_start: 0.6126 (mtm-85) cc_final: 0.5613 (ttm110) REVERT: A 167 GLU cc_start: 0.7188 (tp30) cc_final: 0.5614 (mt-10) REVERT: A 183 HIS cc_start: 0.6741 (t70) cc_final: 0.5976 (m-70) REVERT: A 229 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5937 (tt) REVERT: A 236 LYS cc_start: 0.8374 (mttp) cc_final: 0.8032 (mmmt) REVERT: A 625 ARG cc_start: 0.7671 (mmt180) cc_final: 0.7441 (mmm-85) REVERT: A 628 ILE cc_start: 0.7279 (mm) cc_final: 0.6976 (mm) REVERT: A 645 ILE cc_start: 0.8723 (mm) cc_final: 0.8446 (mm) REVERT: A 701 GLU cc_start: 0.7284 (tm-30) cc_final: 0.7042 (tm-30) REVERT: A 704 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7177 (mp0) REVERT: A 708 ARG cc_start: 0.6961 (ttp80) cc_final: 0.6744 (mtm110) REVERT: A 740 MET cc_start: 0.7317 (tpt) cc_final: 0.7043 (tpt) REVERT: A 757 MET cc_start: 0.6900 (ttm) cc_final: 0.6598 (mtp) REVERT: B 60 LYS cc_start: 0.6804 (tptp) cc_final: 0.6256 (ttmt) REVERT: B 146 ILE cc_start: 0.7745 (mm) cc_final: 0.7219 (pt) REVERT: B 154 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7390 (t) REVERT: B 167 GLU cc_start: 0.7219 (tp30) cc_final: 0.5959 (mt-10) REVERT: B 183 HIS cc_start: 0.6536 (t-90) cc_final: 0.5377 (m90) REVERT: B 216 ILE cc_start: 0.8029 (mm) cc_final: 0.7774 (mt) REVERT: B 307 ASP cc_start: 0.7771 (t0) cc_final: 0.7444 (t0) REVERT: B 458 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: B 477 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7524 (mt-10) REVERT: B 504 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8116 (mm) REVERT: B 578 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7440 (mt-10) REVERT: B 701 GLU cc_start: 0.6864 (tp30) cc_final: 0.6587 (tm-30) REVERT: C 60 LYS cc_start: 0.6940 (tptp) cc_final: 0.6216 (tppt) REVERT: C 85 ASN cc_start: 0.5122 (OUTLIER) cc_final: 0.4899 (p0) REVERT: C 89 ARG cc_start: 0.5925 (mtm-85) cc_final: 0.5528 (mtm110) REVERT: C 154 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7519 (t) REVERT: C 167 GLU cc_start: 0.7212 (tp30) cc_final: 0.5546 (mt-10) REVERT: C 183 HIS cc_start: 0.6487 (t-90) cc_final: 0.5448 (m90) REVERT: C 206 ILE cc_start: 0.8169 (mt) cc_final: 0.7864 (mt) REVERT: C 210 ARG cc_start: 0.6670 (mmt180) cc_final: 0.6354 (mmp-170) REVERT: C 222 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7635 (mp) REVERT: C 236 LYS cc_start: 0.8451 (mttm) cc_final: 0.8150 (mmmt) REVERT: C 283 GLU cc_start: 0.5319 (mm-30) cc_final: 0.5091 (mm-30) REVERT: C 321 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5908 (tt0) REVERT: C 386 LYS cc_start: 0.7472 (pttm) cc_final: 0.6937 (mmmt) REVERT: C 426 LYS cc_start: 0.7538 (tppt) cc_final: 0.7277 (mptt) REVERT: C 628 ILE cc_start: 0.7023 (mm) cc_final: 0.6797 (mm) REVERT: C 701 GLU cc_start: 0.7022 (tp30) cc_final: 0.6635 (tm-30) REVERT: C 757 MET cc_start: 0.6755 (ttm) cc_final: 0.6517 (mtp) REVERT: D 27 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5991 (tp) REVERT: D 60 LYS cc_start: 0.6786 (tptp) cc_final: 0.6323 (tppt) REVERT: D 152 PHE cc_start: 0.8050 (p90) cc_final: 0.7574 (p90) REVERT: D 158 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6826 (mtm) REVERT: D 167 GLU cc_start: 0.7193 (tp30) cc_final: 0.5654 (mt-10) REVERT: D 181 VAL cc_start: 0.5511 (OUTLIER) cc_final: 0.4483 (p) REVERT: D 183 HIS cc_start: 0.6359 (t-90) cc_final: 0.5550 (m90) REVERT: D 229 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6033 (mp) REVERT: D 236 LYS cc_start: 0.8331 (mttp) cc_final: 0.7990 (mmmt) REVERT: D 578 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7360 (mt-10) REVERT: D 584 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8186 (ttpp) REVERT: D 624 ASN cc_start: 0.7155 (p0) cc_final: 0.6857 (p0) REVERT: D 625 ARG cc_start: 0.7687 (mmt180) cc_final: 0.7450 (mmm-85) REVERT: D 628 ILE cc_start: 0.7332 (mm) cc_final: 0.7007 (mm) REVERT: D 645 ILE cc_start: 0.8719 (mm) cc_final: 0.8437 (mm) REVERT: D 701 GLU cc_start: 0.7262 (tm-30) cc_final: 0.7017 (tm-30) REVERT: D 704 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7063 (mp0) REVERT: D 708 ARG cc_start: 0.6950 (ttp80) cc_final: 0.6739 (mtm110) REVERT: D 740 MET cc_start: 0.7454 (tpt) cc_final: 0.7236 (tpt) REVERT: D 772 ARG cc_start: 0.6304 (ptm160) cc_final: 0.5861 (tpt170) REVERT: D 773 PHE cc_start: 0.6983 (m-10) cc_final: 0.6716 (m-10) REVERT: E 60 LYS cc_start: 0.6751 (tptp) cc_final: 0.6194 (ttmt) REVERT: E 146 ILE cc_start: 0.7717 (mm) cc_final: 0.7179 (pt) REVERT: E 154 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7433 (t) REVERT: E 158 MET cc_start: 0.7353 (mtm) cc_final: 0.7045 (ttt) REVERT: E 167 GLU cc_start: 0.7139 (tp30) cc_final: 0.5844 (mt-10) REVERT: E 182 ILE cc_start: 0.7027 (mm) cc_final: 0.6776 (mm) REVERT: E 216 ILE cc_start: 0.8034 (mm) cc_final: 0.7771 (mt) REVERT: E 229 LEU cc_start: 0.6876 (tt) cc_final: 0.6533 (mp) REVERT: E 236 LYS cc_start: 0.8643 (mttp) cc_final: 0.8157 (mmmt) REVERT: E 307 ASP cc_start: 0.7806 (t0) cc_final: 0.7484 (t0) REVERT: E 477 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 504 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8101 (mm) REVERT: E 578 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7436 (mt-10) REVERT: E 701 GLU cc_start: 0.6875 (tp30) cc_final: 0.6658 (tm-30) REVERT: E 740 MET cc_start: 0.7186 (tpt) cc_final: 0.6964 (tpt) REVERT: F 60 LYS cc_start: 0.6922 (tptp) cc_final: 0.6130 (tppt) REVERT: F 131 PHE cc_start: 0.7283 (t80) cc_final: 0.6700 (t80) REVERT: F 167 GLU cc_start: 0.7137 (tp30) cc_final: 0.5509 (mt-10) REVERT: F 183 HIS cc_start: 0.6543 (t-90) cc_final: 0.5455 (m90) REVERT: F 210 ARG cc_start: 0.6692 (mmt180) cc_final: 0.6327 (mmp-170) REVERT: F 229 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6224 (mp) REVERT: F 236 LYS cc_start: 0.8461 (mttm) cc_final: 0.8169 (mmmt) REVERT: F 283 GLU cc_start: 0.5289 (mm-30) cc_final: 0.5061 (mm-30) REVERT: F 321 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5976 (tt0) REVERT: F 360 PHE cc_start: 0.7398 (t80) cc_final: 0.7147 (t80) REVERT: F 386 LYS cc_start: 0.7419 (pttm) cc_final: 0.6865 (mmmt) REVERT: F 453 ARG cc_start: 0.7392 (mmm-85) cc_final: 0.7022 (mmm-85) REVERT: F 488 GLU cc_start: 0.7197 (tt0) cc_final: 0.6994 (mt-10) REVERT: F 608 MET cc_start: 0.7266 (mtt) cc_final: 0.7018 (mtp) REVERT: F 628 ILE cc_start: 0.7115 (mm) cc_final: 0.6883 (mm) REVERT: F 701 GLU cc_start: 0.6953 (tp30) cc_final: 0.6605 (tm-30) REVERT: F 757 MET cc_start: 0.6717 (ttm) cc_final: 0.6470 (mtp) outliers start: 176 outliers final: 101 residues processed: 769 average time/residue: 0.2344 time to fit residues: 287.4586 Evaluate side-chains 693 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 575 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 771 PHE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 771 PHE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 771 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 400 optimal weight: 0.5980 chunk 236 optimal weight: 6.9990 chunk 363 optimal weight: 0.9990 chunk 417 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 chunk 398 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 404 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 404 HIS ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS E 404 HIS ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.230769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.198255 restraints weight = 40123.105| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.12 r_work: 0.4080 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36210 Z= 0.152 Angle : 0.695 7.257 48942 Z= 0.335 Chirality : 0.046 0.151 5436 Planarity : 0.005 0.048 6420 Dihedral : 11.943 153.957 5221 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.82 % Allowed : 16.69 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.58 (0.13), residues: 4434 helix: -0.24 (0.12), residues: 1842 sheet: -2.24 (0.19), residues: 696 loop : -1.24 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 287 TYR 0.014 0.002 TYR D 134 PHE 0.023 0.001 PHE A 674 TRP 0.010 0.002 TRP A 551 HIS 0.006 0.001 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (36210) covalent geometry : angle 0.69486 / 0.34 (48942) hydrogen bonds : bond 0.03793 / 2.49 ( 1379) hydrogen bonds : angle 5.27223 / 3.75 ( 3846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 616 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.6005 (tp) REVERT: A 60 LYS cc_start: 0.6914 (tptp) cc_final: 0.6496 (tppt) REVERT: A 167 GLU cc_start: 0.7276 (tp30) cc_final: 0.5745 (mt-10) REVERT: A 183 HIS cc_start: 0.6798 (t70) cc_final: 0.6081 (m-70) REVERT: A 236 LYS cc_start: 0.8302 (mttp) cc_final: 0.8028 (mmmt) REVERT: A 628 ILE cc_start: 0.7301 (mm) cc_final: 0.6932 (mm) REVERT: A 701 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6987 (tm-30) REVERT: A 704 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7018 (mp0) REVERT: A 740 MET cc_start: 0.7350 (tpt) cc_final: 0.7063 (tpt) REVERT: A 757 MET cc_start: 0.6922 (ttm) cc_final: 0.6600 (mtp) REVERT: B 60 LYS cc_start: 0.6919 (tptp) cc_final: 0.6560 (ttmt) REVERT: B 146 ILE cc_start: 0.7763 (mm) cc_final: 0.7260 (pt) REVERT: B 154 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7569 (t) REVERT: B 167 GLU cc_start: 0.7294 (tp30) cc_final: 0.6090 (mt-10) REVERT: B 183 HIS cc_start: 0.6549 (t-90) cc_final: 0.5502 (m90) REVERT: B 216 ILE cc_start: 0.8065 (mm) cc_final: 0.7837 (mt) REVERT: B 307 ASP cc_start: 0.7729 (t0) cc_final: 0.7409 (t0) REVERT: B 458 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7950 (mt0) REVERT: B 477 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7491 (mt-10) REVERT: B 526 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7242 (mm) REVERT: B 578 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 633 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8049 (tt) REVERT: B 701 GLU cc_start: 0.6877 (tp30) cc_final: 0.6652 (tm-30) REVERT: C 27 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5706 (tp) REVERT: C 60 LYS cc_start: 0.7117 (tptp) cc_final: 0.6342 (tppt) REVERT: C 84 MET cc_start: 0.6336 (mtt) cc_final: 0.6023 (mtm) REVERT: C 89 ARG cc_start: 0.6044 (mtm-85) cc_final: 0.5572 (mtm110) REVERT: C 154 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7609 (t) REVERT: C 167 GLU cc_start: 0.7177 (tp30) cc_final: 0.5466 (mt-10) REVERT: C 183 HIS cc_start: 0.6633 (t-90) cc_final: 0.5634 (m90) REVERT: C 222 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7760 (mp) REVERT: C 229 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6300 (tt) REVERT: C 236 LYS cc_start: 0.8433 (mttm) cc_final: 0.8231 (mmmt) REVERT: C 321 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5851 (tt0) REVERT: C 386 LYS cc_start: 0.7388 (pttm) cc_final: 0.6962 (mmmt) REVERT: C 426 LYS cc_start: 0.7676 (tppt) cc_final: 0.7393 (mptt) REVERT: C 453 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.6936 (mmm-85) REVERT: C 572 CYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7662 (t) REVERT: C 628 ILE cc_start: 0.7058 (mm) cc_final: 0.6825 (mm) REVERT: C 701 GLU cc_start: 0.7000 (tp30) cc_final: 0.6658 (tm-30) REVERT: C 757 MET cc_start: 0.6739 (ttm) cc_final: 0.6452 (mtp) REVERT: D 60 LYS cc_start: 0.6933 (tptp) cc_final: 0.6492 (tppt) REVERT: D 131 PHE cc_start: 0.7350 (t80) cc_final: 0.6901 (t80) REVERT: D 167 GLU cc_start: 0.7259 (tp30) cc_final: 0.5744 (mt-10) REVERT: D 181 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.4491 (p) REVERT: D 183 HIS cc_start: 0.6400 (t-90) cc_final: 0.5609 (m90) REVERT: D 229 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6062 (mp) REVERT: D 236 LYS cc_start: 0.8209 (mttp) cc_final: 0.7971 (mmmt) REVERT: D 477 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7513 (mt-10) REVERT: D 578 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7260 (mt-10) REVERT: D 584 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8200 (ttpp) REVERT: D 625 ARG cc_start: 0.7646 (mmt180) cc_final: 0.7406 (mmm-85) REVERT: D 628 ILE cc_start: 0.7312 (mm) cc_final: 0.7052 (mm) REVERT: D 645 ILE cc_start: 0.8714 (mm) cc_final: 0.8425 (mm) REVERT: D 701 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 704 GLU cc_start: 0.7788 (mm-30) cc_final: 0.6985 (mp0) REVERT: D 740 MET cc_start: 0.7407 (tpt) cc_final: 0.7055 (tpt) REVERT: D 772 ARG cc_start: 0.6359 (ptm160) cc_final: 0.5945 (tpt170) REVERT: E 60 LYS cc_start: 0.6873 (tptp) cc_final: 0.6510 (ttmt) REVERT: E 131 PHE cc_start: 0.7298 (t80) cc_final: 0.6796 (t80) REVERT: E 134 TYR cc_start: 0.6858 (m-80) cc_final: 0.6321 (m-10) REVERT: E 154 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7467 (t) REVERT: E 167 GLU cc_start: 0.7284 (tp30) cc_final: 0.6065 (mt-10) REVERT: E 183 HIS cc_start: 0.6701 (t-90) cc_final: 0.5650 (m90) REVERT: E 216 ILE cc_start: 0.8084 (mm) cc_final: 0.7861 (mt) REVERT: E 229 LEU cc_start: 0.6926 (tt) cc_final: 0.6608 (mp) REVERT: E 236 LYS cc_start: 0.8632 (mttp) cc_final: 0.8185 (mmmt) REVERT: E 307 ASP cc_start: 0.7736 (t0) cc_final: 0.7415 (t0) REVERT: E 445 LEU cc_start: 0.8161 (mp) cc_final: 0.7437 (pp) REVERT: E 477 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7535 (mt-10) REVERT: E 526 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7295 (mm) REVERT: E 578 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7429 (mt-10) REVERT: E 633 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8025 (tt) REVERT: F 60 LYS cc_start: 0.7137 (tptp) cc_final: 0.6331 (tppt) REVERT: F 131 PHE cc_start: 0.7267 (t80) cc_final: 0.7038 (t80) REVERT: F 167 GLU cc_start: 0.7186 (tp30) cc_final: 0.5430 (mt-10) REVERT: F 183 HIS cc_start: 0.6683 (t-90) cc_final: 0.5709 (m90) REVERT: F 229 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6338 (mp) REVERT: F 236 LYS cc_start: 0.8407 (mttm) cc_final: 0.8186 (mmmt) REVERT: F 283 GLU cc_start: 0.5378 (mm-30) cc_final: 0.5097 (mm-30) REVERT: F 321 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5808 (tt0) REVERT: F 453 ARG cc_start: 0.7446 (mmm-85) cc_final: 0.7005 (mmm-85) REVERT: F 488 GLU cc_start: 0.7153 (tt0) cc_final: 0.6920 (mt-10) REVERT: F 572 CYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7595 (t) REVERT: F 611 MET cc_start: 0.7760 (tpp) cc_final: 0.7545 (tpp) REVERT: F 628 ILE cc_start: 0.7132 (mm) cc_final: 0.6876 (mm) REVERT: F 701 GLU cc_start: 0.6959 (tp30) cc_final: 0.6657 (tm-30) REVERT: F 757 MET cc_start: 0.6732 (ttm) cc_final: 0.6456 (mtp) outliers start: 183 outliers final: 116 residues processed: 750 average time/residue: 0.2255 time to fit residues: 270.2257 Evaluate side-chains 709 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 574 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 771 PHE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 771 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 771 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 262 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 393 optimal weight: 3.9990 chunk 409 optimal weight: 4.9990 chunk 234 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.4012 > 50:) chunk 299 optimal weight: 9.9990 chunk 410 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 404 HIS ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 404 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.227373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.194716 restraints weight = 40108.368| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.09 r_work: 0.4049 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 36210 Z= 0.204 Angle : 0.721 7.549 48942 Z= 0.350 Chirality : 0.047 0.174 5436 Planarity : 0.005 0.049 6420 Dihedral : 11.708 155.425 5221 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.19 % Allowed : 16.80 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.62 (0.13), residues: 4434 helix: -0.26 (0.12), residues: 1836 sheet: -2.31 (0.18), residues: 690 loop : -1.26 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 287 TYR 0.018 0.002 TYR B 517 PHE 0.030 0.002 PHE B 131 TRP 0.011 0.001 TRP D 551 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (36210) covalent geometry : angle 0.72148 / 0.35 (48942) hydrogen bonds : bond 0.03846 / 2.52 ( 1379) hydrogen bonds : angle 5.32401 / 3.79 ( 3846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 630 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.6010 (tp) REVERT: A 60 LYS cc_start: 0.6873 (tptp) cc_final: 0.6357 (tppt) REVERT: A 89 ARG cc_start: 0.6607 (mtm110) cc_final: 0.6244 (ttm110) REVERT: A 131 PHE cc_start: 0.7291 (t80) cc_final: 0.6957 (t80) REVERT: A 152 PHE cc_start: 0.8084 (p90) cc_final: 0.7712 (p90) REVERT: A 158 MET cc_start: 0.6961 (mtm) cc_final: 0.6690 (ttt) REVERT: A 167 GLU cc_start: 0.7281 (tp30) cc_final: 0.5730 (mt-10) REVERT: A 183 HIS cc_start: 0.6892 (t70) cc_final: 0.6158 (m-70) REVERT: A 229 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6180 (mp) REVERT: A 236 LYS cc_start: 0.8337 (mttp) cc_final: 0.8023 (mmmt) REVERT: A 258 VAL cc_start: 0.8055 (t) cc_final: 0.7725 (m) REVERT: A 283 GLU cc_start: 0.5403 (mm-30) cc_final: 0.5054 (mm-30) REVERT: A 307 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: A 445 LEU cc_start: 0.8363 (mt) cc_final: 0.7691 (pp) REVERT: A 628 ILE cc_start: 0.7413 (mm) cc_final: 0.7181 (mm) REVERT: A 701 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7092 (tm-30) REVERT: A 704 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7242 (mp0) REVERT: A 740 MET cc_start: 0.7309 (tpt) cc_final: 0.7040 (tpt) REVERT: A 757 MET cc_start: 0.6838 (ttm) cc_final: 0.6523 (mtp) REVERT: B 60 LYS cc_start: 0.6973 (tptp) cc_final: 0.6466 (ttmt) REVERT: B 154 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7502 (t) REVERT: B 167 GLU cc_start: 0.7262 (tp30) cc_final: 0.6020 (mt-10) REVERT: B 183 HIS cc_start: 0.6677 (t-90) cc_final: 0.5618 (m90) REVERT: B 216 ILE cc_start: 0.8076 (mm) cc_final: 0.7854 (mt) REVERT: B 229 LEU cc_start: 0.6985 (tt) cc_final: 0.6601 (mp) REVERT: B 307 ASP cc_start: 0.7782 (t0) cc_final: 0.7451 (t0) REVERT: B 442 MET cc_start: 0.7563 (tpp) cc_final: 0.7295 (tpt) REVERT: B 458 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: B 477 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 526 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7289 (mm) REVERT: B 578 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7525 (mt-10) REVERT: B 633 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8060 (tt) REVERT: B 701 GLU cc_start: 0.6941 (tp30) cc_final: 0.6725 (tm-30) REVERT: B 772 ARG cc_start: 0.6211 (ptm-80) cc_final: 0.5988 (tpt170) REVERT: C 27 ILE cc_start: 0.5988 (OUTLIER) cc_final: 0.5703 (tp) REVERT: C 60 LYS cc_start: 0.7229 (tptp) cc_final: 0.6555 (tppt) REVERT: C 84 MET cc_start: 0.6294 (mtt) cc_final: 0.5968 (mtm) REVERT: C 167 GLU cc_start: 0.7244 (tp30) cc_final: 0.5586 (mt-10) REVERT: C 183 HIS cc_start: 0.6921 (t-90) cc_final: 0.5801 (m90) REVERT: C 222 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7790 (mp) REVERT: C 229 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6616 (tt) REVERT: C 236 LYS cc_start: 0.8429 (mttm) cc_final: 0.8219 (mmmt) REVERT: C 321 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5930 (tt0) REVERT: C 386 LYS cc_start: 0.7489 (pttm) cc_final: 0.7049 (mmmt) REVERT: C 453 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.6997 (mmm-85) REVERT: C 508 MET cc_start: 0.7614 (tpt) cc_final: 0.7412 (tpt) REVERT: C 572 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7692 (t) REVERT: C 628 ILE cc_start: 0.7171 (mm) cc_final: 0.6935 (mm) REVERT: C 701 GLU cc_start: 0.7031 (tp30) cc_final: 0.6724 (tm-30) REVERT: C 757 MET cc_start: 0.6734 (ttm) cc_final: 0.6446 (mtp) REVERT: D 27 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.6001 (tp) REVERT: D 60 LYS cc_start: 0.6896 (tptp) cc_final: 0.6423 (tppt) REVERT: D 131 PHE cc_start: 0.7323 (t80) cc_final: 0.7007 (t80) REVERT: D 152 PHE cc_start: 0.8089 (p90) cc_final: 0.7784 (p90) REVERT: D 158 MET cc_start: 0.7045 (mtm) cc_final: 0.6769 (ttt) REVERT: D 167 GLU cc_start: 0.7236 (tp30) cc_final: 0.5692 (mt-10) REVERT: D 181 VAL cc_start: 0.5547 (OUTLIER) cc_final: 0.4769 (p) REVERT: D 183 HIS cc_start: 0.6616 (t-90) cc_final: 0.5742 (m90) REVERT: D 229 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6246 (mp) REVERT: D 236 LYS cc_start: 0.8292 (mttp) cc_final: 0.7997 (mmmt) REVERT: D 300 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8205 (mt) REVERT: D 307 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: D 578 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7354 (mt-10) REVERT: D 584 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8228 (ttpp) REVERT: D 625 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7445 (mmm-85) REVERT: D 628 ILE cc_start: 0.7340 (mm) cc_final: 0.7082 (mm) REVERT: D 645 ILE cc_start: 0.8817 (mm) cc_final: 0.8535 (mm) REVERT: D 682 PHE cc_start: 0.7769 (m-80) cc_final: 0.7539 (m-80) REVERT: D 701 GLU cc_start: 0.7276 (tm-30) cc_final: 0.7060 (tm-30) REVERT: D 704 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7176 (mp0) REVERT: D 740 MET cc_start: 0.7379 (tpt) cc_final: 0.7009 (tpt) REVERT: D 772 ARG cc_start: 0.6399 (ptm160) cc_final: 0.6137 (ptm160) REVERT: E 60 LYS cc_start: 0.6918 (tptp) cc_final: 0.6401 (ttmt) REVERT: E 131 PHE cc_start: 0.7386 (t80) cc_final: 0.7089 (t80) REVERT: E 154 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7584 (t) REVERT: E 167 GLU cc_start: 0.7214 (tp30) cc_final: 0.5939 (mt-10) REVERT: E 216 ILE cc_start: 0.8125 (mm) cc_final: 0.7882 (mt) REVERT: E 229 LEU cc_start: 0.7092 (tt) cc_final: 0.6763 (mp) REVERT: E 236 LYS cc_start: 0.8641 (mttp) cc_final: 0.8191 (mmmt) REVERT: E 307 ASP cc_start: 0.7751 (t0) cc_final: 0.7423 (t0) REVERT: E 477 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7561 (mt-10) REVERT: E 526 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7344 (mm) REVERT: E 578 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7483 (mt-10) REVERT: E 633 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8056 (tt) REVERT: E 740 MET cc_start: 0.6964 (tpt) cc_final: 0.6744 (tpt) REVERT: F 60 LYS cc_start: 0.7269 (tptp) cc_final: 0.6587 (tppt) REVERT: F 95 ARG cc_start: 0.7334 (mmm-85) cc_final: 0.6500 (mmt180) REVERT: F 167 GLU cc_start: 0.7209 (tp30) cc_final: 0.5554 (mt-10) REVERT: F 183 HIS cc_start: 0.6926 (t-90) cc_final: 0.5806 (m90) REVERT: F 236 LYS cc_start: 0.8412 (mttm) cc_final: 0.8169 (mmmt) REVERT: F 321 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5837 (tt0) REVERT: F 453 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.6937 (mmm-85) REVERT: F 488 GLU cc_start: 0.7169 (tt0) cc_final: 0.6871 (mt-10) REVERT: F 572 CYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7662 (t) REVERT: F 628 ILE cc_start: 0.7258 (mm) cc_final: 0.7020 (mm) REVERT: F 701 GLU cc_start: 0.6989 (tp30) cc_final: 0.6679 (tm-30) REVERT: F 753 ARG cc_start: 0.7494 (mmt90) cc_final: 0.7204 (mtp-110) REVERT: F 757 MET cc_start: 0.6658 (ttm) cc_final: 0.6360 (mtp) outliers start: 197 outliers final: 137 residues processed: 770 average time/residue: 0.2225 time to fit residues: 275.0377 Evaluate side-chains 764 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 604 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 771 PHE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 625 ARG Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 771 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 771 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 336 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 208 optimal weight: 0.2980 chunk 263 optimal weight: 0.3980 chunk 319 optimal weight: 0.9980 chunk 429 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 chunk 408 optimal weight: 6.9990 chunk 433 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 404 HIS ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 473 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 404 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.228986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.196316 restraints weight = 40045.410| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.07 r_work: 0.4070 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36210 Z= 0.156 Angle : 0.697 9.212 48942 Z= 0.336 Chirality : 0.046 0.151 5436 Planarity : 0.005 0.052 6420 Dihedral : 11.265 153.898 5219 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.48 % Allowed : 18.25 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.56 (0.13), residues: 4434 helix: -0.18 (0.12), residues: 1830 sheet: -2.18 (0.19), residues: 690 loop : -1.30 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 287 TYR 0.014 0.002 TYR A 134 PHE 0.026 0.002 PHE E 682 TRP 0.010 0.001 TRP E 551 HIS 0.017 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (36210) covalent geometry : angle 0.69706 / 0.34 (48942) hydrogen bonds : bond 0.03679 / 2.42 ( 1379) hydrogen bonds : angle 5.24004 / 3.74 ( 3846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 612 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.5993 (tp) REVERT: A 60 LYS cc_start: 0.6811 (tptp) cc_final: 0.6325 (tppt) REVERT: A 89 ARG cc_start: 0.6511 (mtm110) cc_final: 0.6135 (ttm110) REVERT: A 152 PHE cc_start: 0.8083 (p90) cc_final: 0.7577 (p90) REVERT: A 158 MET cc_start: 0.6951 (mtm) cc_final: 0.6734 (ttt) REVERT: A 167 GLU cc_start: 0.7256 (tp30) cc_final: 0.5677 (mt-10) REVERT: A 183 HIS cc_start: 0.6841 (t70) cc_final: 0.6038 (m-70) REVERT: A 229 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6198 (tt) REVERT: A 236 LYS cc_start: 0.8320 (mttp) cc_final: 0.8059 (mmmt) REVERT: A 283 GLU cc_start: 0.5360 (mm-30) cc_final: 0.5068 (mm-30) REVERT: A 300 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8131 (mt) REVERT: A 307 ASP cc_start: 0.7645 (t0) cc_final: 0.7335 (m-30) REVERT: A 628 ILE cc_start: 0.7370 (mm) cc_final: 0.7137 (mm) REVERT: A 701 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7089 (tm-30) REVERT: A 704 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7161 (mp0) REVERT: A 740 MET cc_start: 0.7278 (tpt) cc_final: 0.6906 (tpt) REVERT: A 753 ARG cc_start: 0.7611 (mmt90) cc_final: 0.7121 (mtp-110) REVERT: A 757 MET cc_start: 0.6898 (ttm) cc_final: 0.6565 (mtp) REVERT: B 60 LYS cc_start: 0.6950 (tptp) cc_final: 0.6538 (tppt) REVERT: B 131 PHE cc_start: 0.7465 (t80) cc_final: 0.7148 (t80) REVERT: B 134 TYR cc_start: 0.6872 (m-80) cc_final: 0.6332 (m-10) REVERT: B 144 ARG cc_start: 0.7230 (ptt180) cc_final: 0.7006 (ptt180) REVERT: B 146 ILE cc_start: 0.7803 (mm) cc_final: 0.7510 (pt) REVERT: B 167 GLU cc_start: 0.7252 (tp30) cc_final: 0.6001 (mt-10) REVERT: B 183 HIS cc_start: 0.6605 (t-90) cc_final: 0.5563 (m90) REVERT: B 216 ILE cc_start: 0.8108 (mm) cc_final: 0.7855 (mt) REVERT: B 229 LEU cc_start: 0.7036 (tt) cc_final: 0.6603 (mp) REVERT: B 307 ASP cc_start: 0.7690 (t0) cc_final: 0.7363 (t0) REVERT: B 445 LEU cc_start: 0.8094 (mp) cc_final: 0.7594 (pp) REVERT: B 458 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: B 477 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7529 (mt-10) REVERT: B 526 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7277 (mm) REVERT: B 546 GLU cc_start: 0.7341 (mp0) cc_final: 0.7114 (mp0) REVERT: B 578 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7403 (mt-10) REVERT: B 633 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 772 ARG cc_start: 0.6180 (ptm-80) cc_final: 0.5963 (tpt170) REVERT: C 27 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5753 (tp) REVERT: C 60 LYS cc_start: 0.7229 (tptp) cc_final: 0.6582 (tppt) REVERT: C 84 MET cc_start: 0.6230 (mtt) cc_final: 0.5942 (mtm) REVERT: C 134 TYR cc_start: 0.6950 (m-80) cc_final: 0.6395 (m-10) REVERT: C 167 GLU cc_start: 0.7217 (tp30) cc_final: 0.5539 (mt-10) REVERT: C 183 HIS cc_start: 0.6823 (t-90) cc_final: 0.5775 (m90) REVERT: C 213 LEU cc_start: 0.8055 (tp) cc_final: 0.7854 (tp) REVERT: C 222 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7793 (mp) REVERT: C 229 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6594 (tt) REVERT: C 321 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: C 386 LYS cc_start: 0.7420 (pttm) cc_final: 0.6971 (mmmt) REVERT: C 397 GLU cc_start: 0.7201 (mp0) cc_final: 0.6739 (mp0) REVERT: C 453 ARG cc_start: 0.7502 (mmm-85) cc_final: 0.6939 (mmm-85) REVERT: C 572 CYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7747 (t) REVERT: C 628 ILE cc_start: 0.7121 (mm) cc_final: 0.6887 (mm) REVERT: C 701 GLU cc_start: 0.6946 (tp30) cc_final: 0.6725 (tm-30) REVERT: C 757 MET cc_start: 0.6678 (ttm) cc_final: 0.6401 (mtp) REVERT: D 27 ILE cc_start: 0.6325 (OUTLIER) cc_final: 0.6010 (tp) REVERT: D 60 LYS cc_start: 0.6910 (tptp) cc_final: 0.6366 (tppt) REVERT: D 131 PHE cc_start: 0.7232 (t80) cc_final: 0.6945 (t80) REVERT: D 152 PHE cc_start: 0.8082 (p90) cc_final: 0.7641 (p90) REVERT: D 167 GLU cc_start: 0.7263 (tp30) cc_final: 0.5680 (mt-10) REVERT: D 181 VAL cc_start: 0.5519 (OUTLIER) cc_final: 0.4924 (p) REVERT: D 183 HIS cc_start: 0.6592 (t-90) cc_final: 0.5693 (m90) REVERT: D 229 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6183 (mp) REVERT: D 236 LYS cc_start: 0.8226 (mttp) cc_final: 0.7987 (mmmt) REVERT: D 300 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8134 (mt) REVERT: D 307 ASP cc_start: 0.7531 (t0) cc_final: 0.7248 (m-30) REVERT: D 578 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7319 (mt-10) REVERT: D 584 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8176 (ttpp) REVERT: D 625 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7473 (mmm-85) REVERT: D 628 ILE cc_start: 0.7288 (mm) cc_final: 0.7042 (mm) REVERT: D 645 ILE cc_start: 0.8721 (mm) cc_final: 0.8429 (mm) REVERT: D 682 PHE cc_start: 0.7691 (m-80) cc_final: 0.7481 (m-80) REVERT: D 701 GLU cc_start: 0.7297 (tm-30) cc_final: 0.7058 (tm-30) REVERT: D 704 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7182 (mp0) REVERT: D 740 MET cc_start: 0.7329 (tpt) cc_final: 0.6968 (tpt) REVERT: D 753 ARG cc_start: 0.7614 (mmt90) cc_final: 0.7212 (mtp-110) REVERT: D 772 ARG cc_start: 0.6448 (ptm160) cc_final: 0.6193 (ptm160) REVERT: E 60 LYS cc_start: 0.6907 (tptp) cc_final: 0.6474 (tppt) REVERT: E 131 PHE cc_start: 0.7322 (t80) cc_final: 0.7028 (t80) REVERT: E 134 TYR cc_start: 0.6836 (m-80) cc_final: 0.6307 (m-10) REVERT: E 144 ARG cc_start: 0.7205 (ptt180) cc_final: 0.6967 (ptt180) REVERT: E 146 ILE cc_start: 0.7827 (mm) cc_final: 0.7502 (pt) REVERT: E 167 GLU cc_start: 0.7269 (tp30) cc_final: 0.6023 (mt-10) REVERT: E 183 HIS cc_start: 0.6806 (t-90) cc_final: 0.5676 (m90) REVERT: E 216 ILE cc_start: 0.8125 (mm) cc_final: 0.7884 (mt) REVERT: E 229 LEU cc_start: 0.7098 (tt) cc_final: 0.6781 (mp) REVERT: E 236 LYS cc_start: 0.8654 (mttp) cc_final: 0.8234 (mmmt) REVERT: E 307 ASP cc_start: 0.7678 (t0) cc_final: 0.7336 (t0) REVERT: E 442 MET cc_start: 0.7653 (tpp) cc_final: 0.7374 (tpt) REVERT: E 526 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7323 (mm) REVERT: E 578 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7405 (mt-10) REVERT: E 633 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7857 (tt) REVERT: F 46 MET cc_start: 0.6186 (ptp) cc_final: 0.5958 (ptp) REVERT: F 60 LYS cc_start: 0.7264 (tptp) cc_final: 0.6623 (tppt) REVERT: F 134 TYR cc_start: 0.6798 (m-80) cc_final: 0.6139 (m-10) REVERT: F 167 GLU cc_start: 0.7232 (tp30) cc_final: 0.5519 (mt-10) REVERT: F 183 HIS cc_start: 0.6826 (t-90) cc_final: 0.5746 (m90) REVERT: F 213 LEU cc_start: 0.8027 (tp) cc_final: 0.7827 (tp) REVERT: F 229 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6451 (mp) REVERT: F 321 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5737 (tt0) REVERT: F 453 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.6927 (mmm-85) REVERT: F 488 GLU cc_start: 0.7189 (tt0) cc_final: 0.6907 (mt-10) REVERT: F 508 MET cc_start: 0.7764 (tpt) cc_final: 0.7221 (tpt) REVERT: F 572 CYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7624 (t) REVERT: F 628 ILE cc_start: 0.7224 (mm) cc_final: 0.6974 (mm) REVERT: F 701 GLU cc_start: 0.6958 (tp30) cc_final: 0.6751 (tm-30) REVERT: F 753 ARG cc_start: 0.7466 (mmt90) cc_final: 0.6824 (mtp-110) REVERT: F 757 MET cc_start: 0.6680 (ttm) cc_final: 0.6306 (mtp) outliers start: 170 outliers final: 111 residues processed: 732 average time/residue: 0.2114 time to fit residues: 249.2050 Evaluate side-chains 715 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 583 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 771 PHE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 625 ARG Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 771 PHE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 771 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 129 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 300 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 284 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 186 optimal weight: 9.9990 chunk 383 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 424 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN D 43 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 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 = 0.4544 r_free = 0.4544 target = 0.229758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.197390 restraints weight = 40165.325| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.09 r_work: 0.4075 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36210 Z= 0.147 Angle : 0.704 9.559 48942 Z= 0.339 Chirality : 0.046 0.180 5436 Planarity : 0.005 0.060 6420 Dihedral : 11.025 152.383 5216 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.11 % Allowed : 18.72 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.41 (0.13), residues: 4434 helix: -0.02 (0.12), residues: 1800 sheet: -2.16 (0.19), residues: 702 loop : -1.20 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 287 TYR 0.013 0.001 TYR A 134 PHE 0.032 0.002 PHE D 674 TRP 0.012 0.002 TRP A 551 HIS 0.016 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (36210) covalent geometry : angle 0.70415 / 0.34 (48942) hydrogen bonds : bond 0.03602 / 2.36 ( 1379) hydrogen bonds : angle 5.20699 / 3.71 ( 3846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 606 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5982 (tp) REVERT: A 60 LYS cc_start: 0.6769 (tptp) cc_final: 0.6283 (tppt) REVERT: A 152 PHE cc_start: 0.8072 (p90) cc_final: 0.7605 (p90) REVERT: A 167 GLU cc_start: 0.7227 (tp30) cc_final: 0.5650 (mt-10) REVERT: A 183 HIS cc_start: 0.6786 (t70) cc_final: 0.5996 (m-70) REVERT: A 229 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6314 (tt) REVERT: A 236 LYS cc_start: 0.8306 (mttp) cc_final: 0.8054 (mmmt) REVERT: A 258 VAL cc_start: 0.7815 (t) cc_final: 0.7561 (m) REVERT: A 283 GLU cc_start: 0.5379 (mm-30) cc_final: 0.5031 (mm-30) REVERT: A 628 ILE cc_start: 0.7376 (mm) cc_final: 0.7133 (mm) REVERT: A 701 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 704 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7087 (mp0) REVERT: A 740 MET cc_start: 0.7412 (tpt) cc_final: 0.6877 (tpt) REVERT: A 753 ARG cc_start: 0.7561 (mmt90) cc_final: 0.7079 (mtp-110) REVERT: A 757 MET cc_start: 0.6847 (ttm) cc_final: 0.6514 (mtp) REVERT: B 60 LYS cc_start: 0.6889 (tptp) cc_final: 0.6508 (tppt) REVERT: B 131 PHE cc_start: 0.7255 (t80) cc_final: 0.6979 (t80) REVERT: B 134 TYR cc_start: 0.6902 (m-80) cc_final: 0.6329 (m-10) REVERT: B 144 ARG cc_start: 0.7336 (ptt180) cc_final: 0.6974 (mtm-85) REVERT: B 146 ILE cc_start: 0.7882 (mm) cc_final: 0.7583 (pt) REVERT: B 154 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7463 (m) REVERT: B 167 GLU cc_start: 0.7192 (tp30) cc_final: 0.5945 (mt-10) REVERT: B 183 HIS cc_start: 0.6600 (t-90) cc_final: 0.5488 (m90) REVERT: B 216 ILE cc_start: 0.8093 (mm) cc_final: 0.7840 (mt) REVERT: B 229 LEU cc_start: 0.7087 (tt) cc_final: 0.6662 (mp) REVERT: B 236 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7727 (mmtm) REVERT: B 307 ASP cc_start: 0.7665 (t0) cc_final: 0.7346 (t0) REVERT: B 458 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: B 526 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7231 (mm) REVERT: B 546 GLU cc_start: 0.7327 (mp0) cc_final: 0.7096 (mp0) REVERT: B 578 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7392 (mt-10) REVERT: B 633 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7820 (tt) REVERT: B 772 ARG cc_start: 0.6190 (ptm-80) cc_final: 0.5946 (tpt170) REVERT: C 27 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5756 (tp) REVERT: C 60 LYS cc_start: 0.7218 (tptp) cc_final: 0.6597 (tppt) REVERT: C 84 MET cc_start: 0.6261 (mtt) cc_final: 0.6017 (mtm) REVERT: C 134 TYR cc_start: 0.6886 (m-80) cc_final: 0.6362 (m-10) REVERT: C 154 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7648 (m) REVERT: C 159 ARG cc_start: 0.4762 (OUTLIER) cc_final: 0.4543 (mtt180) REVERT: C 167 GLU cc_start: 0.7250 (tp30) cc_final: 0.5425 (mt-10) REVERT: C 183 HIS cc_start: 0.6763 (t-90) cc_final: 0.5751 (m90) REVERT: C 222 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7801 (mp) REVERT: C 229 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6653 (tt) REVERT: C 236 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7776 (mttp) REVERT: C 321 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5923 (tt0) REVERT: C 397 GLU cc_start: 0.7274 (mp0) cc_final: 0.6817 (pm20) REVERT: C 426 LYS cc_start: 0.7714 (tppt) cc_final: 0.7407 (mptt) REVERT: C 453 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.6966 (mmm-85) REVERT: C 508 MET cc_start: 0.7781 (tpt) cc_final: 0.7082 (tpt) REVERT: C 572 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7680 (t) REVERT: C 628 ILE cc_start: 0.7163 (mm) cc_final: 0.6942 (mm) REVERT: C 701 GLU cc_start: 0.6968 (tp30) cc_final: 0.6736 (tm-30) REVERT: C 753 ARG cc_start: 0.7404 (mmt90) cc_final: 0.7090 (mtp-110) REVERT: C 757 MET cc_start: 0.6680 (ttm) cc_final: 0.6412 (mtp) REVERT: D 27 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6058 (tp) REVERT: D 60 LYS cc_start: 0.6855 (tptp) cc_final: 0.6364 (tppt) REVERT: D 131 PHE cc_start: 0.7225 (t80) cc_final: 0.6967 (t80) REVERT: D 152 PHE cc_start: 0.8074 (p90) cc_final: 0.7674 (p90) REVERT: D 167 GLU cc_start: 0.7224 (tp30) cc_final: 0.5616 (mt-10) REVERT: D 183 HIS cc_start: 0.6524 (t-90) cc_final: 0.5705 (m-70) REVERT: D 229 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6283 (mp) REVERT: D 236 LYS cc_start: 0.8228 (mttp) cc_final: 0.7983 (mmmt) REVERT: D 578 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7277 (mt-10) REVERT: D 625 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7441 (mmm-85) REVERT: D 628 ILE cc_start: 0.7291 (mm) cc_final: 0.7055 (mm) REVERT: D 701 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7051 (tm-30) REVERT: D 704 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7205 (mp0) REVERT: D 740 MET cc_start: 0.7401 (tpt) cc_final: 0.7037 (tpt) REVERT: D 753 ARG cc_start: 0.7635 (mmt90) cc_final: 0.7214 (mtp-110) REVERT: D 772 ARG cc_start: 0.6382 (ptm160) cc_final: 0.6131 (ptm160) REVERT: E 60 LYS cc_start: 0.6848 (tptp) cc_final: 0.6449 (tppt) REVERT: E 131 PHE cc_start: 0.7362 (t80) cc_final: 0.7068 (t80) REVERT: E 134 TYR cc_start: 0.6867 (m-80) cc_final: 0.6299 (m-10) REVERT: E 144 ARG cc_start: 0.7341 (ptt180) cc_final: 0.6908 (mtm-85) REVERT: E 146 ILE cc_start: 0.7819 (mm) cc_final: 0.7503 (pt) REVERT: E 154 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7428 (m) REVERT: E 167 GLU cc_start: 0.7266 (tp30) cc_final: 0.6014 (mt-10) REVERT: E 183 HIS cc_start: 0.6797 (t-90) cc_final: 0.5651 (m90) REVERT: E 216 ILE cc_start: 0.8100 (mm) cc_final: 0.7861 (mt) REVERT: E 229 LEU cc_start: 0.7097 (tt) cc_final: 0.6802 (mp) REVERT: E 236 LYS cc_start: 0.8633 (mttp) cc_final: 0.8273 (mmmt) REVERT: E 307 ASP cc_start: 0.7672 (t0) cc_final: 0.7335 (t0) REVERT: E 442 MET cc_start: 0.7562 (tpp) cc_final: 0.7345 (tpp) REVERT: E 445 LEU cc_start: 0.8140 (mp) cc_final: 0.7723 (pp) REVERT: E 526 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7271 (mm) REVERT: E 546 GLU cc_start: 0.7345 (mp0) cc_final: 0.7109 (mp0) REVERT: E 578 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7416 (mt-10) REVERT: E 633 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7818 (tt) REVERT: F 46 MET cc_start: 0.6290 (ptp) cc_final: 0.6057 (ptp) REVERT: F 60 LYS cc_start: 0.7224 (tptp) cc_final: 0.6577 (tppt) REVERT: F 95 ARG cc_start: 0.7120 (mmm-85) cc_final: 0.6501 (mmt-90) REVERT: F 134 TYR cc_start: 0.6765 (m-80) cc_final: 0.6259 (m-10) REVERT: F 167 GLU cc_start: 0.7219 (tp30) cc_final: 0.5380 (mt-10) REVERT: F 183 HIS cc_start: 0.6765 (t-90) cc_final: 0.5691 (m90) REVERT: F 213 LEU cc_start: 0.8008 (tp) cc_final: 0.7805 (tp) REVERT: F 229 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6492 (mp) REVERT: F 321 GLU cc_start: 0.6053 (OUTLIER) cc_final: 0.5740 (tt0) REVERT: F 426 LYS cc_start: 0.7743 (tppt) cc_final: 0.7388 (mptt) REVERT: F 488 GLU cc_start: 0.7133 (tt0) cc_final: 0.6848 (mt-10) REVERT: F 508 MET cc_start: 0.7779 (tpt) cc_final: 0.7250 (tpt) REVERT: F 572 CYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7661 (t) REVERT: F 628 ILE cc_start: 0.7288 (mm) cc_final: 0.7052 (mm) REVERT: F 701 GLU cc_start: 0.7008 (tp30) cc_final: 0.6760 (tm-30) REVERT: F 704 GLU cc_start: 0.7554 (mp0) cc_final: 0.7253 (mp0) REVERT: F 753 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6968 (mtp-110) REVERT: F 757 MET cc_start: 0.6607 (ttm) cc_final: 0.6317 (mtp) outliers start: 156 outliers final: 107 residues processed: 713 average time/residue: 0.2162 time to fit residues: 248.2560 Evaluate side-chains 707 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 578 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 159 ARG Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 771 PHE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 625 ARG Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 771 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain F residue 771 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 131 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 303 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 46 optimal weight: 0.0970 chunk 3 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.229493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.197230 restraints weight = 40059.557| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.29 r_work: 0.4070 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36210 Z= 0.154 Angle : 0.704 8.983 48942 Z= 0.338 Chirality : 0.046 0.198 5436 Planarity : 0.005 0.061 6420 Dihedral : 10.789 151.722 5214 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.71 % Allowed : 19.12 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.36 (0.13), residues: 4434 helix: 0.02 (0.12), residues: 1800 sheet: -2.15 (0.19), residues: 702 loop : -1.19 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 732 TYR 0.013 0.002 TYR F 244 PHE 0.032 0.002 PHE A 674 TRP 0.011 0.002 TRP E 551 HIS 0.018 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (36210) covalent geometry : angle 0.70363 / 0.34 (48942) hydrogen bonds : bond 0.03569 / 2.34 ( 1379) hydrogen bonds : angle 5.18686 / 3.69 ( 3846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 599 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.6049 (tp) REVERT: A 60 LYS cc_start: 0.6638 (tptp) cc_final: 0.6087 (tppt) REVERT: A 152 PHE cc_start: 0.8071 (p90) cc_final: 0.7604 (p90) REVERT: A 167 GLU cc_start: 0.7234 (tp30) cc_final: 0.5602 (mt-10) REVERT: A 183 HIS cc_start: 0.6808 (t70) cc_final: 0.6008 (m-70) REVERT: A 229 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6397 (tt) REVERT: A 236 LYS cc_start: 0.8299 (mttp) cc_final: 0.8043 (mmmt) REVERT: A 258 VAL cc_start: 0.7798 (t) cc_final: 0.7544 (m) REVERT: A 283 GLU cc_start: 0.5488 (mm-30) cc_final: 0.5124 (mm-30) REVERT: A 508 MET cc_start: 0.7553 (tpt) cc_final: 0.7351 (tpt) REVERT: A 628 ILE cc_start: 0.7397 (mm) cc_final: 0.7164 (mm) REVERT: A 701 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 704 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7184 (mp0) REVERT: A 740 MET cc_start: 0.7352 (tpt) cc_final: 0.6996 (tpt) REVERT: A 753 ARG cc_start: 0.7593 (mmt90) cc_final: 0.7092 (mtp-110) REVERT: A 757 MET cc_start: 0.6883 (ttm) cc_final: 0.6553 (mtp) REVERT: B 60 LYS cc_start: 0.6928 (tptp) cc_final: 0.6509 (tppt) REVERT: B 131 PHE cc_start: 0.7254 (t80) cc_final: 0.7020 (t80) REVERT: B 134 TYR cc_start: 0.6890 (m-80) cc_final: 0.6317 (m-10) REVERT: B 144 ARG cc_start: 0.7471 (ptt180) cc_final: 0.6746 (ptt180) REVERT: B 146 ILE cc_start: 0.7865 (mm) cc_final: 0.7557 (pt) REVERT: B 154 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7517 (m) REVERT: B 167 GLU cc_start: 0.7153 (tp30) cc_final: 0.5886 (mt-10) REVERT: B 183 HIS cc_start: 0.6625 (t-90) cc_final: 0.5522 (m90) REVERT: B 216 ILE cc_start: 0.8100 (mm) cc_final: 0.7842 (mt) REVERT: B 229 LEU cc_start: 0.7237 (tt) cc_final: 0.6856 (mp) REVERT: B 236 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7805 (mmtm) REVERT: B 307 ASP cc_start: 0.7665 (t0) cc_final: 0.7347 (t0) REVERT: B 445 LEU cc_start: 0.8036 (mp) cc_final: 0.7561 (pp) REVERT: B 458 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: B 526 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7235 (mm) REVERT: B 578 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7413 (mt-10) REVERT: B 753 ARG cc_start: 0.7370 (mmt90) cc_final: 0.7117 (mmt90) REVERT: B 772 ARG cc_start: 0.6148 (ptm-80) cc_final: 0.5900 (tpt90) REVERT: C 27 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5820 (tp) REVERT: C 60 LYS cc_start: 0.7238 (tptp) cc_final: 0.6638 (tppt) REVERT: C 84 MET cc_start: 0.6187 (mtt) cc_final: 0.5937 (mtm) REVERT: C 134 TYR cc_start: 0.6893 (m-80) cc_final: 0.6425 (m-10) REVERT: C 154 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7680 (m) REVERT: C 167 GLU cc_start: 0.7357 (tp30) cc_final: 0.5673 (mt-10) REVERT: C 183 HIS cc_start: 0.6726 (t-90) cc_final: 0.5679 (m90) REVERT: C 222 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7793 (mp) REVERT: C 229 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6758 (tt) REVERT: C 236 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7763 (mttp) REVERT: C 321 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5938 (tt0) REVERT: C 323 ARG cc_start: 0.6412 (ttm110) cc_final: 0.5924 (ttm-80) REVERT: C 397 GLU cc_start: 0.7240 (mp0) cc_final: 0.6811 (pm20) REVERT: C 426 LYS cc_start: 0.7734 (tppt) cc_final: 0.7451 (mptt) REVERT: C 445 LEU cc_start: 0.8275 (mp) cc_final: 0.8032 (pp) REVERT: C 453 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.6953 (mmm-85) REVERT: C 508 MET cc_start: 0.7708 (tpt) cc_final: 0.7260 (tpt) REVERT: C 572 CYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7631 (t) REVERT: C 628 ILE cc_start: 0.7212 (mm) cc_final: 0.6992 (mm) REVERT: C 701 GLU cc_start: 0.6959 (tp30) cc_final: 0.6723 (tm-30) REVERT: C 753 ARG cc_start: 0.7403 (mmt90) cc_final: 0.7054 (mtp-110) REVERT: C 757 MET cc_start: 0.6627 (ttm) cc_final: 0.6360 (mtp) REVERT: D 27 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.6057 (tp) REVERT: D 60 LYS cc_start: 0.6837 (tptp) cc_final: 0.6365 (tppt) REVERT: D 131 PHE cc_start: 0.7235 (t80) cc_final: 0.6993 (t80) REVERT: D 152 PHE cc_start: 0.8067 (p90) cc_final: 0.7691 (p90) REVERT: D 158 MET cc_start: 0.6895 (mtm) cc_final: 0.6645 (ttt) REVERT: D 167 GLU cc_start: 0.7177 (tp30) cc_final: 0.5631 (mt-10) REVERT: D 183 HIS cc_start: 0.6626 (t-90) cc_final: 0.5784 (m-70) REVERT: D 229 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6239 (mp) REVERT: D 236 LYS cc_start: 0.8232 (mttp) cc_final: 0.7994 (mmmt) REVERT: D 287 ARG cc_start: 0.6628 (mtm110) cc_final: 0.6379 (ttp80) REVERT: D 504 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8104 (mm) REVERT: D 578 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7332 (mt-10) REVERT: D 584 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8147 (ttpp) REVERT: D 625 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7457 (mmm-85) REVERT: D 628 ILE cc_start: 0.7342 (mm) cc_final: 0.7090 (mm) REVERT: D 701 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7108 (tm-30) REVERT: D 704 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7208 (mp0) REVERT: D 740 MET cc_start: 0.7419 (tpt) cc_final: 0.7018 (tpt) REVERT: D 753 ARG cc_start: 0.7612 (mmt90) cc_final: 0.7229 (mtp-110) REVERT: D 772 ARG cc_start: 0.6402 (ptm160) cc_final: 0.6154 (ptm160) REVERT: E 60 LYS cc_start: 0.6812 (tptp) cc_final: 0.6433 (tppt) REVERT: E 131 PHE cc_start: 0.7371 (t80) cc_final: 0.7092 (t80) REVERT: E 134 TYR cc_start: 0.6884 (m-80) cc_final: 0.6328 (m-10) REVERT: E 144 ARG cc_start: 0.7366 (ptt180) cc_final: 0.6738 (ptt180) REVERT: E 146 ILE cc_start: 0.7836 (mm) cc_final: 0.7522 (pt) REVERT: E 167 GLU cc_start: 0.7356 (tp30) cc_final: 0.6128 (mt-10) REVERT: E 183 HIS cc_start: 0.6774 (t-90) cc_final: 0.5651 (m90) REVERT: E 216 ILE cc_start: 0.8111 (mm) cc_final: 0.7876 (mt) REVERT: E 229 LEU cc_start: 0.7142 (tt) cc_final: 0.6897 (mp) REVERT: E 236 LYS cc_start: 0.8623 (mttp) cc_final: 0.8214 (mmmt) REVERT: E 307 ASP cc_start: 0.7626 (t0) cc_final: 0.7289 (t0) REVERT: E 397 GLU cc_start: 0.7165 (mp0) cc_final: 0.6915 (pm20) REVERT: E 445 LEU cc_start: 0.8111 (mp) cc_final: 0.7675 (pp) REVERT: E 526 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7267 (mm) REVERT: E 546 GLU cc_start: 0.7383 (mp0) cc_final: 0.7138 (mp0) REVERT: E 578 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7388 (mt-10) REVERT: E 633 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8096 (mt) REVERT: F 46 MET cc_start: 0.6302 (ptp) cc_final: 0.6045 (ptp) REVERT: F 60 LYS cc_start: 0.7168 (tptp) cc_final: 0.6516 (tppt) REVERT: F 134 TYR cc_start: 0.6800 (m-80) cc_final: 0.6274 (m-10) REVERT: F 167 GLU cc_start: 0.7310 (tp30) cc_final: 0.5618 (mt-10) REVERT: F 183 HIS cc_start: 0.6806 (t-90) cc_final: 0.5714 (m90) REVERT: F 229 LEU cc_start: 0.6957 (tt) cc_final: 0.6536 (mp) REVERT: F 321 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5955 (tt0) REVERT: F 426 LYS cc_start: 0.7734 (tppt) cc_final: 0.7419 (mptt) REVERT: F 488 GLU cc_start: 0.7033 (tt0) cc_final: 0.6779 (mt-10) REVERT: F 508 MET cc_start: 0.7802 (tpt) cc_final: 0.7246 (tpt) REVERT: F 572 CYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7661 (t) REVERT: F 628 ILE cc_start: 0.7366 (mm) cc_final: 0.7145 (mm) REVERT: F 701 GLU cc_start: 0.6969 (tp30) cc_final: 0.6706 (tm-30) REVERT: F 704 GLU cc_start: 0.7575 (mp0) cc_final: 0.7270 (mp0) REVERT: F 753 ARG cc_start: 0.7423 (mmt90) cc_final: 0.6938 (mtp-110) REVERT: F 757 MET cc_start: 0.6568 (ttm) cc_final: 0.6275 (mtp) outliers start: 141 outliers final: 106 residues processed: 693 average time/residue: 0.2262 time to fit residues: 252.2946 Evaluate side-chains 703 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 578 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 771 PHE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 771 PHE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 625 ARG Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 771 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 180 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 350 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 398 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 415 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 438 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 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 = 0.4542 r_free = 0.4542 target = 0.229473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.196985 restraints weight = 40336.749| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.32 r_work: 0.4068 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36210 Z= 0.153 Angle : 0.704 8.803 48942 Z= 0.339 Chirality : 0.046 0.212 5436 Planarity : 0.005 0.084 6420 Dihedral : 10.497 151.176 5214 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.63 % Allowed : 19.19 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.32 (0.13), residues: 4434 helix: 0.06 (0.12), residues: 1800 sheet: -2.12 (0.19), residues: 702 loop : -1.17 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 732 TYR 0.013 0.001 TYR A 134 PHE 0.044 0.002 PHE E 674 TRP 0.011 0.002 TRP F 551 HIS 0.019 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (36210) covalent geometry : angle 0.70394 / 0.34 (48942) hydrogen bonds : bond 0.03546 / 2.33 ( 1379) hydrogen bonds : angle 5.16945 / 3.68 ( 3846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 586 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.6043 (tp) REVERT: A 60 LYS cc_start: 0.6606 (tptp) cc_final: 0.6059 (tppt) REVERT: A 152 PHE cc_start: 0.8073 (p90) cc_final: 0.7617 (p90) REVERT: A 158 MET cc_start: 0.7037 (mtm) cc_final: 0.6756 (ttt) REVERT: A 167 GLU cc_start: 0.7214 (tp30) cc_final: 0.5608 (mt-10) REVERT: A 183 HIS cc_start: 0.6796 (t70) cc_final: 0.6006 (m-70) REVERT: A 229 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6410 (tt) REVERT: A 236 LYS cc_start: 0.8300 (mttp) cc_final: 0.8026 (mmmt) REVERT: A 258 VAL cc_start: 0.7796 (t) cc_final: 0.7541 (m) REVERT: A 283 GLU cc_start: 0.5636 (mm-30) cc_final: 0.5303 (mm-30) REVERT: A 287 ARG cc_start: 0.6661 (mtm110) cc_final: 0.6448 (ttp80) REVERT: A 628 ILE cc_start: 0.7368 (mm) cc_final: 0.7149 (mm) REVERT: A 634 LEU cc_start: 0.8167 (mm) cc_final: 0.7962 (mt) REVERT: A 701 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 704 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7158 (mp0) REVERT: A 740 MET cc_start: 0.7373 (tpt) cc_final: 0.6965 (tpt) REVERT: A 753 ARG cc_start: 0.7586 (mmt90) cc_final: 0.7087 (mtp-110) REVERT: A 757 MET cc_start: 0.6848 (ttm) cc_final: 0.6518 (mtp) REVERT: B 60 LYS cc_start: 0.6930 (tptp) cc_final: 0.6430 (ttmt) REVERT: B 131 PHE cc_start: 0.7249 (t80) cc_final: 0.7020 (t80) REVERT: B 134 TYR cc_start: 0.6886 (m-80) cc_final: 0.6334 (m-10) REVERT: B 144 ARG cc_start: 0.7505 (ptt180) cc_final: 0.6769 (ptt180) REVERT: B 146 ILE cc_start: 0.7872 (mm) cc_final: 0.7560 (pt) REVERT: B 167 GLU cc_start: 0.7218 (tp30) cc_final: 0.5964 (mt-10) REVERT: B 183 HIS cc_start: 0.6587 (t-90) cc_final: 0.5499 (m90) REVERT: B 216 ILE cc_start: 0.8113 (mm) cc_final: 0.7861 (mt) REVERT: B 229 LEU cc_start: 0.7243 (tt) cc_final: 0.6707 (mp) REVERT: B 236 LYS cc_start: 0.8428 (mmmt) cc_final: 0.7746 (mmtm) REVERT: B 307 ASP cc_start: 0.7663 (t0) cc_final: 0.7344 (t0) REVERT: B 458 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: B 526 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7255 (mm) REVERT: B 578 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7414 (mt-10) REVERT: B 753 ARG cc_start: 0.7361 (mmt90) cc_final: 0.7154 (mmt90) REVERT: C 27 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5830 (tp) REVERT: C 60 LYS cc_start: 0.7235 (tptp) cc_final: 0.6626 (tppt) REVERT: C 84 MET cc_start: 0.6194 (mtt) cc_final: 0.5924 (mtm) REVERT: C 134 TYR cc_start: 0.6876 (m-80) cc_final: 0.6416 (m-10) REVERT: C 154 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7626 (m) REVERT: C 167 GLU cc_start: 0.7320 (tp30) cc_final: 0.5577 (mt-10) REVERT: C 183 HIS cc_start: 0.6716 (t-90) cc_final: 0.5678 (m90) REVERT: C 222 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7789 (mp) REVERT: C 229 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6811 (tt) REVERT: C 236 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7751 (mttp) REVERT: C 321 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5822 (tt0) REVERT: C 323 ARG cc_start: 0.6421 (ttm110) cc_final: 0.5927 (ttm-80) REVERT: C 397 GLU cc_start: 0.7244 (mp0) cc_final: 0.6822 (pm20) REVERT: C 426 LYS cc_start: 0.7725 (tppt) cc_final: 0.7441 (mptt) REVERT: C 445 LEU cc_start: 0.8238 (mp) cc_final: 0.7984 (pp) REVERT: C 453 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.6953 (mmm-85) REVERT: C 508 MET cc_start: 0.7730 (tpt) cc_final: 0.7294 (tpt) REVERT: C 572 CYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7666 (t) REVERT: C 628 ILE cc_start: 0.7260 (mm) cc_final: 0.7044 (mm) REVERT: C 701 GLU cc_start: 0.6902 (tp30) cc_final: 0.6695 (tm-30) REVERT: C 753 ARG cc_start: 0.7421 (mmt90) cc_final: 0.7027 (mtp-110) REVERT: C 757 MET cc_start: 0.6632 (ttm) cc_final: 0.6370 (mtp) REVERT: D 27 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.6103 (tp) REVERT: D 60 LYS cc_start: 0.6836 (tptp) cc_final: 0.6350 (tppt) REVERT: D 131 PHE cc_start: 0.7189 (t80) cc_final: 0.6929 (t80) REVERT: D 152 PHE cc_start: 0.8073 (p90) cc_final: 0.7626 (p90) REVERT: D 158 MET cc_start: 0.6852 (mtm) cc_final: 0.6647 (ttt) REVERT: D 167 GLU cc_start: 0.7200 (tp30) cc_final: 0.5593 (mt-10) REVERT: D 183 HIS cc_start: 0.6646 (t-90) cc_final: 0.5801 (m-70) REVERT: D 229 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6243 (mp) REVERT: D 236 LYS cc_start: 0.8301 (mttp) cc_final: 0.8056 (mmmt) REVERT: D 287 ARG cc_start: 0.6635 (mtm110) cc_final: 0.6384 (ttp80) REVERT: D 504 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8116 (mm) REVERT: D 578 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7320 (mt-10) REVERT: D 584 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8144 (ttpp) REVERT: D 625 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7461 (mmm-85) REVERT: D 628 ILE cc_start: 0.7348 (mm) cc_final: 0.7098 (mm) REVERT: D 701 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7126 (tm-30) REVERT: D 704 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7166 (mp0) REVERT: D 740 MET cc_start: 0.7388 (tpt) cc_final: 0.7098 (tpt) REVERT: D 753 ARG cc_start: 0.7599 (mmt90) cc_final: 0.7225 (mtp-110) REVERT: E 60 LYS cc_start: 0.6798 (tptp) cc_final: 0.6428 (tppt) REVERT: E 131 PHE cc_start: 0.7373 (t80) cc_final: 0.7096 (t80) REVERT: E 134 TYR cc_start: 0.6877 (m-80) cc_final: 0.6329 (m-10) REVERT: E 144 ARG cc_start: 0.7357 (ptt180) cc_final: 0.6636 (ptt180) REVERT: E 146 ILE cc_start: 0.7832 (mm) cc_final: 0.7517 (pt) REVERT: E 167 GLU cc_start: 0.7368 (tp30) cc_final: 0.6136 (mt-10) REVERT: E 183 HIS cc_start: 0.6772 (t-90) cc_final: 0.5649 (m90) REVERT: E 216 ILE cc_start: 0.8101 (mm) cc_final: 0.7863 (mt) REVERT: E 229 LEU cc_start: 0.7124 (tt) cc_final: 0.6874 (mp) REVERT: E 236 LYS cc_start: 0.8652 (mttp) cc_final: 0.8235 (mmmt) REVERT: E 307 ASP cc_start: 0.7622 (t0) cc_final: 0.7275 (t0) REVERT: E 397 GLU cc_start: 0.7188 (mp0) cc_final: 0.6929 (pm20) REVERT: E 445 LEU cc_start: 0.8105 (mp) cc_final: 0.7695 (pp) REVERT: E 458 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: E 526 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7281 (mm) REVERT: E 546 GLU cc_start: 0.7383 (mp0) cc_final: 0.7142 (mp0) REVERT: E 753 ARG cc_start: 0.7424 (mmt90) cc_final: 0.7029 (mtp-110) REVERT: F 46 MET cc_start: 0.6414 (ptp) cc_final: 0.6154 (ptp) REVERT: F 60 LYS cc_start: 0.7160 (tptp) cc_final: 0.6469 (tppt) REVERT: F 134 TYR cc_start: 0.6803 (m-80) cc_final: 0.6286 (m-10) REVERT: F 167 GLU cc_start: 0.7260 (tp30) cc_final: 0.5509 (mt-10) REVERT: F 183 HIS cc_start: 0.6814 (t-90) cc_final: 0.5718 (m90) REVERT: F 229 LEU cc_start: 0.6943 (tt) cc_final: 0.6533 (mp) REVERT: F 321 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5979 (tt0) REVERT: F 426 LYS cc_start: 0.7611 (tppt) cc_final: 0.7344 (mptt) REVERT: F 442 MET cc_start: 0.7976 (tpp) cc_final: 0.7689 (tpp) REVERT: F 453 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.6960 (mmm-85) REVERT: F 488 GLU cc_start: 0.6990 (tt0) cc_final: 0.6738 (mt-10) REVERT: F 508 MET cc_start: 0.7787 (tpt) cc_final: 0.7228 (tpt) REVERT: F 572 CYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7661 (t) REVERT: F 628 ILE cc_start: 0.7395 (mm) cc_final: 0.7180 (mm) REVERT: F 701 GLU cc_start: 0.6992 (tp30) cc_final: 0.6723 (tm-30) REVERT: F 704 GLU cc_start: 0.7562 (mp0) cc_final: 0.7159 (mm-30) REVERT: F 753 ARG cc_start: 0.7415 (mmt90) cc_final: 0.6928 (mtp-110) REVERT: F 757 MET cc_start: 0.6594 (ttm) cc_final: 0.6285 (mtp) outliers start: 138 outliers final: 106 residues processed: 679 average time/residue: 0.2223 time to fit residues: 241.4757 Evaluate side-chains 701 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 577 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 572 CYS Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 771 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 625 ARG Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 771 PHE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 266 PHE Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 624 ASN Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 771 PHE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 522 CYS Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 572 CYS Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 94 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 203 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 315 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 353 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 406 HIS ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 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 = 0.4526 r_free = 0.4526 target = 0.228324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.194133 restraints weight = 40272.077| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.32 r_work: 0.4073 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36210 Z= 0.135 Angle : 0.689 8.409 48942 Z= 0.332 Chirality : 0.046 0.206 5436 Planarity : 0.005 0.062 6420 Dihedral : 10.176 149.264 5214 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.19 % Allowed : 19.62 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 4434 helix: 0.17 (0.12), residues: 1800 sheet: -2.01 (0.19), residues: 702 loop : -1.13 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 708 TYR 0.013 0.001 TYR A 134 PHE 0.029 0.002 PHE C 674 TRP 0.013 0.002 TRP E 476 HIS 0.017 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (36210) covalent geometry : angle 0.68919 / 0.33 (48942) hydrogen bonds : bond 0.03495 / 2.29 ( 1379) hydrogen bonds : angle 5.13717 / 3.66 ( 3846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8443.38 seconds wall clock time: 145 minutes 39.52 seconds (8739.52 seconds total)