Starting phenix.real_space_refine on Tue Oct 27 14:12:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oll_70596/10_2026/9oll_70596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oll_70596/10_2026/9oll_70596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oll_70596/10_2026/9oll_70596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oll_70596/10_2026/9oll_70596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oll_70596/10_2026/9oll_70596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oll_70596/10_2026/9oll_70596.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 132 5.16 5 C 16040 2.51 5 N 3892 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24564 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6001 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 2 Chain: "D" Number of atoms: 6001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6001 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'CPL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'CPL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Restraints were copied for chains: B, C Time building chain proxies: 7.90, per 1000 atoms: 0.32 Number of scatterers: 24564 At special positions: 0 Unit cell: (116.64, 117.72, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 12 15.00 O 4488 8.00 N 3892 7.00 C 16040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 196 " distance=3.00 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 196 " distance=3.00 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 196 " distance=3.00 Simple disulfide: pdb=" SG CYS D 194 " - pdb=" SG CYS D 196 " distance=3.00 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 841.3 milliseconds 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5696 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 75.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 51 through 62 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.538A pdb=" N ASN A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.657A pdb=" N ALA A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 172 through 181 Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 206 through 222 removed outlier: 4.064A pdb=" N HIS A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.679A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 4.056A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 removed outlier: 4.121A pdb=" N TYR A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 306 through 316 Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.712A pdb=" N VAL A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.525A pdb=" N LEU A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.974A pdb=" N ALA A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 381 through 403 Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 435 through 459 Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 469 through 505 removed outlier: 3.640A pdb=" N TYR A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.544A pdb=" N TRP A 529 " --> pdb=" O ARG A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 550 removed outlier: 3.693A pdb=" N PHE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.937A pdb=" N ALA A 554 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 557 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 562 through 600 removed outlier: 4.254A pdb=" N LEU A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A 576 " --> pdb=" O ARG A 572 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 623 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.590A pdb=" N SER A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 676 removed outlier: 4.104A pdb=" N SER A 673 " --> pdb=" O MET A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 694 Processing helix chain 'A' and resid 773 through 796 removed outlier: 3.673A pdb=" N GLU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 837 removed outlier: 3.667A pdb=" N LEU A 804 " --> pdb=" O ASN A 800 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.538A pdb=" N ASN B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.657A pdb=" N ALA B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 196 through 205 Processing helix chain 'B' and resid 206 through 222 removed outlier: 4.064A pdb=" N HIS B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.679A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 4.056A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 4.121A pdb=" N TYR B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.712A pdb=" N VAL B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 335 removed outlier: 3.525A pdb=" N LEU B 330 " --> pdb=" O CYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 359 through 370 removed outlier: 3.974A pdb=" N ALA B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 381 Processing helix chain 'B' and resid 381 through 403 Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 435 through 459 Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 469 through 505 removed outlier: 3.640A pdb=" N TYR B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 525 through 529 removed outlier: 3.544A pdb=" N TRP B 529 " --> pdb=" O ARG B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 550 removed outlier: 3.693A pdb=" N PHE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 removed outlier: 3.937A pdb=" N ALA B 554 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 557 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Proline residue: B 558 - end of helix Processing helix chain 'B' and resid 562 through 600 removed outlier: 4.254A pdb=" N LEU B 566 " --> pdb=" O SER B 562 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU B 583 " --> pdb=" O LYS B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 623 Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.590A pdb=" N SER B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 676 removed outlier: 4.104A pdb=" N SER B 673 " --> pdb=" O MET B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 773 through 796 removed outlier: 3.673A pdb=" N GLU B 795 " --> pdb=" O GLN B 791 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 837 removed outlier: 3.667A pdb=" N LEU B 804 " --> pdb=" O ASN B 800 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 816 " --> pdb=" O SER B 812 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 821 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 51 through 62 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 86 through 95 Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.538A pdb=" N ASN C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.657A pdb=" N ALA C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 196 through 205 Processing helix chain 'C' and resid 206 through 222 removed outlier: 4.064A pdb=" N HIS C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.679A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 removed outlier: 4.056A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 276 removed outlier: 4.121A pdb=" N TYR C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 270 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 274 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 289 Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'C' and resid 317 through 322 removed outlier: 3.712A pdb=" N VAL C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 335 removed outlier: 3.525A pdb=" N LEU C 330 " --> pdb=" O CYS C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 359 Processing helix chain 'C' and resid 359 through 370 removed outlier: 3.974A pdb=" N ALA C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 381 through 403 Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 435 through 459 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 469 through 505 removed outlier: 3.640A pdb=" N TYR C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 521 Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 525 through 529 removed outlier: 3.544A pdb=" N TRP C 529 " --> pdb=" O ARG C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 550 removed outlier: 3.693A pdb=" N PHE C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 560 removed outlier: 3.937A pdb=" N ALA C 554 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 557 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Proline residue: C 558 - end of helix Processing helix chain 'C' and resid 562 through 600 removed outlier: 4.254A pdb=" N LEU C 566 " --> pdb=" O SER C 562 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 571 " --> pdb=" O GLN C 567 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG C 572 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS C 575 " --> pdb=" O GLY C 571 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 576 " --> pdb=" O ARG C 572 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 582 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU C 583 " --> pdb=" O LYS C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 623 Processing helix chain 'C' and resid 630 through 634 removed outlier: 3.590A pdb=" N SER C 633 " --> pdb=" O GLU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 676 removed outlier: 4.104A pdb=" N SER C 673 " --> pdb=" O MET C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 694 Processing helix chain 'C' and resid 773 through 796 removed outlier: 3.673A pdb=" N GLU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 837 removed outlier: 3.667A pdb=" N LEU C 804 " --> pdb=" O ASN C 800 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 806 " --> pdb=" O GLY C 802 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 816 " --> pdb=" O SER C 812 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 819 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 821 " --> pdb=" O GLU C 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 51 through 62 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.538A pdb=" N ASN D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.657A pdb=" N ALA D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 144 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 196 through 205 Processing helix chain 'D' and resid 206 through 222 removed outlier: 4.064A pdb=" N HIS D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.679A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.056A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 4.121A pdb=" N TYR D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 270 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 274 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 289 Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 317 through 322 removed outlier: 3.712A pdb=" N VAL D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 335 removed outlier: 3.525A pdb=" N LEU D 330 " --> pdb=" O CYS D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 359 Processing helix chain 'D' and resid 359 through 370 removed outlier: 3.974A pdb=" N ALA D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 381 Processing helix chain 'D' and resid 381 through 403 Processing helix chain 'D' and resid 426 through 432 Processing helix chain 'D' and resid 435 through 459 Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 469 through 505 removed outlier: 3.640A pdb=" N TYR D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 505 " --> pdb=" O VAL D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 522 through 524 No H-bonds generated for 'chain 'D' and resid 522 through 524' Processing helix chain 'D' and resid 525 through 529 removed outlier: 3.544A pdb=" N TRP D 529 " --> pdb=" O ARG D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 550 removed outlier: 3.693A pdb=" N PHE D 550 " --> pdb=" O VAL D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 560 removed outlier: 3.937A pdb=" N ALA D 554 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU D 557 " --> pdb=" O ALA D 554 " (cutoff:3.500A) Proline residue: D 558 - end of helix Processing helix chain 'D' and resid 562 through 600 removed outlier: 4.255A pdb=" N LEU D 566 " --> pdb=" O SER D 562 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 571 " --> pdb=" O GLN D 567 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG D 572 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 575 " --> pdb=" O GLY D 571 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP D 576 " --> pdb=" O ARG D 572 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 582 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU D 583 " --> pdb=" O LYS D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 623 Processing helix chain 'D' and resid 630 through 634 removed outlier: 3.590A pdb=" N SER D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 676 removed outlier: 4.104A pdb=" N SER D 673 " --> pdb=" O MET D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 694 Processing helix chain 'D' and resid 773 through 796 removed outlier: 3.674A pdb=" N GLU D 795 " --> pdb=" O GLN D 791 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 837 removed outlier: 3.667A pdb=" N LEU D 804 " --> pdb=" O ASN D 800 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 816 " --> pdb=" O SER D 812 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 819 " --> pdb=" O ARG D 815 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 820 " --> pdb=" O TYR D 816 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 821 " --> pdb=" O GLU D 817 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3960 1.29 - 1.42: 6387 1.42 - 1.55: 14493 1.55 - 1.68: 28 1.68 - 1.81: 216 Bond restraints: 25084 Sorted by residual: bond pdb=" C LEU A 666 " pdb=" O LEU A 666 " ideal model delta sigma weight residual 1.236 1.162 0.075 1.18e-02 7.18e+03 4.01e+01 bond pdb=" C LEU D 666 " pdb=" O LEU D 666 " ideal model delta sigma weight residual 1.236 1.162 0.075 1.18e-02 7.18e+03 4.01e+01 bond pdb=" C LEU C 666 " pdb=" O LEU C 666 " ideal model delta sigma weight residual 1.236 1.162 0.075 1.18e-02 7.18e+03 4.01e+01 bond pdb=" C LEU B 666 " pdb=" O LEU B 666 " ideal model delta sigma weight residual 1.236 1.162 0.075 1.18e-02 7.18e+03 4.01e+01 bond pdb=" N PRO A 324 " pdb=" CD PRO A 324 " ideal model delta sigma weight residual 1.473 1.386 0.087 1.40e-02 5.10e+03 3.90e+01 ... (remaining 25079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 30653 2.43 - 4.86: 2823 4.86 - 7.28: 292 7.28 - 9.71: 64 9.71 - 12.14: 32 Bond angle restraints: 33864 Sorted by residual: angle pdb=" CA LEU D 666 " pdb=" C LEU D 666 " pdb=" O LEU D 666 " ideal model delta sigma weight residual 120.63 111.37 9.26 1.08e+00 8.57e-01 7.35e+01 angle pdb=" CA LEU C 666 " pdb=" C LEU C 666 " pdb=" O LEU C 666 " ideal model delta sigma weight residual 120.63 111.37 9.26 1.08e+00 8.57e-01 7.35e+01 angle pdb=" CA LEU A 666 " pdb=" C LEU A 666 " pdb=" O LEU A 666 " ideal model delta sigma weight residual 120.63 111.37 9.26 1.08e+00 8.57e-01 7.35e+01 angle pdb=" CA LEU B 666 " pdb=" C LEU B 666 " pdb=" O LEU B 666 " ideal model delta sigma weight residual 120.63 111.37 9.26 1.08e+00 8.57e-01 7.35e+01 angle pdb=" CA PHE C 687 " pdb=" C PHE C 687 " pdb=" O PHE C 687 " ideal model delta sigma weight residual 120.70 112.51 8.19 1.03e+00 9.43e-01 6.33e+01 ... (remaining 33859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 14420 33.64 - 67.28: 656 67.28 - 100.91: 100 100.91 - 134.55: 4 134.55 - 168.19: 20 Dihedral angle restraints: 15200 sinusoidal: 6404 harmonic: 8796 Sorted by residual: dihedral pdb=" CD ARG D 278 " pdb=" NE ARG D 278 " pdb=" CZ ARG D 278 " pdb=" NH1 ARG D 278 " ideal model delta sinusoidal sigma weight residual 0.00 55.90 -55.90 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CD ARG B 278 " pdb=" NE ARG B 278 " pdb=" CZ ARG B 278 " pdb=" NH1 ARG B 278 " ideal model delta sinusoidal sigma weight residual 0.00 55.86 -55.86 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CD ARG A 278 " pdb=" NE ARG A 278 " pdb=" CZ ARG A 278 " pdb=" NH1 ARG A 278 " ideal model delta sinusoidal sigma weight residual 0.00 55.86 -55.86 1 1.00e+01 1.00e-02 4.21e+01 ... (remaining 15197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2135 0.051 - 0.103: 907 0.103 - 0.154: 506 0.154 - 0.206: 168 0.206 - 0.257: 48 Chirality restraints: 3764 Sorted by residual: chirality pdb=" CA ARG A 572 " pdb=" N ARG A 572 " pdb=" C ARG A 572 " pdb=" CB ARG A 572 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ARG B 572 " pdb=" N ARG B 572 " pdb=" C ARG B 572 " pdb=" CB ARG B 572 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ARG D 572 " pdb=" N ARG D 572 " pdb=" C ARG D 572 " pdb=" CB ARG D 572 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 3761 not shown) Planarity restraints: 4228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 CPL D 902 " -0.101 2.00e-02 2.50e+03 2.31e-01 5.36e+02 pdb=" C39 CPL D 902 " 0.311 2.00e-02 2.50e+03 pdb=" C40 CPL D 902 " -0.312 2.00e-02 2.50e+03 pdb=" C41 CPL D 902 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL C 903 " 0.101 2.00e-02 2.50e+03 2.31e-01 5.34e+02 pdb=" C39 CPL C 903 " -0.311 2.00e-02 2.50e+03 pdb=" C40 CPL C 903 " 0.311 2.00e-02 2.50e+03 pdb=" C41 CPL C 903 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL A 903 " -0.101 2.00e-02 2.50e+03 2.31e-01 5.34e+02 pdb=" C39 CPL A 903 " 0.310 2.00e-02 2.50e+03 pdb=" C40 CPL A 903 " -0.311 2.00e-02 2.50e+03 pdb=" C41 CPL A 903 " 0.102 2.00e-02 2.50e+03 ... (remaining 4225 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 8 2.21 - 2.88: 9248 2.88 - 3.55: 34844 3.55 - 4.23: 53706 4.23 - 4.90: 95640 Nonbonded interactions: 193446 Sorted by model distance: nonbonded pdb=" CE LYS B 822 " pdb=" OD2 ASP C 821 " model vdw 1.532 2.752 nonbonded pdb=" CE LYS A 822 " pdb=" OD2 ASP B 821 " model vdw 1.532 2.752 nonbonded pdb=" OD2 ASP A 821 " pdb=" CE LYS D 822 " model vdw 1.533 2.752 nonbonded pdb=" CE LYS C 822 " pdb=" OD2 ASP D 821 " model vdw 1.533 2.752 nonbonded pdb=" CE LYS B 822 " pdb=" CB ASP C 821 " model vdw 1.607 3.072 ... (remaining 193441 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' and (resid 23 through 838 or (resid 901 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C \ 43 or name C44 or name C45 or name C46 or name C5 or name C6 or name C7 or name \ C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name \ O3P or name O4P or name P )) or (resid 902 and (name N or name C1 or name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or n \ ame C44 or name C45 or name C5 or name C6 or name C7 or name C8 or name O11 or n \ ame O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or \ name P )) or resid 903)) selection = (chain 'B' and (resid 23 through 838 or (resid 901 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C \ 43 or name C44 or name C45 or name C46 or name C5 or name C6 or name C7 or name \ C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name \ O3P or name O4P or name P )) or (resid 902 and (name N or name C1 or name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or n \ ame C44 or name C45 or name C5 or name C6 or name C7 or name C8 or name O11 or n \ ame O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or \ name P )) or resid 903)) selection = (chain 'C' and (resid 23 through 838 or (resid 901 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C \ 43 or name C44 or name C45 or name C46 or name C5 or name C6 or name C7 or name \ C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name \ O3P or name O4P or name P )) or (resid 902 and (name N or name C1 or name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or n \ ame C44 or name C45 or name C5 or name C6 or name C7 or name C8 or name O11 or n \ ame O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or \ name P )) or resid 903)) selection = (chain 'D' and (resid 23 through 838 or (resid 901 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C \ 43 or name C44 or name C45 or name C46 or name C5 or name C6 or name C7 or name \ C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name \ O3P or name O4P or name P )) or (resid 902 and (name N or name C1 or name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or n \ ame C44 or name C45 or name C5 or name C6 or name C7 or name C8 or name O11 or n \ ame O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or \ name P )) or (resid 903 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name \ C41 or name C42 or name C43 or name C44 or name C45 or name C5 or name C6 or na \ me C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or na \ me O31 or name O3P or name O4P or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.290 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.968 25096 Z= 1.245 Angle : 1.473 17.720 33872 Z= 1.080 Chirality : 0.077 0.257 3764 Planarity : 0.025 0.404 4228 Dihedral : 19.570 168.190 9492 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.19 % Favored : 93.40 % Rotamer: Outliers : 1.67 % Allowed : 17.35 % Favored : 80.97 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.14), residues: 2956 helix: -0.76 (0.11), residues: 2076 sheet: None (None), residues: 0 loop : -2.53 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 552 TYR 0.032 0.002 TYR D 150 PHE 0.043 0.002 PHE C 402 TRP 0.014 0.001 TRP A 444 HIS 0.007 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.01009 / 0.74 (25084) covalent geometry : angle 1.45523 / 1.07 (33864) SS BOND : bond 0.96800 / 48.49 ( 4) SS BOND : angle 15.10570 / 9.40 ( 8) hydrogen bonds : bond 0.20284 / 13.88 ( 1464) hydrogen bonds : angle 7.59868 / 5.41 ( 4344) Misc. bond : bond 0.44726 / 23.89 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 488 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.8152 (p0) cc_final: 0.7923 (p0) REVERT: A 86 HIS cc_start: 0.7216 (m-70) cc_final: 0.6970 (m-70) REVERT: A 641 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6523 (mtpt) REVERT: B 86 HIS cc_start: 0.7168 (m-70) cc_final: 0.6930 (m-70) REVERT: B 641 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6546 (mtpt) REVERT: C 86 HIS cc_start: 0.7260 (m-70) cc_final: 0.6966 (m-70) REVERT: C 641 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6484 (mtpt) REVERT: C 808 LYS cc_start: 0.8292 (tttp) cc_final: 0.8071 (pttp) REVERT: D 71 ASP cc_start: 0.8106 (p0) cc_final: 0.7873 (p0) REVERT: D 86 HIS cc_start: 0.7297 (m-70) cc_final: 0.7007 (m-70) REVERT: D 641 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6484 (mtpt) REVERT: D 808 LYS cc_start: 0.8334 (tttp) cc_final: 0.8112 (pttp) outliers start: 44 outliers final: 12 residues processed: 512 average time/residue: 0.1718 time to fit residues: 133.6692 Evaluate side-chains 332 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 674 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 177 HIS A 205 HIS A 327 GLN A 403 ASN A 470 ASN A 800 ASN B 171 GLN B 177 HIS B 327 GLN B 403 ASN B 470 ASN B 800 ASN C 171 GLN C 177 HIS C 327 GLN C 403 ASN C 470 ASN C 800 ASN D 171 GLN D 177 HIS D 403 ASN D 470 ASN D 800 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.259931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.215128 restraints weight = 28914.939| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.34 r_work: 0.4097 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25096 Z= 0.169 Angle : 0.656 9.400 33872 Z= 0.334 Chirality : 0.041 0.177 3764 Planarity : 0.005 0.046 4228 Dihedral : 17.036 168.158 3716 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 3.54 % Allowed : 15.18 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2956 helix: 1.11 (0.11), residues: 2092 sheet: None (None), residues: 0 loop : -1.85 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 278 TYR 0.018 0.001 TYR D 150 PHE 0.036 0.002 PHE B 484 TRP 0.017 0.002 TRP B 693 HIS 0.013 0.002 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (25084) covalent geometry : angle 0.65506 / 0.33 (33864) SS BOND : bond 0.00421 / 0.21 ( 4) SS BOND : angle 1.72666 / 1.18 ( 8) hydrogen bonds : bond 0.06064 / 4.15 ( 1464) hydrogen bonds : angle 4.45665 / 3.19 ( 4344) Misc. bond : bond 0.00516 / 0.27 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 328 time to evaluate : 0.871 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: A 442 MET cc_start: 0.7415 (tpt) cc_final: 0.7092 (tpt) REVERT: A 449 MET cc_start: 0.7725 (tpt) cc_final: 0.7505 (tpt) REVERT: A 484 PHE cc_start: 0.6954 (m-80) cc_final: 0.6543 (m-80) REVERT: A 592 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6262 (mtm) REVERT: A 684 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8143 (mm-30) REVERT: A 779 MET cc_start: 0.6254 (tpt) cc_final: 0.5867 (mmt) REVERT: A 794 LYS cc_start: 0.7641 (tptp) cc_final: 0.6735 (mtpt) REVERT: B 442 MET cc_start: 0.7396 (tpt) cc_final: 0.7108 (tpt) REVERT: B 449 MET cc_start: 0.7666 (tpt) cc_final: 0.7459 (tpt) REVERT: B 484 PHE cc_start: 0.6918 (m-80) cc_final: 0.6577 (m-80) REVERT: B 592 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6234 (mtm) REVERT: B 684 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8196 (mm-30) REVERT: B 779 MET cc_start: 0.6214 (tpt) cc_final: 0.5833 (mmt) REVERT: B 794 LYS cc_start: 0.7613 (tptp) cc_final: 0.6723 (mtpt) REVERT: C 55 VAL cc_start: 0.8138 (p) cc_final: 0.7861 (t) REVERT: C 442 MET cc_start: 0.7394 (tpt) cc_final: 0.7037 (tpt) REVERT: C 449 MET cc_start: 0.7712 (tpt) cc_final: 0.7491 (tpt) REVERT: C 484 PHE cc_start: 0.6912 (m-80) cc_final: 0.6591 (m-80) REVERT: C 592 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6221 (mtm) REVERT: C 641 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6143 (mtpt) REVERT: C 684 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8170 (mm-30) REVERT: C 779 MET cc_start: 0.6223 (tpt) cc_final: 0.5843 (mmt) REVERT: C 794 LYS cc_start: 0.7617 (tptp) cc_final: 0.6734 (mtpt) REVERT: D 55 VAL cc_start: 0.8158 (p) cc_final: 0.7876 (t) REVERT: D 442 MET cc_start: 0.7411 (tpt) cc_final: 0.7084 (tpt) REVERT: D 449 MET cc_start: 0.7685 (tpt) cc_final: 0.7479 (tpt) REVERT: D 484 PHE cc_start: 0.6936 (m-80) cc_final: 0.6611 (m-80) REVERT: D 592 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6249 (mtm) REVERT: D 684 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8166 (mm-30) REVERT: D 779 MET cc_start: 0.6262 (tpt) cc_final: 0.5877 (mmt) REVERT: D 794 LYS cc_start: 0.7659 (tptp) cc_final: 0.6750 (mtpt) outliers start: 93 outliers final: 24 residues processed: 401 average time/residue: 0.1482 time to fit residues: 95.8336 Evaluate side-chains 311 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 469 TRP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 592 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [261, 41, 294, 177, 206, 64, 163, 208, 265, 2, 22] chunk 261 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 294 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN A 403 ASN B 205 HIS B 327 GLN B 403 ASN C 203 GLN C 205 HIS C 327 GLN C 403 ASN D 205 HIS D 403 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.235145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.192941 restraints weight = 27971.004| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.85 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 25096 Z= 0.234 Angle : 0.763 14.537 33872 Z= 0.375 Chirality : 0.044 0.192 3764 Planarity : 0.005 0.057 4228 Dihedral : 16.289 171.402 3692 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 3.50 % Allowed : 17.35 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 2956 helix: 1.10 (0.11), residues: 2088 sheet: None (None), residues: 0 loop : -1.61 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 308 TYR 0.028 0.002 TYR C 150 PHE 0.025 0.002 PHE B 588 TRP 0.020 0.002 TRP C 334 HIS 0.011 0.002 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (25084) covalent geometry : angle 0.76103 / 0.37 (33864) SS BOND : bond 0.01456 / 0.73 ( 4) SS BOND : angle 3.49675 / 2.32 ( 8) hydrogen bonds : bond 0.07238 / 4.94 ( 1464) hydrogen bonds : angle 4.41889 / 3.17 ( 4344) Misc. bond : bond 0.00227 / 0.12 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 363 time to evaluate : 0.891 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: A 57 LYS cc_start: 0.7626 (ttmt) cc_final: 0.7220 (tmmt) REVERT: A 58 MET cc_start: 0.8893 (mtp) cc_final: 0.8625 (mtp) REVERT: A 60 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: A 264 MET cc_start: 0.7593 (mpp) cc_final: 0.7170 (mpp) REVERT: A 794 LYS cc_start: 0.8068 (tptp) cc_final: 0.7038 (mtmt) REVERT: B 58 MET cc_start: 0.8883 (mtp) cc_final: 0.8563 (mtp) REVERT: B 60 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: B 264 MET cc_start: 0.7594 (mpp) cc_final: 0.7169 (mpp) REVERT: B 641 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6159 (mttt) REVERT: B 684 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 794 LYS cc_start: 0.8068 (tptp) cc_final: 0.7032 (mtmt) REVERT: C 57 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7223 (tmmt) REVERT: C 58 MET cc_start: 0.8933 (mtp) cc_final: 0.8667 (mtp) REVERT: C 60 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: C 264 MET cc_start: 0.7584 (mpp) cc_final: 0.7137 (mpp) REVERT: C 480 PHE cc_start: 0.7457 (m-80) cc_final: 0.7181 (m-80) REVERT: C 794 LYS cc_start: 0.8067 (tptp) cc_final: 0.7037 (mtmt) REVERT: D 57 LYS cc_start: 0.7637 (ttmt) cc_final: 0.7224 (tmmt) REVERT: D 58 MET cc_start: 0.8936 (mtp) cc_final: 0.8664 (mtp) REVERT: D 60 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: D 264 MET cc_start: 0.7591 (mpp) cc_final: 0.7164 (mpp) REVERT: D 480 PHE cc_start: 0.7513 (m-80) cc_final: 0.7233 (m-80) REVERT: D 641 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6147 (mttt) REVERT: D 794 LYS cc_start: 0.8081 (tptp) cc_final: 0.7056 (mtmt) outliers start: 92 outliers final: 44 residues processed: 438 average time/residue: 0.1452 time to fit residues: 102.7701 Evaluate side-chains 367 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 317 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 469 TRP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 641 LYS Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [164, 213, 114, 215, 202, 282, 36, 177, 168, 210, 184] chunk 164 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.236272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.193724 restraints weight = 27742.977| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.84 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25096 Z= 0.160 Angle : 0.627 11.516 33872 Z= 0.311 Chirality : 0.040 0.259 3764 Planarity : 0.004 0.044 4228 Dihedral : 15.872 170.698 3688 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 2.13 % Allowed : 19.56 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 2956 helix: 1.45 (0.11), residues: 2096 sheet: None (None), residues: 0 loop : -1.49 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 308 TYR 0.013 0.001 TYR D 150 PHE 0.042 0.001 PHE B 484 TRP 0.014 0.001 TRP D 334 HIS 0.020 0.002 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (25084) covalent geometry : angle 0.62639 / 0.31 (33864) SS BOND : bond 0.00414 / 0.21 ( 4) SS BOND : angle 1.67160 / 1.04 ( 8) hydrogen bonds : bond 0.05732 / 3.90 ( 1464) hydrogen bonds : angle 4.09240 / 2.94 ( 4344) Misc. bond : bond 0.00231 / 0.12 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 333 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7622 (ttmt) cc_final: 0.7201 (tmmt) REVERT: A 58 MET cc_start: 0.8908 (mtp) cc_final: 0.8593 (mtp) REVERT: A 264 MET cc_start: 0.7492 (mpp) cc_final: 0.7146 (mpp) REVERT: A 484 PHE cc_start: 0.6832 (m-80) cc_final: 0.6568 (m-80) REVERT: B 57 LYS cc_start: 0.7619 (ttmt) cc_final: 0.7179 (tmmt) REVERT: B 58 MET cc_start: 0.8901 (mtp) cc_final: 0.8598 (mtp) REVERT: B 60 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: B 264 MET cc_start: 0.7482 (mpp) cc_final: 0.7161 (mpp) REVERT: B 484 PHE cc_start: 0.6816 (m-80) cc_final: 0.6528 (m-80) REVERT: B 665 MET cc_start: 0.7232 (tpp) cc_final: 0.6877 (ttm) REVERT: B 684 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7296 (mm-30) REVERT: C 57 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7231 (tmmt) REVERT: C 58 MET cc_start: 0.8909 (mtp) cc_final: 0.8605 (mtp) REVERT: C 60 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: C 264 MET cc_start: 0.7508 (mpp) cc_final: 0.7173 (mpp) REVERT: C 442 MET cc_start: 0.6732 (tpt) cc_final: 0.6470 (tpt) REVERT: C 665 MET cc_start: 0.7198 (tpp) cc_final: 0.6870 (ttm) REVERT: D 57 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7233 (tmmt) REVERT: D 58 MET cc_start: 0.8890 (mtp) cc_final: 0.8566 (mtp) REVERT: D 264 MET cc_start: 0.7491 (mpp) cc_final: 0.7160 (mpp) REVERT: D 442 MET cc_start: 0.6742 (tpt) cc_final: 0.6447 (tpt) outliers start: 56 outliers final: 42 residues processed: 373 average time/residue: 0.1414 time to fit residues: 86.3355 Evaluate side-chains 361 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 469 TRP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [2, 87, 117, 174, 50, 43, 226, 283, 221, 246, 109] chunk 2 optimal weight: 0.9990 chunk 87 optimal weight: 0.0870 chunk 117 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 HIS B 403 ASN C 205 HIS D 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.232089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.187141 restraints weight = 27443.624| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.04 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25096 Z= 0.191 Angle : 0.664 11.912 33872 Z= 0.325 Chirality : 0.041 0.202 3764 Planarity : 0.004 0.041 4228 Dihedral : 15.657 171.275 3688 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.92 % Favored : 95.94 % Rotamer: Outliers : 3.31 % Allowed : 18.87 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 2956 helix: 1.44 (0.11), residues: 2096 sheet: None (None), residues: 0 loop : -1.36 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 308 TYR 0.014 0.002 TYR B 150 PHE 0.027 0.002 PHE B 484 TRP 0.017 0.001 TRP C 334 HIS 0.016 0.002 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (25084) covalent geometry : angle 0.66287 / 0.32 (33864) SS BOND : bond 0.00943 / 0.47 ( 4) SS BOND : angle 2.07083 / 1.36 ( 8) hydrogen bonds : bond 0.06123 / 4.17 ( 1464) hydrogen bonds : angle 4.04992 / 2.91 ( 4344) Misc. bond : bond 0.00201 / 0.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 335 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7649 (ttmt) cc_final: 0.7253 (tmmt) REVERT: A 58 MET cc_start: 0.8945 (mtp) cc_final: 0.8474 (mtp) REVERT: A 60 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: A 264 MET cc_start: 0.7409 (mpp) cc_final: 0.7031 (mpp) REVERT: A 442 MET cc_start: 0.7098 (tpt) cc_final: 0.6700 (tpt) REVERT: A 448 MET cc_start: 0.7458 (mtt) cc_final: 0.7158 (mtt) REVERT: B 57 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7237 (tmmt) REVERT: B 58 MET cc_start: 0.8919 (mtp) cc_final: 0.8471 (mtp) REVERT: B 60 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: B 264 MET cc_start: 0.7394 (mpp) cc_final: 0.6990 (mpp) REVERT: B 442 MET cc_start: 0.6991 (tpt) cc_final: 0.6636 (tpt) REVERT: B 448 MET cc_start: 0.7567 (mtt) cc_final: 0.7255 (mtt) REVERT: B 579 LYS cc_start: 0.6818 (mmmt) cc_final: 0.6359 (mmtt) REVERT: C 57 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7256 (tmmt) REVERT: C 58 MET cc_start: 0.8945 (mtp) cc_final: 0.8597 (mtp) REVERT: C 60 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: C 264 MET cc_start: 0.7400 (mpp) cc_final: 0.7007 (mpp) REVERT: C 448 MET cc_start: 0.7422 (mtt) cc_final: 0.7142 (mtt) REVERT: D 57 LYS cc_start: 0.7610 (ttmt) cc_final: 0.7209 (tmmt) REVERT: D 58 MET cc_start: 0.8939 (mtp) cc_final: 0.8496 (mtp) REVERT: D 60 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: D 264 MET cc_start: 0.7445 (mpp) cc_final: 0.7075 (mpp) REVERT: D 448 MET cc_start: 0.7657 (mtt) cc_final: 0.7389 (mtt) REVERT: D 555 TYR cc_start: 0.6687 (t80) cc_final: 0.6451 (t80) REVERT: D 579 LYS cc_start: 0.6666 (mmmt) cc_final: 0.6229 (mmtt) outliers start: 87 outliers final: 56 residues processed: 401 average time/residue: 0.1415 time to fit residues: 92.8527 Evaluate side-chains 366 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 306 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 469 TRP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [46, 195, 122, 179, 209, 212, 173, 268, 228, 125, 91] chunk 46 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 212 optimal weight: 0.3980 chunk 173 optimal weight: 0.9980 chunk 268 optimal weight: 20.0000 chunk 228 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN C 403 ASN D 403 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.234024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.188033 restraints weight = 27711.460| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.02 r_work: 0.3694 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25096 Z= 0.144 Angle : 0.595 10.123 33872 Z= 0.297 Chirality : 0.039 0.147 3764 Planarity : 0.004 0.042 4228 Dihedral : 15.488 172.045 3688 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.70 % Allowed : 19.63 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 2956 helix: 1.57 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : -1.37 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 308 TYR 0.013 0.001 TYR C 524 PHE 0.036 0.001 PHE A 484 TRP 0.013 0.001 TRP C 334 HIS 0.021 0.001 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (25084) covalent geometry : angle 0.59410 / 0.30 (33864) SS BOND : bond 0.00588 / 0.29 ( 4) SS BOND : angle 1.54680 / 1.04 ( 8) hydrogen bonds : bond 0.05283 / 3.59 ( 1464) hydrogen bonds : angle 3.91592 / 2.81 ( 4344) Misc. bond : bond 0.00216 / 0.11 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 334 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7248 (tmmt) REVERT: A 58 MET cc_start: 0.9250 (mtp) cc_final: 0.8909 (mtp) REVERT: A 60 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: A 63 LYS cc_start: 0.8088 (mtmm) cc_final: 0.7833 (mptt) REVERT: A 75 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: A 264 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8255 (mpp) REVERT: A 402 PHE cc_start: 0.7530 (t80) cc_final: 0.7278 (t80) REVERT: A 442 MET cc_start: 0.7829 (tpt) cc_final: 0.7258 (tpt) REVERT: A 448 MET cc_start: 0.8001 (mtt) cc_final: 0.7635 (mtt) REVERT: B 57 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7177 (tmmt) REVERT: B 58 MET cc_start: 0.9223 (mtp) cc_final: 0.8916 (mtp) REVERT: B 60 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: B 63 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7813 (mptt) REVERT: B 75 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: B 264 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8299 (mpp) REVERT: B 442 MET cc_start: 0.7872 (tpt) cc_final: 0.7297 (tpt) REVERT: B 448 MET cc_start: 0.8090 (mtt) cc_final: 0.7681 (mtt) REVERT: B 555 TYR cc_start: 0.6853 (t80) cc_final: 0.6321 (t80) REVERT: B 579 LYS cc_start: 0.7660 (mmmt) cc_final: 0.7060 (ptpt) REVERT: B 674 TYR cc_start: 0.5007 (OUTLIER) cc_final: 0.4013 (p90) REVERT: C 57 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7201 (tmmt) REVERT: C 58 MET cc_start: 0.9223 (mtp) cc_final: 0.8905 (mtp) REVERT: C 60 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: C 264 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8273 (mpp) REVERT: C 402 PHE cc_start: 0.7491 (t80) cc_final: 0.7245 (t80) REVERT: C 442 MET cc_start: 0.7733 (tpt) cc_final: 0.7225 (tpt) REVERT: C 555 TYR cc_start: 0.6784 (t80) cc_final: 0.6296 (t80) REVERT: C 651 TYR cc_start: 0.8278 (t80) cc_final: 0.7895 (t80) REVERT: D 57 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7253 (tmmt) REVERT: D 58 MET cc_start: 0.9259 (mtp) cc_final: 0.8921 (mtp) REVERT: D 60 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: D 75 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: D 264 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8281 (mpp) REVERT: D 402 PHE cc_start: 0.7452 (t80) cc_final: 0.7214 (t80) REVERT: D 442 MET cc_start: 0.7725 (tpt) cc_final: 0.7236 (tpt) REVERT: D 448 MET cc_start: 0.8103 (mtt) cc_final: 0.7736 (mtt) REVERT: D 579 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7164 (ptpt) outliers start: 71 outliers final: 42 residues processed: 382 average time/residue: 0.1397 time to fit residues: 86.6365 Evaluate side-chains 368 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 314 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 469 TRP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [133, 26, 131, 77, 96, 82, 86, 294, 206, 49, 137] chunk 133 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 77 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 294 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN A 344 GLN B 344 GLN B 403 ASN C 344 GLN D 344 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.236334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.194892 restraints weight = 27695.008| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.59 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25096 Z= 0.116 Angle : 0.561 9.247 33872 Z= 0.281 Chirality : 0.038 0.164 3764 Planarity : 0.004 0.042 4228 Dihedral : 15.145 173.697 3680 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.47 % Allowed : 19.86 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.16), residues: 2956 helix: 1.83 (0.11), residues: 2096 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 204 TYR 0.010 0.001 TYR C 192 PHE 0.019 0.001 PHE A 484 TRP 0.011 0.001 TRP C 334 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (25084) covalent geometry : angle 0.56075 / 0.28 (33864) SS BOND : bond 0.00449 / 0.22 ( 4) SS BOND : angle 1.15557 / 0.80 ( 8) hydrogen bonds : bond 0.04463 / 3.04 ( 1464) hydrogen bonds : angle 3.75929 / 2.70 ( 4344) Misc. bond : bond 0.00228 / 0.12 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 350 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7290 (tmmt) REVERT: A 58 MET cc_start: 0.8899 (mtp) cc_final: 0.8522 (mtp) REVERT: A 60 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: A 75 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: A 264 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7106 (mpp) REVERT: A 402 PHE cc_start: 0.7556 (t80) cc_final: 0.7292 (t80) REVERT: A 442 MET cc_start: 0.7064 (tpt) cc_final: 0.6690 (tpt) REVERT: A 448 MET cc_start: 0.7421 (mtt) cc_final: 0.7171 (mtt) REVERT: A 484 PHE cc_start: 0.7194 (m-80) cc_final: 0.6834 (m-80) REVERT: A 651 TYR cc_start: 0.8246 (t80) cc_final: 0.7875 (t80) REVERT: A 794 LYS cc_start: 0.7831 (tptp) cc_final: 0.6807 (mttt) REVERT: A 810 ASP cc_start: 0.6017 (m-30) cc_final: 0.5711 (m-30) REVERT: B 57 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7273 (tmmt) REVERT: B 58 MET cc_start: 0.8894 (mtp) cc_final: 0.8519 (mtp) REVERT: B 60 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: B 264 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7134 (mpp) REVERT: B 442 MET cc_start: 0.7012 (tpt) cc_final: 0.6762 (tpt) REVERT: B 484 PHE cc_start: 0.7206 (m-80) cc_final: 0.6957 (m-80) REVERT: B 555 TYR cc_start: 0.6617 (t80) cc_final: 0.6404 (t80) REVERT: B 651 TYR cc_start: 0.8214 (t80) cc_final: 0.7852 (t80) REVERT: B 674 TYR cc_start: 0.4192 (OUTLIER) cc_final: 0.3579 (p90) REVERT: B 794 LYS cc_start: 0.7838 (tptp) cc_final: 0.6790 (mttt) REVERT: B 810 ASP cc_start: 0.6218 (m-30) cc_final: 0.5869 (m-30) REVERT: C 57 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7284 (tmmt) REVERT: C 58 MET cc_start: 0.8915 (mtp) cc_final: 0.8532 (mtp) REVERT: C 60 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: C 75 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: C 264 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7110 (mpp) REVERT: C 402 PHE cc_start: 0.7597 (t80) cc_final: 0.7341 (t80) REVERT: C 442 MET cc_start: 0.7100 (tpt) cc_final: 0.6781 (tpt) REVERT: C 448 MET cc_start: 0.7411 (mtt) cc_final: 0.7145 (mtt) REVERT: C 651 TYR cc_start: 0.8236 (t80) cc_final: 0.7885 (t80) REVERT: C 674 TYR cc_start: 0.4182 (OUTLIER) cc_final: 0.3638 (p90) REVERT: C 794 LYS cc_start: 0.7831 (tptp) cc_final: 0.6795 (mttt) REVERT: C 810 ASP cc_start: 0.5956 (m-30) cc_final: 0.5639 (m-30) REVERT: D 57 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7258 (tmmt) REVERT: D 58 MET cc_start: 0.8899 (mtp) cc_final: 0.8512 (mtp) REVERT: D 60 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: D 264 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7118 (mpp) REVERT: D 402 PHE cc_start: 0.7564 (t80) cc_final: 0.7314 (t80) REVERT: D 442 MET cc_start: 0.7023 (tpt) cc_final: 0.6787 (tpt) REVERT: D 448 MET cc_start: 0.7433 (mtt) cc_final: 0.7196 (mtt) REVERT: D 794 LYS cc_start: 0.7844 (tptp) cc_final: 0.6812 (mttt) REVERT: D 810 ASP cc_start: 0.5986 (m-30) cc_final: 0.5641 (m-30) outliers start: 65 outliers final: 41 residues processed: 389 average time/residue: 0.1441 time to fit residues: 90.8630 Evaluate side-chains 378 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 641 LYS Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 469 TRP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 674 TYR Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [240, 274, 289, 33, 144, 228, 42, 174, 84, 86, 54] chunk 240 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.227314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.183692 restraints weight = 27815.688| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.99 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 25096 Z= 0.290 Angle : 0.768 16.502 33872 Z= 0.379 Chirality : 0.045 0.185 3764 Planarity : 0.005 0.039 4228 Dihedral : 15.301 173.652 3680 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.70 % Rotamer: Outliers : 2.82 % Allowed : 19.37 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 2956 helix: 1.35 (0.11), residues: 2096 sheet: None (None), residues: 0 loop : -1.53 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 278 TYR 0.018 0.002 TYR B 226 PHE 0.020 0.002 PHE A 320 TRP 0.018 0.002 TRP B 444 HIS 0.007 0.002 HIS D 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.29 (25084) covalent geometry : angle 0.76718 / 0.38 (33864) SS BOND : bond 0.01020 / 0.51 ( 4) SS BOND : angle 2.38770 / 1.60 ( 8) hydrogen bonds : bond 0.07340 / 5.00 ( 1464) hydrogen bonds : angle 4.22266 / 3.03 ( 4344) Misc. bond : bond 0.00146 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 339 time to evaluate : 0.917 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 57 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7466 (tmmt) REVERT: A 58 MET cc_start: 0.8979 (mtp) cc_final: 0.8546 (mtp) REVERT: A 60 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: A 402 PHE cc_start: 0.7670 (t80) cc_final: 0.7409 (t80) REVERT: A 442 MET cc_start: 0.7212 (tpt) cc_final: 0.6792 (tpt) REVERT: A 448 MET cc_start: 0.7702 (mtt) cc_final: 0.7428 (mtt) REVERT: A 484 PHE cc_start: 0.7357 (m-80) cc_final: 0.6998 (m-80) REVERT: A 709 LEU cc_start: 0.2679 (OUTLIER) cc_final: 0.2398 (pp) REVERT: B 57 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7445 (tmmt) REVERT: B 58 MET cc_start: 0.8986 (mtp) cc_final: 0.8562 (mtp) REVERT: B 60 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: B 442 MET cc_start: 0.7096 (tpt) cc_final: 0.6802 (tpt) REVERT: B 444 TRP cc_start: 0.6951 (t-100) cc_final: 0.6724 (t-100) REVERT: B 484 PHE cc_start: 0.7268 (m-80) cc_final: 0.6829 (m-80) REVERT: B 674 TYR cc_start: 0.4301 (OUTLIER) cc_final: 0.3478 (p90) REVERT: B 709 LEU cc_start: 0.2686 (OUTLIER) cc_final: 0.2433 (pp) REVERT: C 57 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7459 (tmmt) REVERT: C 58 MET cc_start: 0.8996 (mtp) cc_final: 0.8566 (mtp) REVERT: C 60 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: C 264 MET cc_start: 0.7362 (mpp) cc_final: 0.7158 (mpp) REVERT: C 442 MET cc_start: 0.7063 (tpt) cc_final: 0.6645 (tpt) REVERT: C 448 MET cc_start: 0.7751 (mtt) cc_final: 0.7399 (mtt) REVERT: C 651 TYR cc_start: 0.8254 (t80) cc_final: 0.7957 (t80) REVERT: C 674 TYR cc_start: 0.4390 (OUTLIER) cc_final: 0.3617 (p90) REVERT: C 709 LEU cc_start: 0.2726 (OUTLIER) cc_final: 0.2468 (pp) REVERT: D 57 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7433 (tmmt) REVERT: D 58 MET cc_start: 0.8976 (mtp) cc_final: 0.8539 (mtp) REVERT: D 60 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: D 402 PHE cc_start: 0.7643 (t80) cc_final: 0.7379 (t80) REVERT: D 442 MET cc_start: 0.7000 (tpt) cc_final: 0.6605 (tpt) REVERT: D 444 TRP cc_start: 0.6900 (t-100) cc_final: 0.6678 (t-100) REVERT: D 709 LEU cc_start: 0.2722 (OUTLIER) cc_final: 0.2464 (pp) outliers start: 74 outliers final: 58 residues processed: 393 average time/residue: 0.1493 time to fit residues: 94.3505 Evaluate side-chains 407 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 339 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 469 TRP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [209, 26, 83, 62, 254, 255, 122, 42, 63, 118, 92] chunk 209 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN B 403 ASN C 403 ASN D 403 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.230187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.186052 restraints weight = 27884.006| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.03 r_work: 0.3632 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25096 Z= 0.180 Angle : 0.648 14.775 33872 Z= 0.319 Chirality : 0.040 0.163 3764 Planarity : 0.004 0.039 4228 Dihedral : 15.038 174.201 3680 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 3.01 % Allowed : 19.22 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 2956 helix: 1.48 (0.11), residues: 2096 sheet: None (None), residues: 0 loop : -1.45 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 278 TYR 0.016 0.002 TYR D 150 PHE 0.014 0.001 PHE A 320 TRP 0.014 0.001 TRP C 334 HIS 0.004 0.001 HIS B 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (25084) covalent geometry : angle 0.64711 / 0.32 (33864) SS BOND : bond 0.00693 / 0.35 ( 4) SS BOND : angle 1.73901 / 1.19 ( 8) hydrogen bonds : bond 0.05756 / 3.92 ( 1464) hydrogen bonds : angle 3.96709 / 2.84 ( 4344) Misc. bond : bond 0.00194 / 0.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 343 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7424 (tmmt) REVERT: A 58 MET cc_start: 0.9268 (mtp) cc_final: 0.8900 (mtp) REVERT: A 60 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: A 264 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8544 (mpp) REVERT: A 402 PHE cc_start: 0.7607 (t80) cc_final: 0.7374 (t80) REVERT: A 442 MET cc_start: 0.8135 (tpt) cc_final: 0.7706 (tpt) REVERT: A 448 MET cc_start: 0.8299 (mtt) cc_final: 0.7890 (mtt) REVERT: A 651 TYR cc_start: 0.8308 (t80) cc_final: 0.8008 (t80) REVERT: A 709 LEU cc_start: 0.3495 (OUTLIER) cc_final: 0.3274 (pp) REVERT: B 57 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7381 (tmmt) REVERT: B 58 MET cc_start: 0.9250 (mtp) cc_final: 0.8888 (mtp) REVERT: B 60 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: B 264 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8519 (mpp) REVERT: B 444 TRP cc_start: 0.7358 (t-100) cc_final: 0.6718 (t60) REVERT: B 484 PHE cc_start: 0.7417 (m-80) cc_final: 0.6886 (m-80) REVERT: B 651 TYR cc_start: 0.8268 (t80) cc_final: 0.7995 (t80) REVERT: B 674 TYR cc_start: 0.4971 (OUTLIER) cc_final: 0.3861 (p90) REVERT: B 709 LEU cc_start: 0.3500 (OUTLIER) cc_final: 0.3278 (pp) REVERT: C 57 LYS cc_start: 0.8033 (ttmt) cc_final: 0.7395 (tmmt) REVERT: C 58 MET cc_start: 0.9265 (mtp) cc_final: 0.8893 (mtp) REVERT: C 60 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: C 264 MET cc_start: 0.8778 (mpp) cc_final: 0.8395 (mpp) REVERT: C 442 MET cc_start: 0.8108 (tpt) cc_final: 0.7625 (tpt) REVERT: C 448 MET cc_start: 0.8340 (mtt) cc_final: 0.7905 (mtt) REVERT: C 651 TYR cc_start: 0.8270 (t80) cc_final: 0.7957 (t80) REVERT: C 674 TYR cc_start: 0.5029 (OUTLIER) cc_final: 0.3983 (p90) REVERT: C 709 LEU cc_start: 0.3488 (OUTLIER) cc_final: 0.3271 (pp) REVERT: D 57 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7390 (tmmt) REVERT: D 58 MET cc_start: 0.9267 (mtp) cc_final: 0.8906 (mtp) REVERT: D 60 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: D 264 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8525 (mpp) REVERT: D 402 PHE cc_start: 0.7585 (t80) cc_final: 0.7350 (t80) REVERT: D 442 MET cc_start: 0.8092 (tpt) cc_final: 0.7599 (tpt) REVERT: D 444 TRP cc_start: 0.7361 (t-100) cc_final: 0.6850 (t-100) REVERT: D 709 LEU cc_start: 0.3505 (OUTLIER) cc_final: 0.3287 (pp) outliers start: 79 outliers final: 57 residues processed: 390 average time/residue: 0.1440 time to fit residues: 90.4385 Evaluate side-chains 402 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 332 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 469 TRP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [34, 140, 51, 135, 46, 111, 174, 176, 158, 90, 71] chunk 34 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 176 optimal weight: 0.3980 chunk 158 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.233982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.191092 restraints weight = 27760.841| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.74 r_work: 0.3720 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25096 Z= 0.123 Angle : 0.595 13.847 33872 Z= 0.296 Chirality : 0.039 0.170 3764 Planarity : 0.004 0.042 4228 Dihedral : 14.705 175.242 3680 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 2.28 % Allowed : 20.21 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.16), residues: 2956 helix: 1.75 (0.11), residues: 2096 sheet: None (None), residues: 0 loop : -1.31 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 380 TYR 0.011 0.001 TYR A 674 PHE 0.015 0.001 PHE B 484 TRP 0.014 0.001 TRP B 334 HIS 0.003 0.001 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (25084) covalent geometry : angle 0.59460 / 0.30 (33864) SS BOND : bond 0.00431 / 0.22 ( 4) SS BOND : angle 1.25518 / 0.88 ( 8) hydrogen bonds : bond 0.04624 / 3.15 ( 1464) hydrogen bonds : angle 3.80629 / 2.73 ( 4344) Misc. bond : bond 0.00222 / 0.11 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 337 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7403 (tmmt) REVERT: A 60 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: A 264 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8430 (mpp) REVERT: A 402 PHE cc_start: 0.7535 (t80) cc_final: 0.7290 (t80) REVERT: A 448 MET cc_start: 0.8307 (mtt) cc_final: 0.7864 (mtt) REVERT: A 651 TYR cc_start: 0.8247 (t80) cc_final: 0.7936 (t80) REVERT: A 709 LEU cc_start: 0.3480 (OUTLIER) cc_final: 0.3254 (pp) REVERT: A 794 LYS cc_start: 0.7757 (tptp) cc_final: 0.6457 (mttt) REVERT: A 810 ASP cc_start: 0.6647 (m-30) cc_final: 0.6368 (m-30) REVERT: B 57 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7347 (tmmt) REVERT: B 60 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: B 264 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8445 (mpp) REVERT: B 444 TRP cc_start: 0.7028 (t-100) cc_final: 0.6681 (t60) REVERT: B 651 TYR cc_start: 0.8227 (t80) cc_final: 0.7933 (t80) REVERT: B 674 TYR cc_start: 0.4996 (OUTLIER) cc_final: 0.4055 (p90) REVERT: B 709 LEU cc_start: 0.3453 (OUTLIER) cc_final: 0.3227 (pp) REVERT: B 794 LYS cc_start: 0.7763 (tptp) cc_final: 0.6475 (mttt) REVERT: C 57 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7354 (tmmt) REVERT: C 60 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: C 264 MET cc_start: 0.8718 (mpp) cc_final: 0.8366 (mpp) REVERT: C 442 MET cc_start: 0.8014 (tpt) cc_final: 0.7648 (tpt) REVERT: C 448 MET cc_start: 0.8301 (mtt) cc_final: 0.7851 (mtt) REVERT: C 651 TYR cc_start: 0.8283 (t80) cc_final: 0.7921 (t80) REVERT: C 674 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.4133 (p90) REVERT: C 709 LEU cc_start: 0.3447 (OUTLIER) cc_final: 0.3224 (pp) REVERT: C 794 LYS cc_start: 0.7745 (tptp) cc_final: 0.6457 (mttt) REVERT: D 57 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7358 (tmmt) REVERT: D 60 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: D 264 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8416 (mpp) REVERT: D 402 PHE cc_start: 0.7514 (t80) cc_final: 0.7273 (t80) REVERT: D 442 MET cc_start: 0.7964 (tpt) cc_final: 0.7615 (tpt) REVERT: D 444 TRP cc_start: 0.7332 (t-100) cc_final: 0.6693 (t-100) REVERT: D 448 MET cc_start: 0.7778 (mtt) cc_final: 0.7206 (mtt) REVERT: D 449 MET cc_start: 0.7609 (tpt) cc_final: 0.7369 (tpt) REVERT: D 709 LEU cc_start: 0.3458 (OUTLIER) cc_final: 0.3238 (pp) REVERT: D 794 LYS cc_start: 0.7738 (tptp) cc_final: 0.6453 (mttt) outliers start: 60 outliers final: 44 residues processed: 374 average time/residue: 0.1576 time to fit residues: 94.3949 Evaluate side-chains 386 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 329 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 669 MET Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 669 MET Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: [207, 57, 241, 225, 137, 103, 171, 280, 13, 270, 190] chunk 207 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 171 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.231874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.190756 restraints weight = 27731.845| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.95 r_work: 0.3673 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25096 Z= 0.149 Angle : 0.628 17.305 33872 Z= 0.309 Chirality : 0.040 0.215 3764 Planarity : 0.004 0.039 4228 Dihedral : 14.620 175.556 3680 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.42 % Favored : 96.45 % Rotamer: Outliers : 2.66 % Allowed : 20.24 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.16), residues: 2956 helix: 1.71 (0.11), residues: 2096 sheet: None (None), residues: 0 loop : -1.28 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.014 0.001 TYR D 150 PHE 0.019 0.001 PHE B 484 TRP 0.016 0.001 TRP A 444 HIS 0.004 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (25084) covalent geometry : angle 0.62721 / 0.31 (33864) SS BOND : bond 0.00565 / 0.28 ( 4) SS BOND : angle 1.59480 / 1.10 ( 8) hydrogen bonds : bond 0.05155 / 3.51 ( 1464) hydrogen bonds : angle 3.89045 / 2.80 ( 4344) Misc. bond : bond 0.00201 / 0.10 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4954.96 seconds wall clock time: 85 minutes 43.33 seconds (5143.33 seconds total)