Starting phenix.real_space_refine on Tue Apr 7 05:01:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oll_70596/04_2026/9oll_70596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oll_70596/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9oll_70596/04_2026/9oll_70596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oll_70596/04_2026/9oll_70596.map" model { file = "/net/cci-nas-00/data/ceres_data/9oll_70596/04_2026/9oll_70596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oll_70596/04_2026/9oll_70596.cif" } 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-2.1rc1-6017/lib/python3.9/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: 8.06, per 1000 atoms: 0.33 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=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 196 " distance=3.00 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 69 " distance=0.00 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 138 " distance=0.00 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 170 " distance=0.00 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 196 " distance=3.00 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 194 " distance=0.00 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 196 " distance=3.00 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 194 " distance=3.00 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 196 " distance=0.00 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 199 " distance=0.00 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 266 " distance=0.00 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 277 " distance=0.00 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 326 " distance=0.00 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 350 " distance=0.00 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 372 " distance=0.00 Simple disulfide: pdb=" SG CYS B 453 " - pdb=" SG CYS B 453 " distance=0.00 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 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.68 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: 4.54 Time building geometry restraints manager: 2.86 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: 14442 33.64 - 67.28: 655 67.28 - 100.91: 100 100.91 - 134.55: 4 134.55 - 168.19: 20 Dihedral angle restraints: 15221 sinusoidal: 6425 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 15218 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: 34845 3.55 - 4.23: 53707 4.23 - 4.90: 95641 Nonbonded interactions: 193449 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 193444 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.190 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 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 : 0.017 0.968 25095 Z= 1.207 Angle : 1.469 17.720 33882 Z= 1.079 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 : 7.79 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 covalent geometry : bond 0.01009 (25084) covalent geometry : angle 1.45523 (33864) SS BOND : bond 0.96800 ( 3) SS BOND : angle 8.72128 ( 18) hydrogen bonds : bond 0.20284 ( 1464) hydrogen bonds : angle 7.59868 ( 4344) Misc. bond : bond 0.44726 ( 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 : 1.054 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: 0.1860 time to fit residues: 143.8051 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 : 0.849 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 177 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.259589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.216264 restraints weight = 28881.709| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 2.32 r_work: 0.4099 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25095 Z= 0.171 Angle : 0.655 8.786 33882 Z= 0.333 Chirality : 0.041 0.167 3764 Planarity : 0.005 0.045 4228 Dihedral : 16.979 168.171 3716 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Rotamer: Outliers : 3.50 % Allowed : 15.30 % Favored : 81.20 % 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: 0.41 (0.15), residues: 2956 helix: 1.12 (0.11), residues: 2092 sheet: None (None), residues: 0 loop : -1.84 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 278 TYR 0.017 0.001 TYR A 150 PHE 0.038 0.002 PHE B 484 TRP 0.016 0.002 TRP B 693 HIS 0.014 0.002 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00358 (25084) covalent geometry : angle 0.65518 (33864) SS BOND : bond 0.02355 ( 3) SS BOND : angle 1.09360 ( 18) hydrogen bonds : bond 0.05897 ( 1464) hydrogen bonds : angle 4.43820 ( 4344) Misc. bond : bond 0.00470 ( 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 426 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 334 time to evaluate : 0.951 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: 0.7417 (tpt) cc_final: 0.7110 (tpt) REVERT: A 449 MET cc_start: 0.7703 (tpt) cc_final: 0.7486 (tpt) REVERT: A 484 PHE cc_start: 0.6972 (m-80) cc_final: 0.6542 (m-80) REVERT: A 592 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6222 (mtm) REVERT: A 641 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.6082 (mtpt) REVERT: A 684 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 779 MET cc_start: 0.6328 (tpt) cc_final: 0.5933 (mmt) REVERT: A 794 LYS cc_start: 0.7656 (tptp) cc_final: 0.6634 (mtpt) REVERT: B 442 MET cc_start: 0.7395 (tpt) cc_final: 0.7111 (tpt) REVERT: B 449 MET cc_start: 0.7650 (tpt) cc_final: 0.7441 (tpt) REVERT: B 484 PHE cc_start: 0.6955 (m-80) cc_final: 0.6584 (m-80) REVERT: B 592 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6229 (mtm) REVERT: B 641 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.6060 (mtpt) REVERT: B 684 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8162 (mm-30) REVERT: B 779 MET cc_start: 0.6281 (tpt) cc_final: 0.5888 (mmt) REVERT: B 794 LYS cc_start: 0.7622 (tptp) cc_final: 0.6616 (mtpt) REVERT: C 55 VAL cc_start: 0.8114 (p) cc_final: 0.7854 (t) REVERT: C 442 MET cc_start: 0.7433 (tpt) cc_final: 0.7092 (tpt) REVERT: C 449 MET cc_start: 0.7690 (tpt) cc_final: 0.7469 (tpt) REVERT: C 484 PHE cc_start: 0.6961 (m-80) cc_final: 0.6610 (m-80) REVERT: C 592 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6210 (mtm) REVERT: C 684 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8164 (mm-30) REVERT: C 779 MET cc_start: 0.6298 (tpt) cc_final: 0.5921 (mmt) REVERT: C 794 LYS cc_start: 0.7632 (tptp) cc_final: 0.6628 (mtpt) REVERT: D 55 VAL cc_start: 0.8129 (p) cc_final: 0.7874 (t) REVERT: D 442 MET cc_start: 0.7449 (tpt) cc_final: 0.7130 (tpt) REVERT: D 449 MET cc_start: 0.7654 (tpt) cc_final: 0.7443 (tpt) REVERT: D 484 PHE cc_start: 0.6983 (m-80) cc_final: 0.6620 (m-80) REVERT: D 592 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6220 (mtm) REVERT: D 684 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8144 (mm-30) REVERT: D 779 MET cc_start: 0.6258 (tpt) cc_final: 0.5857 (mmt) REVERT: D 794 LYS cc_start: 0.7651 (tptp) cc_final: 0.6643 (mtpt) outliers start: 92 outliers final: 22 residues processed: 406 average time/residue: 0.1583 time to fit residues: 103.1809 Evaluate side-chains 318 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 A residue 641 LYS Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 134 THR 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 641 LYS 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 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: chunk 261 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 294 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 403 ASN B 327 GLN B 403 ASN C 205 HIS C 210 HIS C 403 ASN D 403 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.236974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.195201 restraints weight = 28041.392| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.87 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25095 Z= 0.208 Angle : 0.710 13.733 33882 Z= 0.352 Chirality : 0.043 0.170 3764 Planarity : 0.005 0.040 4228 Dihedral : 16.092 171.132 3696 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.23 % Favored : 95.64 % Rotamer: Outliers : 3.46 % Allowed : 17.28 % Favored : 79.26 % 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: 0.64 (0.15), residues: 2956 helix: 1.23 (0.11), residues: 2088 sheet: None (None), residues: 0 loop : -1.54 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 278 TYR 0.029 0.002 TYR B 150 PHE 0.025 0.002 PHE B 484 TRP 0.019 0.002 TRP C 334 HIS 0.008 0.002 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00488 (25084) covalent geometry : angle 0.70816 (33864) SS BOND : bond 0.00061 ( 3) SS BOND : angle 2.13901 ( 18) hydrogen bonds : bond 0.06641 ( 1464) hydrogen bonds : angle 4.28478 ( 4344) Misc. bond : bond 0.00227 ( 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: 91 poor density : 364 time to evaluate : 0.855 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 58 MET cc_start: 0.8872 (mtp) cc_final: 0.8556 (mtp) REVERT: A 60 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: A 264 MET cc_start: 0.7605 (mpp) cc_final: 0.7168 (mpp) REVERT: A 684 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 794 LYS cc_start: 0.8017 (tptp) cc_final: 0.7007 (mtmt) REVERT: B 58 MET cc_start: 0.8858 (mtp) cc_final: 0.8546 (mtp) REVERT: B 60 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: B 264 MET cc_start: 0.7637 (mpp) cc_final: 0.7214 (mpp) REVERT: B 402 PHE cc_start: 0.7202 (t80) cc_final: 0.6982 (t80) REVERT: B 684 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7416 (mm-30) REVERT: B 794 LYS cc_start: 0.8019 (tptp) cc_final: 0.7014 (mtmt) REVERT: C 58 MET cc_start: 0.8883 (mtp) cc_final: 0.8581 (mtp) REVERT: C 60 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: C 264 MET cc_start: 0.7620 (mpp) cc_final: 0.7206 (mpp) REVERT: C 402 PHE cc_start: 0.7206 (t80) cc_final: 0.6973 (t80) REVERT: C 794 LYS cc_start: 0.7997 (tptp) cc_final: 0.7011 (mtmt) REVERT: D 57 LYS cc_start: 0.7605 (ttmt) cc_final: 0.7188 (tmmt) REVERT: D 58 MET cc_start: 0.8921 (mtp) cc_final: 0.8665 (mtp) REVERT: D 60 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: D 264 MET cc_start: 0.7599 (mpp) cc_final: 0.7204 (mpp) REVERT: D 402 PHE cc_start: 0.7214 (t80) cc_final: 0.6989 (t80) REVERT: D 684 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7481 (mm-30) REVERT: D 794 LYS cc_start: 0.8026 (tptp) cc_final: 0.7029 (mtmt) outliers start: 91 outliers final: 42 residues processed: 439 average time/residue: 0.1544 time to fit residues: 110.0316 Evaluate side-chains 369 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 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 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 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: chunk 164 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 282 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN C 205 HIS D 403 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.239295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.195450 restraints weight = 27705.509| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.63 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25095 Z= 0.134 Angle : 0.591 10.893 33882 Z= 0.294 Chirality : 0.039 0.164 3764 Planarity : 0.004 0.039 4228 Dihedral : 15.720 170.270 3688 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.25 % Favored : 96.62 % Rotamer: Outliers : 2.44 % Allowed : 19.03 % Favored : 78.54 % 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: 1.15 (0.15), residues: 2956 helix: 1.64 (0.11), residues: 2080 sheet: None (None), residues: 0 loop : -1.41 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.013 0.001 TYR A 192 PHE 0.043 0.001 PHE B 484 TRP 0.013 0.001 TRP B 685 HIS 0.009 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00295 (25084) covalent geometry : angle 0.59079 (33864) SS BOND : bond 0.00761 ( 3) SS BOND : angle 0.72131 ( 18) hydrogen bonds : bond 0.05186 ( 1464) hydrogen bonds : angle 3.97123 ( 4344) Misc. bond : bond 0.00241 ( 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 387 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 323 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8836 (mtp) cc_final: 0.8511 (mtp) REVERT: A 264 MET cc_start: 0.7451 (mpp) cc_final: 0.7093 (mpp) REVERT: A 484 PHE cc_start: 0.6809 (m-80) cc_final: 0.6526 (m-80) REVERT: A 595 MET cc_start: 0.8129 (mmt) cc_final: 0.7774 (mmt) REVERT: A 665 MET cc_start: 0.7442 (tpp) cc_final: 0.7008 (ttp) REVERT: A 684 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 58 MET cc_start: 0.8830 (mtp) cc_final: 0.8514 (mtp) REVERT: B 60 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: B 264 MET cc_start: 0.7449 (mpp) cc_final: 0.7115 (mpp) REVERT: B 484 PHE cc_start: 0.6777 (m-80) cc_final: 0.6478 (m-80) REVERT: B 595 MET cc_start: 0.8066 (mmt) cc_final: 0.7697 (mmt) REVERT: B 684 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7443 (mm-30) REVERT: C 57 LYS cc_start: 0.7612 (ttmt) cc_final: 0.7185 (tmmt) REVERT: C 58 MET cc_start: 0.8879 (mtp) cc_final: 0.8609 (mtp) REVERT: C 60 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: C 178 MET cc_start: 0.6063 (mtm) cc_final: 0.5847 (mtm) REVERT: C 264 MET cc_start: 0.7454 (mpp) cc_final: 0.7099 (mpp) REVERT: C 595 MET cc_start: 0.8116 (mmt) cc_final: 0.7749 (mmt) REVERT: D 57 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7193 (tmmt) REVERT: D 58 MET cc_start: 0.8858 (mtp) cc_final: 0.8578 (mtp) REVERT: D 264 MET cc_start: 0.7444 (mpp) cc_final: 0.7108 (mpp) REVERT: D 595 MET cc_start: 0.8054 (mmt) cc_final: 0.7688 (mmt) REVERT: D 684 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7601 (mm-30) outliers start: 64 outliers final: 41 residues processed: 369 average time/residue: 0.1512 time to fit residues: 91.4526 Evaluate side-chains 346 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 303 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 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 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 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 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 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 134 THR Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 205 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 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: chunk 2 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS D 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.231344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.187216 restraints weight = 27358.209| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.00 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25095 Z= 0.225 Angle : 0.706 13.744 33882 Z= 0.348 Chirality : 0.043 0.189 3764 Planarity : 0.004 0.037 4228 Dihedral : 15.670 170.304 3688 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % Rotamer: Outliers : 3.31 % Allowed : 18.49 % Favored : 78.20 % 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: 0.77 (0.15), residues: 2956 helix: 1.32 (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 0.007 0.001 ARG B 308 TYR 0.015 0.002 TYR A 150 PHE 0.043 0.002 PHE D 484 TRP 0.020 0.002 TRP D 334 HIS 0.009 0.002 HIS D 210 Details of bonding type rmsd covalent geometry : bond 0.00545 (25084) covalent geometry : angle 0.70579 (33864) SS BOND : bond 0.01171 ( 3) SS BOND : angle 1.38313 ( 18) hydrogen bonds : bond 0.06738 ( 1464) hydrogen bonds : angle 4.12918 ( 4344) Misc. bond : bond 0.00171 ( 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 427 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 340 time to evaluate : 0.930 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: 0.7673 (ttmt) cc_final: 0.7271 (tmmt) REVERT: A 58 MET cc_start: 0.8961 (mtp) cc_final: 0.8507 (mtp) REVERT: A 60 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: A 264 MET cc_start: 0.7461 (mpp) cc_final: 0.7059 (mpp) REVERT: A 579 LYS cc_start: 0.6653 (mmmt) cc_final: 0.6225 (mmtt) REVERT: A 595 MET cc_start: 0.8365 (mmt) cc_final: 0.7985 (mmt) REVERT: A 794 LYS cc_start: 0.7902 (tptp) cc_final: 0.6945 (mttt) REVERT: B 57 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7260 (tmmt) REVERT: B 58 MET cc_start: 0.8959 (mtp) cc_final: 0.8505 (mtp) REVERT: B 60 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: B 264 MET cc_start: 0.7470 (mpp) cc_final: 0.7087 (mpp) REVERT: B 595 MET cc_start: 0.8331 (mmt) cc_final: 0.7975 (mmt) REVERT: B 674 TYR cc_start: 0.4072 (OUTLIER) cc_final: 0.3377 (p90) REVERT: B 794 LYS cc_start: 0.7900 (tptp) cc_final: 0.6948 (mttt) REVERT: C 57 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7272 (tmmt) REVERT: C 58 MET cc_start: 0.8973 (mtp) cc_final: 0.8504 (mtp) REVERT: C 60 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: C 264 MET cc_start: 0.7447 (mpp) cc_final: 0.7039 (mpp) REVERT: C 448 MET cc_start: 0.7398 (mtt) cc_final: 0.7019 (mtt) REVERT: C 555 TYR cc_start: 0.6661 (t80) cc_final: 0.6385 (t80) REVERT: C 579 LYS cc_start: 0.6673 (mmmt) cc_final: 0.6232 (mmtt) REVERT: C 595 MET cc_start: 0.8369 (mmt) cc_final: 0.8010 (mmt) REVERT: C 665 MET cc_start: 0.7476 (tpp) cc_final: 0.7040 (ttt) REVERT: C 794 LYS cc_start: 0.7893 (tptp) cc_final: 0.6928 (mttt) REVERT: D 57 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7265 (tmmt) REVERT: D 58 MET cc_start: 0.8964 (mtp) cc_final: 0.8498 (mtp) REVERT: D 60 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: D 264 MET cc_start: 0.7459 (mpp) cc_final: 0.7067 (mpp) REVERT: D 579 LYS cc_start: 0.6659 (mmmt) cc_final: 0.6217 (mmtt) REVERT: D 595 MET cc_start: 0.8333 (mmt) cc_final: 0.7983 (mmt) REVERT: D 665 MET cc_start: 0.7468 (tpp) cc_final: 0.7082 (ttt) REVERT: D 794 LYS cc_start: 0.7920 (tptp) cc_final: 0.6959 (mttt) outliers start: 87 outliers final: 69 residues processed: 400 average time/residue: 0.1447 time to fit residues: 95.4001 Evaluate side-chains 388 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 314 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 A residue 779 MET 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 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 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 B residue 779 MET 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 205 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 547 VAL Chi-restraints excluded: chain C residue 662 LEU 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 C residue 779 MET 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 196 CYS Chi-restraints excluded: chain D residue 205 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 547 VAL Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 663 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 Chi-restraints excluded: chain D residue 779 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 46 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 173 optimal weight: 0.0970 chunk 268 optimal weight: 20.0000 chunk 228 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 403 ASN B 205 HIS B 403 ASN C 403 ASN D 403 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.233970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.192363 restraints weight = 27549.178| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.72 r_work: 0.3694 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25095 Z= 0.144 Angle : 0.596 11.320 33882 Z= 0.298 Chirality : 0.039 0.156 3764 Planarity : 0.004 0.039 4228 Dihedral : 15.485 170.437 3688 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.62 % 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: 1.06 (0.15), residues: 2956 helix: 1.55 (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 0.003 0.000 ARG A 308 TYR 0.014 0.001 TYR A 150 PHE 0.043 0.001 PHE B 484 TRP 0.036 0.002 TRP B 444 HIS 0.011 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00325 (25084) covalent geometry : angle 0.59535 (33864) SS BOND : bond 0.00597 ( 3) SS BOND : angle 0.91980 ( 18) hydrogen bonds : bond 0.05389 ( 1464) hydrogen bonds : angle 3.92020 ( 4344) Misc. bond : bond 0.00215 ( 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: 74 poor density : 331 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7248 (tmmt) REVERT: A 58 MET cc_start: 0.9261 (mtp) cc_final: 0.8928 (mtp) REVERT: A 60 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: A 63 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7798 (mptt) REVERT: A 264 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8240 (mpp) REVERT: A 442 MET cc_start: 0.7508 (tpt) cc_final: 0.7159 (tpt) REVERT: A 579 LYS cc_start: 0.7676 (mmmt) cc_final: 0.7177 (ptpt) REVERT: A 595 MET cc_start: 0.8449 (mmt) cc_final: 0.8067 (mmt) REVERT: B 57 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7253 (tmmt) REVERT: B 58 MET cc_start: 0.9265 (mtp) cc_final: 0.8935 (mtp) REVERT: B 60 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: B 63 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7787 (mptt) REVERT: B 264 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8271 (mpp) REVERT: B 442 MET cc_start: 0.7481 (tpt) cc_final: 0.7242 (tpt) REVERT: B 444 TRP cc_start: 0.6974 (t60) cc_final: 0.6771 (t60) REVERT: B 555 TYR cc_start: 0.6913 (t80) cc_final: 0.6383 (t80) REVERT: B 595 MET cc_start: 0.8471 (mmt) cc_final: 0.8115 (mmt) REVERT: B 674 TYR cc_start: 0.4890 (OUTLIER) cc_final: 0.3901 (p90) REVERT: C 57 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7269 (tmmt) REVERT: C 58 MET cc_start: 0.9270 (mtp) cc_final: 0.8939 (mtp) REVERT: C 60 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: C 63 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7806 (mptt) REVERT: C 264 MET cc_start: 0.8576 (mpp) cc_final: 0.8249 (mpp) REVERT: C 402 PHE cc_start: 0.7463 (t80) cc_final: 0.7226 (t80) REVERT: C 448 MET cc_start: 0.7969 (mtt) cc_final: 0.7493 (mtt) REVERT: C 579 LYS cc_start: 0.7709 (mmmt) cc_final: 0.7191 (ptpt) REVERT: C 595 MET cc_start: 0.8478 (mmt) cc_final: 0.8144 (mmt) REVERT: C 665 MET cc_start: 0.7654 (tpp) cc_final: 0.7447 (ttp) REVERT: C 674 TYR cc_start: 0.4812 (OUTLIER) cc_final: 0.3881 (p90) REVERT: D 57 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7259 (tmmt) REVERT: D 58 MET cc_start: 0.9261 (mtp) cc_final: 0.8925 (mtp) REVERT: D 60 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: D 264 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8255 (mpp) REVERT: D 402 PHE cc_start: 0.7457 (t80) cc_final: 0.7227 (t80) REVERT: D 442 MET cc_start: 0.7512 (tpt) cc_final: 0.7265 (tpt) REVERT: D 579 LYS cc_start: 0.7676 (mmmt) cc_final: 0.7181 (ptpt) REVERT: D 595 MET cc_start: 0.8430 (mmt) cc_final: 0.8107 (mmt) outliers start: 74 outliers final: 53 residues processed: 376 average time/residue: 0.1511 time to fit residues: 92.8429 Evaluate side-chains 377 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 315 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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 669 MET 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 37 THR 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 469 TRP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 663 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 B residue 779 MET 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 205 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 VAL 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 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 C residue 779 MET 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 196 CYS 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 Chi-restraints excluded: chain D residue 779 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 133 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 294 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.235926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.192473 restraints weight = 27634.394| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.77 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25095 Z= 0.121 Angle : 0.562 9.095 33882 Z= 0.283 Chirality : 0.039 0.170 3764 Planarity : 0.004 0.040 4228 Dihedral : 15.284 171.149 3688 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.01 % Allowed : 19.18 % 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: 1.31 (0.16), residues: 2956 helix: 1.74 (0.11), residues: 2092 sheet: None (None), residues: 0 loop : -1.35 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 204 TYR 0.011 0.001 TYR A 150 PHE 0.043 0.001 PHE C 484 TRP 0.028 0.001 TRP D 444 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00261 (25084) covalent geometry : angle 0.56158 (33864) SS BOND : bond 0.00473 ( 3) SS BOND : angle 0.77006 ( 18) hydrogen bonds : bond 0.04803 ( 1464) hydrogen bonds : angle 3.80852 ( 4344) Misc. bond : bond 0.00224 ( 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: 79 poor density : 336 time to evaluate : 0.866 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: 0.7637 (ttmt) cc_final: 0.7229 (tmmt) REVERT: A 58 MET cc_start: 0.8897 (mtp) cc_final: 0.8545 (mtp) REVERT: A 60 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: A 264 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6971 (mpp) REVERT: A 402 PHE cc_start: 0.7489 (t80) cc_final: 0.7236 (t80) REVERT: A 595 MET cc_start: 0.8341 (mmt) cc_final: 0.8052 (mmt) REVERT: A 794 LYS cc_start: 0.7837 (tptp) cc_final: 0.6816 (mttt) REVERT: B 58 MET cc_start: 0.8904 (mtp) cc_final: 0.8504 (mtp) REVERT: B 60 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: B 264 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7013 (mpp) REVERT: B 402 PHE cc_start: 0.7544 (t80) cc_final: 0.7242 (t80) REVERT: B 555 TYR cc_start: 0.6732 (t80) cc_final: 0.6478 (t80) REVERT: B 595 MET cc_start: 0.8310 (mmt) cc_final: 0.8082 (mmt) REVERT: B 674 TYR cc_start: 0.4414 (OUTLIER) cc_final: 0.3828 (p90) REVERT: B 794 LYS cc_start: 0.7835 (tptp) cc_final: 0.6846 (mttt) REVERT: B 810 ASP cc_start: 0.6026 (m-30) cc_final: 0.5647 (m-30) REVERT: C 57 LYS cc_start: 0.7658 (ttmt) cc_final: 0.7250 (tmmt) REVERT: C 58 MET cc_start: 0.8913 (mtp) cc_final: 0.8564 (mtp) REVERT: C 60 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: C 264 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6983 (mpp) REVERT: C 402 PHE cc_start: 0.7524 (t80) cc_final: 0.7277 (t80) REVERT: C 448 MET cc_start: 0.7612 (mtt) cc_final: 0.7281 (mtt) REVERT: C 555 TYR cc_start: 0.6665 (t80) cc_final: 0.6429 (t80) REVERT: C 595 MET cc_start: 0.8334 (mmt) cc_final: 0.8098 (mmt) REVERT: C 674 TYR cc_start: 0.4225 (OUTLIER) cc_final: 0.3638 (p90) REVERT: C 794 LYS cc_start: 0.7825 (tptp) cc_final: 0.6800 (mttt) REVERT: C 810 ASP cc_start: 0.5828 (m-30) cc_final: 0.5443 (m-30) REVERT: D 57 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7248 (tmmt) REVERT: D 58 MET cc_start: 0.8893 (mtp) cc_final: 0.8523 (mtp) REVERT: D 60 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: D 264 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7005 (mpp) REVERT: D 402 PHE cc_start: 0.7570 (t80) cc_final: 0.7329 (t80) REVERT: D 442 MET cc_start: 0.6802 (tpt) cc_final: 0.6525 (tpt) REVERT: D 595 MET cc_start: 0.8321 (mmt) cc_final: 0.8048 (mmt) REVERT: D 794 LYS cc_start: 0.7850 (tptp) cc_final: 0.6849 (mttt) REVERT: D 810 ASP cc_start: 0.5934 (m-30) cc_final: 0.5523 (m-30) outliers start: 79 outliers final: 52 residues processed: 388 average time/residue: 0.1490 time to fit residues: 94.7119 Evaluate side-chains 384 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 322 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 669 MET 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 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 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 663 LEU 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 B residue 779 MET 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 205 HIS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 264 MET 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 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 C residue 779 MET 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 196 CYS 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 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 Chi-restraints excluded: chain D residue 779 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 240 optimal weight: 4.9990 chunk 274 optimal weight: 0.0570 chunk 289 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN B 344 GLN D 344 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.234454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.190629 restraints weight = 27648.229| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.84 r_work: 0.3704 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25095 Z= 0.132 Angle : 0.589 19.055 33882 Z= 0.291 Chirality : 0.039 0.192 3764 Planarity : 0.004 0.038 4228 Dihedral : 15.007 172.150 3680 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.89 % Allowed : 18.84 % Favored : 78.27 % 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: 1.38 (0.16), residues: 2956 helix: 1.77 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : -1.27 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 204 TYR 0.013 0.001 TYR B 150 PHE 0.030 0.001 PHE A 484 TRP 0.043 0.002 TRP A 444 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00298 (25084) covalent geometry : angle 0.58925 (33864) SS BOND : bond 0.00547 ( 3) SS BOND : angle 0.82420 ( 18) hydrogen bonds : bond 0.04879 ( 1464) hydrogen bonds : angle 3.79435 ( 4344) Misc. bond : bond 0.00206 ( 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 400 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 324 time to evaluate : 0.895 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: 0.7944 (ttmt) cc_final: 0.7233 (tmmt) REVERT: A 58 MET cc_start: 0.9230 (mtp) cc_final: 0.8889 (mtp) REVERT: A 60 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: A 63 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7700 (mptt) REVERT: A 264 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8230 (mpp) REVERT: A 402 PHE cc_start: 0.7517 (t80) cc_final: 0.7283 (t80) REVERT: A 444 TRP cc_start: 0.6882 (t60) cc_final: 0.6616 (t60) REVERT: A 595 MET cc_start: 0.8479 (mmt) cc_final: 0.8109 (mmt) REVERT: A 794 LYS cc_start: 0.7647 (tptp) cc_final: 0.6424 (mttt) REVERT: B 57 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7222 (tmmt) REVERT: B 58 MET cc_start: 0.9224 (mtp) cc_final: 0.8889 (mtp) REVERT: B 60 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: B 63 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7702 (mptt) REVERT: B 264 MET cc_start: 0.8556 (mpp) cc_final: 0.8226 (mpp) REVERT: B 402 PHE cc_start: 0.7486 (t80) cc_final: 0.7217 (t80) REVERT: B 595 MET cc_start: 0.8453 (mmt) cc_final: 0.8178 (mmt) REVERT: B 674 TYR cc_start: 0.4995 (OUTLIER) cc_final: 0.4102 (p90) REVERT: B 684 GLU cc_start: 0.8228 (mp0) cc_final: 0.7315 (tp30) REVERT: B 794 LYS cc_start: 0.7648 (tptp) cc_final: 0.6433 (mttt) REVERT: B 810 ASP cc_start: 0.6390 (m-30) cc_final: 0.5778 (m-30) REVERT: C 57 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7238 (tmmt) REVERT: C 58 MET cc_start: 0.9200 (mtp) cc_final: 0.8891 (mtp) REVERT: C 60 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: C 63 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7689 (mptt) REVERT: C 264 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: C 402 PHE cc_start: 0.7492 (t80) cc_final: 0.7255 (t80) REVERT: C 444 TRP cc_start: 0.7192 (t-100) cc_final: 0.6638 (t-100) REVERT: C 448 MET cc_start: 0.8087 (mtt) cc_final: 0.7652 (mtt) REVERT: C 595 MET cc_start: 0.8467 (mmt) cc_final: 0.8172 (mmt) REVERT: C 674 TYR cc_start: 0.5061 (OUTLIER) cc_final: 0.4224 (p90) REVERT: C 794 LYS cc_start: 0.7654 (tptp) cc_final: 0.6434 (mttt) REVERT: C 810 ASP cc_start: 0.6379 (m-30) cc_final: 0.5777 (m-30) REVERT: D 57 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7225 (tmmt) REVERT: D 58 MET cc_start: 0.9225 (mtp) cc_final: 0.8881 (mtp) REVERT: D 60 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: D 63 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7747 (mptt) REVERT: D 264 MET cc_start: 0.8522 (mpp) cc_final: 0.8182 (mpp) REVERT: D 402 PHE cc_start: 0.7523 (t80) cc_final: 0.7286 (t80) REVERT: D 442 MET cc_start: 0.7993 (tpt) cc_final: 0.7714 (tpt) REVERT: D 444 TRP cc_start: 0.6910 (t60) cc_final: 0.6653 (t60) REVERT: D 595 MET cc_start: 0.8479 (mmt) cc_final: 0.8122 (mmt) REVERT: D 794 LYS cc_start: 0.7640 (tptp) cc_final: 0.6429 (mttt) REVERT: D 810 ASP cc_start: 0.6383 (m-30) cc_final: 0.5765 (m-30) outliers start: 76 outliers final: 56 residues processed: 377 average time/residue: 0.1456 time to fit residues: 90.3928 Evaluate side-chains 380 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 316 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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 621 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 779 MET 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 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 669 MET Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 779 MET 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 205 HIS 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 311 LEU 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 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 779 MET 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 196 CYS 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 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 779 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 209 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.228543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.182843 restraints weight = 27840.644| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.21 r_work: 0.3607 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 25095 Z= 0.233 Angle : 0.702 14.792 33882 Z= 0.349 Chirality : 0.043 0.193 3764 Planarity : 0.004 0.039 4228 Dihedral : 15.028 171.339 3680 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 2.59 % Allowed : 18.87 % Favored : 78.54 % 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: 0.91 (0.15), residues: 2956 helix: 1.44 (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 0.005 0.001 ARG C 308 TYR 0.018 0.002 TYR B 150 PHE 0.030 0.002 PHE A 484 TRP 0.036 0.002 TRP A 444 HIS 0.007 0.002 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00564 (25084) covalent geometry : angle 0.70186 (33864) SS BOND : bond 0.00884 ( 3) SS BOND : angle 1.22662 ( 18) hydrogen bonds : bond 0.06643 ( 1464) hydrogen bonds : angle 4.11339 ( 4344) Misc. bond : bond 0.00165 ( 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 412 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 344 time to evaluate : 0.872 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: 0.8037 (ttmt) cc_final: 0.7392 (tmmt) REVERT: A 58 MET cc_start: 0.9284 (mtp) cc_final: 0.8889 (mtp) REVERT: A 60 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: A 63 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7830 (mptt) REVERT: A 402 PHE cc_start: 0.7542 (t80) cc_final: 0.7288 (t80) REVERT: A 444 TRP cc_start: 0.7068 (t60) cc_final: 0.6867 (t60) REVERT: A 579 LYS cc_start: 0.6999 (mmtt) cc_final: 0.6755 (ptpt) REVERT: A 595 MET cc_start: 0.8499 (mmt) cc_final: 0.8098 (mmt) REVERT: A 794 LYS cc_start: 0.7985 (tptp) cc_final: 0.6694 (mttt) REVERT: B 57 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7375 (tmmt) REVERT: B 58 MET cc_start: 0.9288 (mtp) cc_final: 0.8912 (mtp) REVERT: B 60 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: B 63 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7832 (mptt) REVERT: B 402 PHE cc_start: 0.7528 (t80) cc_final: 0.7260 (t80) REVERT: B 595 MET cc_start: 0.8511 (mmt) cc_final: 0.8158 (mmt) REVERT: B 674 TYR cc_start: 0.4929 (OUTLIER) cc_final: 0.3913 (p90) REVERT: B 684 GLU cc_start: 0.8211 (mp0) cc_final: 0.7313 (tp30) REVERT: B 794 LYS cc_start: 0.7996 (tptp) cc_final: 0.6730 (mttt) REVERT: C 57 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7390 (tmmt) REVERT: C 58 MET cc_start: 0.9295 (mtp) cc_final: 0.8913 (mtp) REVERT: C 60 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: C 63 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7833 (mptt) REVERT: C 264 MET cc_start: 0.8523 (mpp) cc_final: 0.8321 (mpp) REVERT: C 402 PHE cc_start: 0.7526 (t80) cc_final: 0.7274 (t80) REVERT: C 448 MET cc_start: 0.8261 (mtt) cc_final: 0.7768 (mtt) REVERT: C 579 LYS cc_start: 0.7092 (mmtt) cc_final: 0.6878 (ptpt) REVERT: C 595 MET cc_start: 0.8509 (mmt) cc_final: 0.8124 (mmt) REVERT: C 674 TYR cc_start: 0.5057 (OUTLIER) cc_final: 0.4014 (p90) REVERT: C 794 LYS cc_start: 0.8005 (tptp) cc_final: 0.6719 (mttt) REVERT: D 57 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7368 (tmmt) REVERT: D 58 MET cc_start: 0.9283 (mtp) cc_final: 0.8891 (mtp) REVERT: D 60 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: D 63 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7840 (mptt) REVERT: D 402 PHE cc_start: 0.7547 (t80) cc_final: 0.7295 (t80) REVERT: D 442 MET cc_start: 0.8017 (tpt) cc_final: 0.7509 (tpt) REVERT: D 595 MET cc_start: 0.8497 (mmt) cc_final: 0.8042 (mmt) REVERT: D 651 TYR cc_start: 0.8269 (t80) cc_final: 0.7871 (t80) REVERT: D 794 LYS cc_start: 0.7991 (tptp) cc_final: 0.6715 (mttt) outliers start: 68 outliers final: 55 residues processed: 389 average time/residue: 0.1497 time to fit residues: 94.3279 Evaluate side-chains 405 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 344 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 231 SER Chi-restraints excluded: chain A residue 235 VAL 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 621 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 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 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 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 205 HIS 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 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 196 CYS 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 34 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 176 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN C 608 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 = 0.4620 r_free = 0.4620 target = 0.234109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191169 restraints weight = 27748.938| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.84 r_work: 0.3703 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25095 Z= 0.126 Angle : 0.582 14.258 33882 Z= 0.291 Chirality : 0.039 0.189 3764 Planarity : 0.004 0.039 4228 Dihedral : 14.608 172.089 3680 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.98 % Allowed : 19.67 % Favored : 78.35 % 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: 1.34 (0.16), residues: 2956 helix: 1.73 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : -1.25 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 308 TYR 0.012 0.001 TYR D 150 PHE 0.034 0.001 PHE D 484 TRP 0.034 0.002 TRP A 444 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00276 (25084) covalent geometry : angle 0.58222 (33864) SS BOND : bond 0.00431 ( 3) SS BOND : angle 0.71553 ( 18) hydrogen bonds : bond 0.04593 ( 1464) hydrogen bonds : angle 3.78721 ( 4344) Misc. bond : bond 0.00222 ( 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 396 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 344 time to evaluate : 0.888 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: 0.7975 (ttmt) cc_final: 0.7258 (tmmt) REVERT: A 60 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: A 63 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7667 (mptt) REVERT: A 264 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8393 (mpp) REVERT: A 402 PHE cc_start: 0.7459 (t80) cc_final: 0.7221 (t80) REVERT: A 444 TRP cc_start: 0.7139 (t60) cc_final: 0.6887 (t60) REVERT: A 595 MET cc_start: 0.8449 (mmt) cc_final: 0.8196 (mmt) REVERT: B 57 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7235 (tmmt) REVERT: B 58 MET cc_start: 0.9184 (mtp) cc_final: 0.8962 (mtm) REVERT: B 60 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: B 63 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7677 (mptt) REVERT: B 264 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8359 (mpp) REVERT: B 402 PHE cc_start: 0.7440 (t80) cc_final: 0.7183 (t80) REVERT: B 579 LYS cc_start: 0.7527 (pttt) cc_final: 0.7310 (mmtt) REVERT: B 674 TYR cc_start: 0.5009 (OUTLIER) cc_final: 0.4133 (p90) REVERT: C 57 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7245 (tmmt) REVERT: C 60 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: C 63 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7679 (mptt) REVERT: C 264 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8283 (mpp) REVERT: C 402 PHE cc_start: 0.7431 (t80) cc_final: 0.7199 (t80) REVERT: C 448 MET cc_start: 0.8228 (mtt) cc_final: 0.7725 (mtt) REVERT: C 579 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6814 (ptpt) REVERT: C 595 MET cc_start: 0.8475 (mmt) cc_final: 0.8219 (mmt) REVERT: C 674 TYR cc_start: 0.5099 (OUTLIER) cc_final: 0.4193 (p90) REVERT: D 57 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7223 (tmmt) REVERT: D 60 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: D 63 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7685 (mptt) REVERT: D 264 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8348 (mpp) REVERT: D 402 PHE cc_start: 0.7438 (t80) cc_final: 0.7201 (t80) REVERT: D 442 MET cc_start: 0.7923 (tpt) cc_final: 0.7520 (tpt) REVERT: D 595 MET cc_start: 0.8465 (mmt) cc_final: 0.8234 (mmt) outliers start: 52 outliers final: 39 residues processed: 368 average time/residue: 0.1535 time to fit residues: 91.3176 Evaluate side-chains 377 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 328 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 231 SER 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 779 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 231 SER 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 779 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 311 LEU 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 779 MET 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 150 TYR Chi-restraints excluded: chain D residue 196 CYS 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 207 optimal weight: 9.9990 chunk 57 optimal weight: 0.0980 chunk 241 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 280 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.231922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.190117 restraints weight = 27753.215| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.90 r_work: 0.3674 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.6764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25095 Z= 0.147 Angle : 0.618 13.856 33882 Z= 0.306 Chirality : 0.040 0.196 3764 Planarity : 0.004 0.040 4228 Dihedral : 14.530 171.348 3680 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 2.47 % Allowed : 19.71 % 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: 1.34 (0.16), residues: 2956 helix: 1.74 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : -1.27 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 308 TYR 0.014 0.001 TYR B 150 PHE 0.034 0.001 PHE D 484 TRP 0.031 0.002 TRP A 444 HIS 0.006 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00341 (25084) covalent geometry : angle 0.61792 (33864) SS BOND : bond 0.00591 ( 3) SS BOND : angle 0.88868 ( 18) hydrogen bonds : bond 0.05065 ( 1464) hydrogen bonds : angle 3.83139 ( 4344) Misc. bond : bond 0.00197 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5423.02 seconds wall clock time: 94 minutes 18.26 seconds (5658.26 seconds total)