Starting phenix.real_space_refine on Fri Jan 17 17:18:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6e_44256/01_2025/9b6e_44256_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6e_44256/01_2025/9b6e_44256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6e_44256/01_2025/9b6e_44256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6e_44256/01_2025/9b6e_44256.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6e_44256/01_2025/9b6e_44256_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6e_44256/01_2025/9b6e_44256_trim.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 116 5.16 5 C 19064 2.51 5 N 4640 2.21 5 O 5020 1.98 5 F 24 1.80 5 H 26380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A ARG 532": not complete - not flipped Residue "B ARG 532": not complete - not flipped Residue "C ARG 532": not complete - not flipped Residue "D ARG 532": not complete - not flipped Time to flip 20 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 55244 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 13638 Classifications: {'peptide': 929} Link IDs: {'PTRANS': 23, 'TRANS': 905} Chain breaks: 9 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 16, 'ASP:plan': 18, 'PHE:plan': 3, 'GLU:plan': 22, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 329 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 173 Unusual residues: {'T14': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: C, B, D Time building chain proxies: 37.95, per 1000 atoms: 0.69 Number of scatterers: 55244 At special positions: 0 Unit cell: (150.12, 150.12, 156.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 F 24 9.00 O 5020 8.00 N 4640 7.00 C 19064 6.00 H 26380 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.78 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.48 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.08 Conformation dependent library (CDL) restraints added in 3.8 seconds 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 8 sheets defined 72.5% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 40 through 49 removed outlier: 3.513A pdb=" N PHE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.641A pdb=" N VAL A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.912A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.666A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.569A pdb=" N ILE A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.554A pdb=" N ILE A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 419 Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.579A pdb=" N LEU A 430 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.706A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 removed outlier: 3.807A pdb=" N THR A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.584A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 587 through 605 removed outlier: 3.894A pdb=" N LYS A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 636 Processing helix chain 'A' and resid 637 through 646 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.577A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.557A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 removed outlier: 4.134A pdb=" N GLY A 706 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 707' Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 765 through 789 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 796 through 817 removed outlier: 3.508A pdb=" N LEU A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 841 removed outlier: 3.895A pdb=" N LEU A 825 " --> pdb=" O ASN A 821 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 827 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 847 removed outlier: 4.048A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 853 through 860 removed outlier: 3.586A pdb=" N LEU A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 952 through 969 removed outlier: 3.640A pdb=" N THR A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) Proline residue: A 958 - end of helix removed outlier: 3.874A pdb=" N ILE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1008 removed outlier: 4.889A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1015 Processing helix chain 'A' and resid 1016 through 1027 Processing helix chain 'A' and resid 1051 through 1073 Processing helix chain 'A' and resid 1076 through 1104 removed outlier: 3.794A pdb=" N HIS A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A1095 " --> pdb=" O ASP A1091 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A1097 " --> pdb=" O LYS A1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.616A pdb=" N ALA B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.641A pdb=" N VAL B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.912A pdb=" N LEU B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.666A pdb=" N SER B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.569A pdb=" N ILE B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.554A pdb=" N ILE B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.579A pdb=" N LEU B 430 " --> pdb=" O TRP B 426 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.706A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 removed outlier: 3.807A pdb=" N THR B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 520 through 534 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.584A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 587 through 605 removed outlier: 3.895A pdb=" N LYS B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 636 Processing helix chain 'B' and resid 637 through 646 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 671 removed outlier: 3.577A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.557A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 removed outlier: 4.134A pdb=" N GLY B 706 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 702 through 707' Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 765 through 789 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 796 through 817 removed outlier: 3.508A pdb=" N LEU B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 841 removed outlier: 3.896A pdb=" N LEU B 825 " --> pdb=" O ASN B 821 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 826 " --> pdb=" O LYS B 822 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 827 " --> pdb=" O SER B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 847 removed outlier: 4.048A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 853 through 860 removed outlier: 3.586A pdb=" N LEU B 860 " --> pdb=" O LYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 952 through 969 removed outlier: 3.640A pdb=" N THR B 956 " --> pdb=" O PRO B 952 " (cutoff:3.500A) Proline residue: B 958 - end of helix removed outlier: 3.874A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1008 removed outlier: 4.889A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B1006 " --> pdb=" O VAL B1002 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B1008 " --> pdb=" O GLU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1015 Processing helix chain 'B' and resid 1016 through 1027 Processing helix chain 'B' and resid 1051 through 1073 Processing helix chain 'B' and resid 1076 through 1104 removed outlier: 3.794A pdb=" N HIS B1080 " --> pdb=" O GLU B1076 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B1094 " --> pdb=" O ASN B1090 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B1095 " --> pdb=" O ASP B1091 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU B1096 " --> pdb=" O LEU B1092 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B1097 " --> pdb=" O LYS B1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.616A pdb=" N ALA C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 201 removed outlier: 3.641A pdb=" N VAL C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.912A pdb=" N LEU C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.666A pdb=" N SER C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.569A pdb=" N ILE C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.554A pdb=" N ILE C 374 " --> pdb=" O PRO C 370 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 419 Processing helix chain 'C' and resid 426 through 436 removed outlier: 3.579A pdb=" N LEU C 430 " --> pdb=" O TRP C 426 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.706A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 removed outlier: 3.807A pdb=" N THR C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 520 through 534 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.584A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 587 through 605 removed outlier: 3.894A pdb=" N LYS C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 636 Processing helix chain 'C' and resid 637 through 646 Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 671 removed outlier: 3.577A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.558A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 707 removed outlier: 4.133A pdb=" N GLY C 706 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS C 707 " --> pdb=" O PRO C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 707' Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 765 through 789 Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 796 through 817 removed outlier: 3.508A pdb=" N LEU C 817 " --> pdb=" O ILE C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 841 removed outlier: 3.895A pdb=" N LEU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C 826 " --> pdb=" O LYS C 822 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 827 " --> pdb=" O SER C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 847 removed outlier: 4.048A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 853 through 860 removed outlier: 3.586A pdb=" N LEU C 860 " --> pdb=" O LYS C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 952 through 969 removed outlier: 3.640A pdb=" N THR C 956 " --> pdb=" O PRO C 952 " (cutoff:3.500A) Proline residue: C 958 - end of helix removed outlier: 3.874A pdb=" N ILE C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1008 removed outlier: 4.889A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C 997 " --> pdb=" O VAL C 993 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS C1006 " --> pdb=" O VAL C1002 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C1008 " --> pdb=" O GLU C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1015 Processing helix chain 'C' and resid 1016 through 1027 Processing helix chain 'C' and resid 1051 through 1073 Processing helix chain 'C' and resid 1076 through 1104 removed outlier: 3.794A pdb=" N HIS C1080 " --> pdb=" O GLU C1076 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C1094 " --> pdb=" O ASN C1090 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C1095 " --> pdb=" O ASP C1091 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C1096 " --> pdb=" O LEU C1092 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C1097 " --> pdb=" O LYS C1093 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.617A pdb=" N ALA D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 137 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.641A pdb=" N VAL D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.912A pdb=" N LEU D 277 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.666A pdb=" N SER D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.569A pdb=" N ILE D 339 " --> pdb=" O ILE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.554A pdb=" N ILE D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 419 Processing helix chain 'D' and resid 426 through 436 removed outlier: 3.579A pdb=" N LEU D 430 " --> pdb=" O TRP D 426 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.706A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 removed outlier: 3.806A pdb=" N THR D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 520 through 534 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.583A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 Processing helix chain 'D' and resid 587 through 605 removed outlier: 3.895A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL D 604 " --> pdb=" O THR D 600 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 636 Processing helix chain 'D' and resid 637 through 646 Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 671 removed outlier: 3.577A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.557A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 707 removed outlier: 4.133A pdb=" N GLY D 706 " --> pdb=" O ILE D 702 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS D 707 " --> pdb=" O PRO D 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 702 through 707' Processing helix chain 'D' and resid 725 through 732 Processing helix chain 'D' and resid 733 through 758 Processing helix chain 'D' and resid 765 through 789 Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 796 through 817 removed outlier: 3.508A pdb=" N LEU D 817 " --> pdb=" O ILE D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 841 removed outlier: 3.894A pdb=" N LEU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D 826 " --> pdb=" O LYS D 822 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER D 827 " --> pdb=" O SER D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 847 removed outlier: 4.048A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 853 through 860 removed outlier: 3.586A pdb=" N LEU D 860 " --> pdb=" O LYS D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 952 through 969 removed outlier: 3.640A pdb=" N THR D 956 " --> pdb=" O PRO D 952 " (cutoff:3.500A) Proline residue: D 958 - end of helix removed outlier: 3.874A pdb=" N ILE D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 1008 removed outlier: 4.889A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 997 " --> pdb=" O VAL D 993 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS D1006 " --> pdb=" O VAL D1002 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D1008 " --> pdb=" O GLU D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1015 Processing helix chain 'D' and resid 1016 through 1027 Processing helix chain 'D' and resid 1051 through 1073 Processing helix chain 'D' and resid 1076 through 1104 removed outlier: 3.794A pdb=" N HIS D1080 " --> pdb=" O GLU D1076 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D1094 " --> pdb=" O ASN D1090 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D1095 " --> pdb=" O ASP D1091 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU D1096 " --> pdb=" O LEU D1092 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS D1097 " --> pdb=" O LYS D1093 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 removed outlier: 6.483A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL A 263 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 215 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 148 removed outlier: 6.313A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 120 removed outlier: 6.483A pdb=" N GLY B 213 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL B 263 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 215 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.313A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.483A pdb=" N GLY C 213 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL C 263 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA C 215 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.313A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 120 removed outlier: 6.483A pdb=" N GLY D 213 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL D 263 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA D 215 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 146 through 148 removed outlier: 6.313A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) 1768 hydrogen bonds defined for protein. 5220 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: 20.26 Time building geometry restraints manager: 14.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26340 1.03 - 1.23: 123 1.23 - 1.42: 12525 1.42 - 1.62: 16820 1.62 - 1.82: 176 Bond restraints: 55984 Sorted by residual: bond pdb=" N20 T14 C1201 " pdb=" O21 T14 C1201 " ideal model delta sigma weight residual 1.347 1.205 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N20 T14 B1201 " pdb=" O21 T14 B1201 " ideal model delta sigma weight residual 1.347 1.205 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N20 T14 D1201 " pdb=" O21 T14 D1201 " ideal model delta sigma weight residual 1.347 1.205 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N20 T14 A1201 " pdb=" O21 T14 A1201 " ideal model delta sigma weight residual 1.347 1.205 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" ND2 ASN D 892 " pdb="HD21 ASN D 892 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 ... (remaining 55979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 99716 2.65 - 5.30: 504 5.30 - 7.94: 92 7.94 - 10.59: 36 10.59 - 13.24: 16 Bond angle restraints: 100364 Sorted by residual: angle pdb=" CAT Y01 B1204 " pdb=" CBH Y01 B1204 " pdb=" CBF Y01 B1204 " ideal model delta sigma weight residual 108.46 95.22 13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CAT Y01 A1204 " pdb=" CBH Y01 A1204 " pdb=" CBF Y01 A1204 " ideal model delta sigma weight residual 108.46 95.22 13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CAT Y01 D1204 " pdb=" CBH Y01 D1204 " pdb=" CBF Y01 D1204 " ideal model delta sigma weight residual 108.46 95.22 13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CAT Y01 C1204 " pdb=" CBH Y01 C1204 " pdb=" CBF Y01 C1204 " ideal model delta sigma weight residual 108.46 95.22 13.24 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CAT Y01 D1202 " pdb=" CBH Y01 D1202 " pdb=" CBF Y01 D1202 " ideal model delta sigma weight residual 108.46 95.24 13.22 3.00e+00 1.11e-01 1.94e+01 ... (remaining 100359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 26996 35.88 - 71.76: 550 71.76 - 107.64: 12 107.64 - 143.53: 0 143.53 - 179.41: 4 Dihedral angle restraints: 27562 sinusoidal: 14190 harmonic: 13372 Sorted by residual: dihedral pdb=" CD ARG A 532 " pdb=" NE ARG A 532 " pdb=" CZ ARG A 532 " pdb=" NH1 ARG A 532 " ideal model delta sinusoidal sigma weight residual 0.00 -179.41 179.41 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG C 532 " pdb=" NE ARG C 532 " pdb=" CZ ARG C 532 " pdb=" NH1 ARG C 532 " ideal model delta sinusoidal sigma weight residual 0.00 -179.41 179.41 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG D 532 " pdb=" NE ARG D 532 " pdb=" CZ ARG D 532 " pdb=" NH1 ARG D 532 " ideal model delta sinusoidal sigma weight residual 0.00 -179.41 179.41 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 27559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4463 0.083 - 0.165: 193 0.165 - 0.248: 20 0.248 - 0.330: 24 0.330 - 0.413: 40 Chirality restraints: 4740 Sorted by residual: chirality pdb=" CBH Y01 D1202 " pdb=" CAT Y01 D1202 " pdb=" CAZ Y01 D1202 " pdb=" CBF Y01 D1202 " both_signs ideal model delta sigma weight residual False -2.85 -3.27 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CBH Y01 C1202 " pdb=" CAT Y01 C1202 " pdb=" CAZ Y01 C1202 " pdb=" CBF Y01 C1202 " both_signs ideal model delta sigma weight residual False -2.85 -3.26 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CBH Y01 C1203 " pdb=" CAT Y01 C1203 " pdb=" CAZ Y01 C1203 " pdb=" CBF Y01 C1203 " both_signs ideal model delta sigma weight residual False -2.85 -3.26 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 4737 not shown) Planarity restraints: 8524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 891 " -0.083 2.00e-02 2.50e+03 8.94e-02 1.20e+02 pdb=" CD GLN C 891 " 0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN C 891 " 0.079 2.00e-02 2.50e+03 pdb=" NE2 GLN C 891 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 891 " -0.133 2.00e-02 2.50e+03 pdb="HE22 GLN C 891 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 891 " 0.083 2.00e-02 2.50e+03 8.93e-02 1.20e+02 pdb=" CD GLN B 891 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN B 891 " -0.079 2.00e-02 2.50e+03 pdb=" NE2 GLN B 891 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 891 " 0.133 2.00e-02 2.50e+03 pdb="HE22 GLN B 891 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 891 " 0.083 2.00e-02 2.50e+03 8.92e-02 1.19e+02 pdb=" CD GLN A 891 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN A 891 " -0.079 2.00e-02 2.50e+03 pdb=" NE2 GLN A 891 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 891 " 0.133 2.00e-02 2.50e+03 pdb="HE22 GLN A 891 " -0.130 2.00e-02 2.50e+03 ... (remaining 8521 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 2026 2.17 - 2.78: 104238 2.78 - 3.39: 150244 3.39 - 3.99: 184420 3.99 - 4.60: 296092 Nonbonded interactions: 737020 Sorted by model distance: nonbonded pdb=" O THR B 584 " pdb=" HZ1 LYS B1060 " model vdw 1.568 2.450 nonbonded pdb=" O THR A 584 " pdb=" HZ1 LYS A1060 " model vdw 1.569 2.450 nonbonded pdb=" O THR C 584 " pdb=" HZ1 LYS C1060 " model vdw 1.569 2.450 nonbonded pdb=" O THR D 584 " pdb=" HZ1 LYS D1060 " model vdw 1.569 2.450 nonbonded pdb=" O GLY D 309 " pdb=" HG1 THR D 312 " model vdw 1.583 2.450 ... (remaining 737015 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.790 Extract box with map and model: 1.610 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 111.730 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.130 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:13.220 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 29604 Z= 0.351 Angle : 0.768 13.239 40516 Z= 0.338 Chirality : 0.055 0.413 4740 Planarity : 0.003 0.025 4944 Dihedral : 12.588 179.407 10736 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.15 % Allowed : 10.13 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.15), residues: 3636 helix: 2.32 (0.11), residues: 2436 sheet: -1.54 (0.39), residues: 196 loop : -1.14 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 217 HIS 0.002 0.000 HIS B1080 PHE 0.012 0.001 PHE C 872 TYR 0.018 0.001 TYR C1022 ARG 0.002 0.000 ARG D 829 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 416 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 412 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 4 outliers final: 0 residues processed: 412 average time/residue: 1.6089 time to fit residues: 835.2076 Evaluate side-chains 261 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 5.9990 chunk 278 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 288 optimal weight: 0.1980 chunk 111 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 334 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 968 ASN A1062 ASN B 199 ASN B 968 ASN B1062 ASN C 199 ASN C 968 ASN C1062 ASN D 199 ASN D 968 ASN D1062 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.150337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096224 restraints weight = 143802.668| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.44 r_work: 0.3254 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29604 Z= 0.258 Angle : 0.531 5.721 40516 Z= 0.280 Chirality : 0.037 0.141 4740 Planarity : 0.003 0.045 4944 Dihedral : 7.815 179.753 5140 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.50 % Allowed : 14.87 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.15), residues: 3636 helix: 2.21 (0.10), residues: 2436 sheet: -1.62 (0.40), residues: 196 loop : -1.28 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 898 HIS 0.002 0.001 HIS B 928 PHE 0.012 0.001 PHE A 870 TYR 0.015 0.001 TYR C1022 ARG 0.003 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 350 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 282 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 615 GLU cc_start: 0.8401 (pp20) cc_final: 0.8091 (pp20) REVERT: A 859 MET cc_start: 0.8806 (ptm) cc_final: 0.8240 (ttp) REVERT: A 1005 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7152 (t80) REVERT: B 615 GLU cc_start: 0.8390 (pp20) cc_final: 0.8076 (pp20) REVERT: B 859 MET cc_start: 0.8807 (ptm) cc_final: 0.8245 (ttp) REVERT: B 1005 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7151 (t80) REVERT: C 615 GLU cc_start: 0.8392 (pp20) cc_final: 0.8080 (pp20) REVERT: C 859 MET cc_start: 0.8806 (ptm) cc_final: 0.8223 (ttp) REVERT: C 1005 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7147 (t80) REVERT: D 615 GLU cc_start: 0.8405 (pp20) cc_final: 0.8095 (pp20) REVERT: D 859 MET cc_start: 0.8813 (ptm) cc_final: 0.8252 (ttp) REVERT: D 1005 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7154 (t80) outliers start: 68 outliers final: 15 residues processed: 322 average time/residue: 1.5837 time to fit residues: 646.5876 Evaluate side-chains 262 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 850 SER Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 173 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 266 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 340 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.149968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095228 restraints weight = 144692.005| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.45 r_work: 0.3231 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29604 Z= 0.221 Angle : 0.498 10.701 40516 Z= 0.265 Chirality : 0.036 0.138 4740 Planarity : 0.003 0.046 4944 Dihedral : 7.438 179.520 5140 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.46 % Allowed : 15.82 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.15), residues: 3636 helix: 2.22 (0.11), residues: 2440 sheet: -1.67 (0.40), residues: 196 loop : -1.38 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 682 HIS 0.002 0.001 HIS A1080 PHE 0.013 0.001 PHE A 304 TYR 0.017 0.001 TYR B1022 ARG 0.006 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 316 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 249 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8781 (ptm) cc_final: 0.8351 (ttp) REVERT: A 1005 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7167 (t80) REVERT: A 1013 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7630 (t80) REVERT: B 859 MET cc_start: 0.8785 (ptm) cc_final: 0.8357 (ttp) REVERT: B 1005 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7163 (t80) REVERT: B 1013 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7629 (t80) REVERT: C 859 MET cc_start: 0.8784 (ptm) cc_final: 0.8356 (ttp) REVERT: C 1005 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7165 (t80) REVERT: C 1013 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7636 (t80) REVERT: D 859 MET cc_start: 0.8778 (ptm) cc_final: 0.8349 (ttp) REVERT: D 1005 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7176 (t80) REVERT: D 1013 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7635 (t80) outliers start: 67 outliers final: 24 residues processed: 281 average time/residue: 1.5625 time to fit residues: 557.8820 Evaluate side-chains 264 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 968 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 968 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1013 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 206 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 290 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 946 HIS B 635 ASN B 946 HIS C 635 ASN D 635 ASN D 946 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.145507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089791 restraints weight = 144793.461| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.39 r_work: 0.3125 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 29604 Z= 0.501 Angle : 0.650 6.322 40516 Z= 0.346 Chirality : 0.042 0.145 4740 Planarity : 0.004 0.051 4944 Dihedral : 8.237 176.675 5140 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.70 % Allowed : 14.46 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3636 helix: 1.61 (0.10), residues: 2432 sheet: -1.94 (0.39), residues: 196 loop : -1.70 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 682 HIS 0.003 0.001 HIS A 765 PHE 0.020 0.002 PHE A 870 TYR 0.020 0.002 TYR B1022 ARG 0.007 0.001 ARG C 816 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 263 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8455 (ttp) REVERT: A 965 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9270 (tp) REVERT: A 1005 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7163 (t80) REVERT: A 1013 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.7739 (t80) REVERT: B 859 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8465 (ttp) REVERT: B 965 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9273 (tp) REVERT: B 1005 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7161 (t80) REVERT: B 1013 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7736 (t80) REVERT: C 859 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8450 (ttp) REVERT: C 965 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9277 (tp) REVERT: C 1005 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7168 (t80) REVERT: C 1013 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7751 (t80) REVERT: D 859 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8459 (ttp) REVERT: D 965 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9272 (tp) REVERT: D 1005 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7175 (t80) REVERT: D 1013 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7745 (t80) outliers start: 128 outliers final: 52 residues processed: 328 average time/residue: 1.4873 time to fit residues: 627.2265 Evaluate side-chains 301 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 233 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1022 TYR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1022 TYR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 850 SER Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1022 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 149 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 139 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 352 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 968 ASN B 619 ASN B 968 ASN C 619 ASN C 968 ASN D 619 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.148859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.093962 restraints weight = 144150.405| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.41 r_work: 0.3208 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 29604 Z= 0.161 Angle : 0.505 10.799 40516 Z= 0.268 Chirality : 0.035 0.173 4740 Planarity : 0.003 0.048 4944 Dihedral : 7.586 179.435 5140 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.31 % Allowed : 16.56 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.14), residues: 3636 helix: 2.06 (0.11), residues: 2440 sheet: -1.87 (0.39), residues: 196 loop : -1.52 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 682 HIS 0.002 0.000 HIS C 946 PHE 0.013 0.001 PHE C 870 TYR 0.014 0.001 TYR D 170 ARG 0.004 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8415 (mm) cc_final: 0.8186 (mm) REVERT: A 859 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8488 (ttp) REVERT: A 1005 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7097 (t80) REVERT: A 1013 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7575 (t80) REVERT: B 120 LEU cc_start: 0.8409 (mm) cc_final: 0.8179 (mm) REVERT: B 859 MET cc_start: 0.8772 (ptm) cc_final: 0.8483 (ttp) REVERT: B 1005 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7092 (t80) REVERT: B 1013 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7584 (t80) REVERT: C 120 LEU cc_start: 0.8415 (mm) cc_final: 0.8186 (mm) REVERT: C 859 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8483 (ttp) REVERT: C 1005 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7099 (t80) REVERT: C 1013 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7589 (t80) REVERT: D 120 LEU cc_start: 0.8421 (mm) cc_final: 0.8191 (mm) REVERT: D 859 MET cc_start: 0.8769 (ptm) cc_final: 0.8482 (ttp) REVERT: D 1005 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7102 (t80) REVERT: D 1013 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7573 (t80) outliers start: 63 outliers final: 30 residues processed: 274 average time/residue: 1.6501 time to fit residues: 567.5036 Evaluate side-chains 257 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1013 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 264 optimal weight: 0.6980 chunk 322 optimal weight: 0.0770 chunk 345 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 619 ASN C 619 ASN C 946 HIS D 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.093878 restraints weight = 144546.989| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.43 r_work: 0.3198 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29604 Z= 0.181 Angle : 0.486 7.684 40516 Z= 0.258 Chirality : 0.035 0.139 4740 Planarity : 0.003 0.054 4944 Dihedral : 7.439 178.752 5140 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.35 % Allowed : 17.14 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.14), residues: 3636 helix: 2.28 (0.11), residues: 2440 sheet: -1.82 (0.39), residues: 196 loop : -1.52 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 682 HIS 0.001 0.000 HIS A 928 PHE 0.013 0.001 PHE B1082 TYR 0.014 0.001 TYR A1022 ARG 0.002 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8417 (mm) cc_final: 0.8187 (mm) REVERT: A 1005 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7098 (t80) REVERT: A 1013 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7532 (t80) REVERT: B 120 LEU cc_start: 0.8418 (mm) cc_final: 0.8186 (mm) REVERT: B 859 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8251 (ttp) REVERT: B 1005 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7091 (t80) REVERT: B 1013 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7532 (t80) REVERT: C 120 LEU cc_start: 0.8416 (mm) cc_final: 0.8185 (mm) REVERT: C 1005 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7102 (t80) REVERT: C 1013 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7537 (t80) REVERT: D 120 LEU cc_start: 0.8428 (mm) cc_final: 0.8196 (mm) REVERT: D 859 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: D 1005 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7106 (t80) REVERT: D 1013 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7538 (t80) outliers start: 64 outliers final: 29 residues processed: 263 average time/residue: 1.5028 time to fit residues: 507.2819 Evaluate side-chains 253 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1013 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 271 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 337 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 510 GLN B 619 ASN C 619 ASN D 619 ASN D 968 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.147179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091736 restraints weight = 143925.476| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.41 r_work: 0.3161 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 29604 Z= 0.301 Angle : 0.535 8.155 40516 Z= 0.283 Chirality : 0.037 0.150 4740 Planarity : 0.003 0.053 4944 Dihedral : 7.679 177.746 5140 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.86 % Allowed : 16.67 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.14), residues: 3636 helix: 2.20 (0.11), residues: 2440 sheet: -1.81 (0.41), residues: 188 loop : -1.66 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 682 HIS 0.002 0.001 HIS A 765 PHE 0.015 0.001 PHE A 870 TYR 0.020 0.001 TYR A 170 ARG 0.004 0.000 ARG C 816 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 312 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8376 (mm) cc_final: 0.8119 (mm) REVERT: A 615 GLU cc_start: 0.8767 (pp20) cc_final: 0.8434 (pp20) REVERT: A 859 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8494 (ttp) REVERT: A 1005 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7134 (t80) REVERT: A 1013 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 120 LEU cc_start: 0.8375 (mm) cc_final: 0.8117 (mm) REVERT: B 615 GLU cc_start: 0.8766 (pp20) cc_final: 0.8432 (pp20) REVERT: B 859 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8386 (ttp) REVERT: B 1005 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7128 (t80) REVERT: B 1013 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7599 (t80) REVERT: C 120 LEU cc_start: 0.8373 (mm) cc_final: 0.8115 (mm) REVERT: C 615 GLU cc_start: 0.8764 (pp20) cc_final: 0.8430 (pp20) REVERT: C 859 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8495 (ttp) REVERT: C 1005 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7135 (t80) REVERT: C 1013 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7600 (t80) REVERT: D 120 LEU cc_start: 0.8412 (mm) cc_final: 0.8156 (mm) REVERT: D 615 GLU cc_start: 0.8769 (pp20) cc_final: 0.8437 (pp20) REVERT: D 859 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8468 (ttp) REVERT: D 1005 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7143 (t80) REVERT: D 1013 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7600 (t80) outliers start: 78 outliers final: 38 residues processed: 271 average time/residue: 1.4504 time to fit residues: 506.5778 Evaluate side-chains 268 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 801 MET Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 240 optimal weight: 5.9990 chunk 343 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 268 optimal weight: 0.5980 chunk 277 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 510 GLN B 619 ASN C 619 ASN D 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.149167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094837 restraints weight = 143685.359| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.38 r_work: 0.3211 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29604 Z= 0.160 Angle : 0.481 7.800 40516 Z= 0.254 Chirality : 0.035 0.139 4740 Planarity : 0.003 0.052 4944 Dihedral : 7.361 179.294 5140 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.24 % Allowed : 17.40 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.15), residues: 3636 helix: 2.43 (0.11), residues: 2452 sheet: -1.87 (0.40), residues: 196 loop : -1.56 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 682 HIS 0.001 0.000 HIS A 667 PHE 0.014 0.001 PHE B1082 TYR 0.014 0.001 TYR A1022 ARG 0.002 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 227 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8437 (mm) cc_final: 0.8173 (mm) REVERT: A 615 GLU cc_start: 0.8794 (pp20) cc_final: 0.8416 (pp20) REVERT: A 859 MET cc_start: 0.8794 (ptm) cc_final: 0.8366 (ttp) REVERT: A 1005 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7065 (t80) REVERT: A 1013 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7496 (t80) REVERT: B 120 LEU cc_start: 0.8487 (mm) cc_final: 0.8231 (mm) REVERT: B 615 GLU cc_start: 0.8786 (pp20) cc_final: 0.8402 (pp20) REVERT: B 859 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8475 (ttp) REVERT: B 1001 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 1005 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7029 (t80) REVERT: B 1013 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7500 (t80) REVERT: C 120 LEU cc_start: 0.8493 (mm) cc_final: 0.8238 (mm) REVERT: C 615 GLU cc_start: 0.8776 (pp20) cc_final: 0.8395 (pp20) REVERT: C 859 MET cc_start: 0.8790 (ptm) cc_final: 0.8363 (ttp) REVERT: C 1001 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8117 (mp) REVERT: C 1005 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7026 (t80) REVERT: C 1013 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7495 (t80) REVERT: D 120 LEU cc_start: 0.8500 (mm) cc_final: 0.8243 (mm) REVERT: D 615 GLU cc_start: 0.8787 (pp20) cc_final: 0.8409 (pp20) REVERT: D 859 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8485 (ttp) REVERT: D 1005 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7076 (t80) REVERT: D 1013 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7498 (t80) outliers start: 61 outliers final: 19 residues processed: 262 average time/residue: 1.6336 time to fit residues: 542.5963 Evaluate side-chains 245 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1013 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 313 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 206 optimal weight: 0.0970 chunk 360 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 288 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 619 ASN C 619 ASN D 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.148025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092885 restraints weight = 144499.793| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.41 r_work: 0.3182 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29604 Z= 0.238 Angle : 0.512 10.262 40516 Z= 0.268 Chirality : 0.036 0.138 4740 Planarity : 0.003 0.049 4944 Dihedral : 7.450 178.221 5140 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.24 % Allowed : 17.73 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.15), residues: 3636 helix: 2.43 (0.11), residues: 2440 sheet: -1.88 (0.40), residues: 196 loop : -1.62 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 896 HIS 0.001 0.000 HIS B 765 PHE 0.014 0.001 PHE B1082 TYR 0.020 0.001 TYR B 170 ARG 0.006 0.000 ARG D 688 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8418 (mm) cc_final: 0.8138 (mm) REVERT: A 615 GLU cc_start: 0.8819 (pp20) cc_final: 0.8438 (pp20) REVERT: A 859 MET cc_start: 0.8783 (ptm) cc_final: 0.8446 (ttp) REVERT: A 1005 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7115 (t80) REVERT: A 1013 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7533 (t80) REVERT: B 120 LEU cc_start: 0.8442 (mm) cc_final: 0.8165 (mm) REVERT: B 615 GLU cc_start: 0.8804 (pp20) cc_final: 0.8419 (pp20) REVERT: B 859 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8302 (ttp) REVERT: B 1005 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7112 (t80) REVERT: B 1013 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7544 (t80) REVERT: C 120 LEU cc_start: 0.8443 (mm) cc_final: 0.8166 (mm) REVERT: C 615 GLU cc_start: 0.8801 (pp20) cc_final: 0.8418 (pp20) REVERT: C 859 MET cc_start: 0.8775 (ptm) cc_final: 0.8436 (ttp) REVERT: C 1005 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7116 (t80) REVERT: C 1013 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7540 (t80) REVERT: D 120 LEU cc_start: 0.8448 (mm) cc_final: 0.8171 (mm) REVERT: D 615 GLU cc_start: 0.8810 (pp20) cc_final: 0.8429 (pp20) REVERT: D 859 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8316 (ttp) REVERT: D 1005 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7128 (t80) REVERT: D 1013 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7540 (t80) outliers start: 61 outliers final: 29 residues processed: 254 average time/residue: 1.5017 time to fit residues: 487.0253 Evaluate side-chains 258 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1067 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 154 optimal weight: 1.9990 chunk 363 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 256 optimal weight: 0.5980 chunk 333 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 619 ASN C 619 ASN D 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.148211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093681 restraints weight = 143038.166| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.38 r_work: 0.3194 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29604 Z= 0.204 Angle : 0.493 10.568 40516 Z= 0.260 Chirality : 0.035 0.136 4740 Planarity : 0.003 0.047 4944 Dihedral : 7.371 178.533 5140 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 2.09 % Allowed : 17.84 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.15), residues: 3636 helix: 2.46 (0.11), residues: 2448 sheet: -1.92 (0.40), residues: 196 loop : -1.62 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 682 HIS 0.001 0.000 HIS D 765 PHE 0.012 0.001 PHE B1082 TYR 0.016 0.001 TYR C1022 ARG 0.004 0.000 ARG B 688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue VAL 604 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 691 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8404 (mm) cc_final: 0.8126 (mm) REVERT: A 615 GLU cc_start: 0.8782 (pp20) cc_final: 0.8407 (pp20) REVERT: A 1001 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8143 (mm) REVERT: A 1005 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7059 (t80) REVERT: A 1013 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7532 (t80) REVERT: B 120 LEU cc_start: 0.8414 (mm) cc_final: 0.8136 (mm) REVERT: B 615 GLU cc_start: 0.8756 (pp20) cc_final: 0.8383 (pp20) REVERT: B 859 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8331 (ttp) REVERT: B 1001 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 1005 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7059 (t80) REVERT: B 1013 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7538 (t80) REVERT: C 120 LEU cc_start: 0.8418 (mm) cc_final: 0.8139 (mm) REVERT: C 615 GLU cc_start: 0.8769 (pp20) cc_final: 0.8392 (pp20) REVERT: C 1001 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8140 (mm) REVERT: C 1005 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7063 (t80) REVERT: C 1013 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7532 (t80) REVERT: D 120 LEU cc_start: 0.8421 (mm) cc_final: 0.8142 (mm) REVERT: D 615 GLU cc_start: 0.8770 (pp20) cc_final: 0.8400 (pp20) REVERT: D 859 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8277 (ttp) REVERT: D 1001 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8143 (mm) REVERT: D 1005 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7073 (t80) REVERT: D 1013 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7532 (t80) outliers start: 57 outliers final: 27 residues processed: 256 average time/residue: 1.4695 time to fit residues: 485.8778 Evaluate side-chains 262 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1082 PHE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1082 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1082 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1082 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 258 optimal weight: 1.9990 chunk 297 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 282 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 510 GLN B 619 ASN C 619 ASN D 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.147390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092257 restraints weight = 144454.069| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.40 r_work: 0.3169 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29604 Z= 0.275 Angle : 0.524 10.461 40516 Z= 0.276 Chirality : 0.037 0.137 4740 Planarity : 0.003 0.047 4944 Dihedral : 7.520 177.516 5140 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 1.91 % Allowed : 17.91 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.14), residues: 3636 helix: 2.39 (0.11), residues: 2440 sheet: -1.92 (0.40), residues: 196 loop : -1.72 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 682 HIS 0.002 0.000 HIS A 765 PHE 0.014 0.001 PHE C 870 TYR 0.021 0.001 TYR B 170 ARG 0.003 0.000 ARG B 688 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37617.27 seconds wall clock time: 639 minutes 8.16 seconds (38348.16 seconds total)