Starting phenix.real_space_refine on Fri Oct 11 15:55:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6e_44256/10_2024/9b6e_44256_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6e_44256/10_2024/9b6e_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6e_44256/10_2024/9b6e_44256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6e_44256/10_2024/9b6e_44256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6e_44256/10_2024/9b6e_44256_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6e_44256/10_2024/9b6e_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): 0.88s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 37.99, 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: 11.38 Conformation dependent library (CDL) restraints added in 3.6 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: 3.47 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: 21.78 Time building geometry restraints manager: 13.80 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.750 Extract box with map and model: 1.840 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 110.300 Find NCS groups from input model: 1.320 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.660 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 412 time to evaluate : 3.354 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: 1.5891 time to fit residues: 823.9142 Evaluate side-chains 261 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 3.777 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 fitting. rotamer outliers: 68 poor density : 282 time to evaluate : 3.333 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: 0.8273 (pp20) cc_final: 0.7938 (pp20) REVERT: A 859 MET cc_start: 0.8803 (ptm) cc_final: 0.8247 (ttp) REVERT: A 1005 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7015 (t80) REVERT: B 615 GLU cc_start: 0.8272 (pp20) cc_final: 0.7936 (pp20) REVERT: B 859 MET cc_start: 0.8802 (ptm) cc_final: 0.8245 (ttp) REVERT: B 1005 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7017 (t80) REVERT: C 615 GLU cc_start: 0.8268 (pp20) cc_final: 0.7934 (pp20) REVERT: C 859 MET cc_start: 0.8804 (ptm) cc_final: 0.8224 (ttp) REVERT: C 1005 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7018 (t80) REVERT: D 615 GLU cc_start: 0.8270 (pp20) cc_final: 0.7934 (pp20) REVERT: D 859 MET cc_start: 0.8802 (ptm) cc_final: 0.8247 (ttp) REVERT: D 1005 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7017 (t80) outliers start: 68 outliers final: 15 residues processed: 322 average time/residue: 1.6123 time to fit residues: 667.6353 Evaluate side-chains 262 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 243 time to evaluate : 3.320 ------------------------------------------------------------------------------- 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 185 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 334 optimal weight: 1.9990 chunk 361 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29604 Z= 0.218 Angle : 0.497 9.703 40516 Z= 0.264 Chirality : 0.036 0.135 4740 Planarity : 0.003 0.048 4944 Dihedral : 7.445 179.663 5140 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.17 % Allowed : 16.12 % 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: 1.60 (0.15), residues: 3636 helix: 2.22 (0.11), residues: 2440 sheet: -1.68 (0.40), residues: 196 loop : -1.37 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 682 HIS 0.003 0.001 HIS A1080 PHE 0.014 0.001 PHE A 304 TYR 0.017 0.001 TYR B1022 ARG 0.007 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 311 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 252 time to evaluate : 3.359 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 615 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: A 859 MET cc_start: 0.8744 (ptm) cc_final: 0.8313 (ttp) REVERT: A 1005 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7040 (t80) REVERT: A 1013 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7450 (t80) REVERT: B 615 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7943 (pp20) REVERT: B 859 MET cc_start: 0.8744 (ptm) cc_final: 0.8312 (ttp) REVERT: B 1005 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7041 (t80) REVERT: B 1013 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7449 (t80) REVERT: C 615 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7944 (pp20) REVERT: C 859 MET cc_start: 0.8744 (ptm) cc_final: 0.8315 (ttp) REVERT: C 1005 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7044 (t80) REVERT: C 1013 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7451 (t80) REVERT: D 615 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7941 (pp20) REVERT: D 859 MET cc_start: 0.8743 (ptm) cc_final: 0.8316 (ttp) REVERT: D 1005 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7043 (t80) REVERT: D 1013 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7450 (t80) outliers start: 59 outliers final: 21 residues processed: 277 average time/residue: 1.5364 time to fit residues: 542.5528 Evaluate side-chains 273 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 615 GLU 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 615 GLU 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 615 GLU 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 615 GLU 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 330 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 335 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 HIS B 946 HIS C 946 HIS D 946 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29604 Z= 0.239 Angle : 0.507 8.623 40516 Z= 0.268 Chirality : 0.036 0.157 4740 Planarity : 0.003 0.051 4944 Dihedral : 7.510 179.140 5140 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.30 % Allowed : 14.79 % Favored : 81.90 % 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: 1.58 (0.15), residues: 3636 helix: 2.23 (0.11), residues: 2440 sheet: -1.82 (0.39), residues: 196 loop : -1.40 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 682 HIS 0.002 0.001 HIS C 389 PHE 0.012 0.001 PHE C 870 TYR 0.015 0.001 TYR B1022 ARG 0.004 0.000 ARG A 167 *********************** 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 339 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 249 time to evaluate : 3.383 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 816 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8694 (ppp80) REVERT: A 859 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8448 (ttp) REVERT: A 1005 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7009 (t80) REVERT: A 1013 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 816 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8695 (ppp80) REVERT: B 859 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8442 (ttp) REVERT: B 1005 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7008 (t80) REVERT: B 1013 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7438 (t80) REVERT: C 816 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8696 (ppp80) REVERT: C 859 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8442 (ttp) REVERT: C 1005 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7012 (t80) REVERT: C 1013 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7439 (t80) REVERT: D 816 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8695 (ppp80) REVERT: D 859 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8444 (ttp) REVERT: D 1005 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7008 (t80) REVERT: D 1013 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7439 (t80) outliers start: 90 outliers final: 29 residues processed: 287 average time/residue: 1.5595 time to fit residues: 569.9783 Evaluate side-chains 263 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 816 ARG 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 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 816 ARG 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 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 816 ARG 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 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 816 ARG 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 264 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 303 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 635 ASN B 619 ASN B 635 ASN C 619 ASN C 635 ASN D 619 ASN D 635 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29604 Z= 0.341 Angle : 0.557 10.607 40516 Z= 0.294 Chirality : 0.038 0.158 4740 Planarity : 0.003 0.046 4944 Dihedral : 7.714 178.148 5140 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.74 % Allowed : 14.43 % Favored : 81.83 % 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: 1.33 (0.14), residues: 3636 helix: 2.07 (0.10), residues: 2432 sheet: -1.88 (0.39), residues: 196 loop : -1.56 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 682 HIS 0.002 0.001 HIS B 765 PHE 0.014 0.001 PHE C 870 TYR 0.017 0.001 TYR C1022 ARG 0.003 0.000 ARG A 816 *********************** 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 340 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 238 time to evaluate : 3.433 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: 0.8910 (mt) cc_final: 0.8700 (mm) REVERT: A 859 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8444 (ttp) REVERT: A 965 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9240 (tp) REVERT: A 1005 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 1013 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 120 LEU cc_start: 0.8907 (mt) cc_final: 0.8696 (mm) REVERT: B 859 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8438 (ttp) REVERT: B 965 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9241 (tp) REVERT: B 1005 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.6964 (t80) REVERT: B 1013 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7430 (t80) REVERT: C 120 LEU cc_start: 0.8908 (mt) cc_final: 0.8697 (mm) REVERT: C 859 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8442 (ttp) REVERT: C 965 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9240 (tp) REVERT: C 1005 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6965 (t80) REVERT: C 1013 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7433 (t80) REVERT: D 120 LEU cc_start: 0.8914 (mt) cc_final: 0.8703 (mm) REVERT: D 859 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8444 (ttp) REVERT: D 965 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9240 (tp) REVERT: D 1005 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6966 (t80) REVERT: D 1013 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7433 (t80) outliers start: 102 outliers final: 55 residues processed: 290 average time/residue: 1.5151 time to fit residues: 560.6475 Evaluate side-chains 292 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 221 time to evaluate : 3.294 ------------------------------------------------------------------------------- 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 303 CYS Chi-restraints excluded: chain A residue 326 CYS 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 801 MET Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 965 LEU 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 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 196 VAL 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 801 MET 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 968 ASN 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 196 VAL 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 801 MET 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 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 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 196 VAL 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 801 MET 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 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 Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 8.9990 chunk 320 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 356 optimal weight: 0.4980 chunk 295 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29604 Z= 0.201 Angle : 0.490 9.533 40516 Z= 0.261 Chirality : 0.036 0.143 4740 Planarity : 0.003 0.042 4944 Dihedral : 7.474 179.002 5140 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.08 % Allowed : 15.42 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.14), residues: 3636 helix: 2.29 (0.11), residues: 2444 sheet: -1.88 (0.39), residues: 196 loop : -1.52 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 682 HIS 0.002 0.000 HIS A 928 PHE 0.012 0.001 PHE B1082 TYR 0.016 0.001 TYR B1022 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 319 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 235 time to evaluate : 3.490 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: A 120 LEU cc_start: 0.8929 (mt) cc_final: 0.8707 (mm) REVERT: A 816 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8597 (ppp80) REVERT: A 859 MET cc_start: 0.8717 (ptm) cc_final: 0.8323 (ttp) REVERT: A 1005 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6950 (t80) REVERT: A 1013 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7361 (t80) REVERT: B 120 LEU cc_start: 0.8943 (mt) cc_final: 0.8714 (mm) REVERT: B 816 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8598 (ppp80) REVERT: B 859 MET cc_start: 0.8721 (ptm) cc_final: 0.8316 (ttp) REVERT: B 1005 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.6950 (t80) REVERT: B 1013 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7362 (t80) REVERT: C 120 LEU cc_start: 0.8942 (mt) cc_final: 0.8714 (mm) REVERT: C 816 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8599 (ppp80) REVERT: C 859 MET cc_start: 0.8718 (ptm) cc_final: 0.8319 (ttp) REVERT: C 1005 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6953 (t80) REVERT: C 1013 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7373 (t80) REVERT: D 120 LEU cc_start: 0.8950 (mt) cc_final: 0.8721 (mm) REVERT: D 816 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8599 (ppp80) REVERT: D 859 MET cc_start: 0.8718 (ptm) cc_final: 0.8322 (ttp) REVERT: D 1005 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6949 (t80) REVERT: D 1013 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7373 (t80) outliers start: 84 outliers final: 49 residues processed: 284 average time/residue: 1.4715 time to fit residues: 536.0019 Evaluate side-chains 274 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 213 time to evaluate : 3.402 ------------------------------------------------------------------------------- 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 303 CYS 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 712 PHE Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 955 ILE 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 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 196 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 816 ARG Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 955 ILE 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 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 196 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 712 PHE Chi-restraints excluded: chain C residue 816 ARG Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 955 ILE 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 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 196 VAL Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 712 PHE Chi-restraints excluded: chain D residue 816 ARG Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 955 ILE 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 Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 260 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 354 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29604 Z= 0.320 Angle : 0.537 9.289 40516 Z= 0.284 Chirality : 0.038 0.149 4740 Planarity : 0.003 0.051 4944 Dihedral : 7.647 177.879 5140 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.63 % Allowed : 15.75 % Favored : 80.62 % 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: 1.48 (0.14), residues: 3636 helix: 2.22 (0.11), residues: 2440 sheet: -1.87 (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 A 682 HIS 0.002 0.001 HIS D 765 PHE 0.013 0.001 PHE C 870 TYR 0.017 0.001 TYR B1022 ARG 0.002 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 326 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 227 time to evaluate : 3.399 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: 0.8788 (OUTLIER) cc_final: 0.8317 (ttp) REVERT: A 965 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9222 (tp) REVERT: A 1005 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.6964 (t80) REVERT: A 1013 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7417 (t80) REVERT: B 120 LEU cc_start: 0.8968 (mt) cc_final: 0.8747 (mm) REVERT: B 859 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8413 (ttp) REVERT: B 965 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9223 (tp) REVERT: B 1005 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6962 (t80) REVERT: B 1013 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7420 (t80) REVERT: C 120 LEU cc_start: 0.8968 (mt) cc_final: 0.8748 (mm) REVERT: C 859 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8315 (ttp) REVERT: C 965 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9221 (tp) REVERT: C 1005 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6963 (t80) REVERT: C 1013 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7422 (t80) REVERT: D 120 LEU cc_start: 0.8974 (mt) cc_final: 0.8755 (mm) REVERT: D 859 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8442 (ttp) REVERT: D 965 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9222 (tp) REVERT: D 1005 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.6966 (t80) REVERT: D 1013 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7420 (t80) outliers start: 99 outliers final: 59 residues processed: 275 average time/residue: 1.4434 time to fit residues: 513.0149 Evaluate side-chains 295 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 220 time to evaluate : 3.374 ------------------------------------------------------------------------------- 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 303 CYS 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 712 PHE Chi-restraints excluded: chain A residue 801 MET 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 955 ILE Chi-restraints excluded: chain A residue 965 LEU 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 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 196 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain B residue 801 MET 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 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 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 196 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 712 PHE Chi-restraints excluded: chain C residue 801 MET 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 968 ASN 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 196 VAL Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 712 PHE Chi-restraints excluded: chain D residue 801 MET 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 968 ASN 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 219 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29604 Z= 0.331 Angle : 0.548 9.056 40516 Z= 0.291 Chirality : 0.038 0.170 4740 Planarity : 0.004 0.050 4944 Dihedral : 7.717 177.522 5140 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.78 % Allowed : 15.68 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.14), residues: 3636 helix: 2.14 (0.11), residues: 2440 sheet: -1.97 (0.40), residues: 196 loop : -1.72 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 682 HIS 0.002 0.001 HIS B 765 PHE 0.015 0.001 PHE B1082 TYR 0.018 0.001 TYR B1022 ARG 0.002 0.000 ARG A 816 *********************** 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 335 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 232 time to evaluate : 3.406 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: 0.8775 (OUTLIER) cc_final: 0.8325 (ttp) REVERT: A 965 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9228 (tp) REVERT: A 1005 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6964 (t80) REVERT: A 1013 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7398 (t80) REVERT: B 120 LEU cc_start: 0.8950 (mt) cc_final: 0.8733 (mm) REVERT: B 859 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8319 (ttp) REVERT: B 965 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9223 (tp) REVERT: B 1005 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6960 (t80) REVERT: B 1013 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7398 (t80) REVERT: C 120 LEU cc_start: 0.8951 (mt) cc_final: 0.8736 (mm) REVERT: C 859 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8318 (ttp) REVERT: C 965 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9227 (tp) REVERT: C 1005 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6958 (t80) REVERT: C 1013 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7402 (t80) REVERT: D 120 LEU cc_start: 0.8955 (mt) cc_final: 0.8737 (mm) REVERT: D 859 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8319 (ttp) REVERT: D 965 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9228 (tp) REVERT: D 1005 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6961 (t80) REVERT: D 1013 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7400 (t80) outliers start: 103 outliers final: 63 residues processed: 284 average time/residue: 1.4768 time to fit residues: 537.3584 Evaluate side-chains 298 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 219 time to evaluate : 3.319 ------------------------------------------------------------------------------- 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 303 CYS Chi-restraints excluded: chain A residue 326 CYS 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 712 PHE Chi-restraints excluded: chain A residue 801 MET 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 955 ILE Chi-restraints excluded: chain A residue 965 LEU 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 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 196 VAL 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 712 PHE Chi-restraints excluded: chain B residue 801 MET 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 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 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 196 VAL 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 712 PHE Chi-restraints excluded: chain C residue 801 MET 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 968 ASN 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 196 VAL 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 712 PHE Chi-restraints excluded: chain D residue 801 MET 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 968 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 312 optimal weight: 1.9990 chunk 329 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29604 Z= 0.277 Angle : 0.530 8.807 40516 Z= 0.279 Chirality : 0.037 0.141 4740 Planarity : 0.004 0.050 4944 Dihedral : 7.615 178.059 5140 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.12 % Allowed : 16.37 % 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: 1.44 (0.14), residues: 3636 helix: 2.23 (0.11), residues: 2440 sheet: -1.92 (0.41), residues: 188 loop : -1.77 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 682 HIS 0.001 0.000 HIS D 765 PHE 0.014 0.001 PHE B1082 TYR 0.022 0.001 TYR D 170 ARG 0.009 0.000 ARG A 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 311 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 226 time to evaluate : 3.487 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 859 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8291 (ttp) REVERT: A 965 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9200 (tp) REVERT: A 1001 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 1005 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.6933 (t80) REVERT: A 1013 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7406 (t80) REVERT: B 120 LEU cc_start: 0.8940 (mt) cc_final: 0.8730 (mm) REVERT: B 859 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8361 (ttp) REVERT: B 965 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9200 (tp) REVERT: B 1001 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 1005 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6931 (t80) REVERT: B 1013 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7407 (t80) REVERT: C 120 LEU cc_start: 0.8941 (mt) cc_final: 0.8733 (mm) REVERT: C 859 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8368 (ttp) REVERT: C 965 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9200 (tp) REVERT: C 1001 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8070 (mm) REVERT: C 1005 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6931 (t80) REVERT: C 1013 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7408 (t80) REVERT: D 120 LEU cc_start: 0.8946 (mt) cc_final: 0.8737 (mm) REVERT: D 859 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8366 (ttp) REVERT: D 965 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9201 (tp) REVERT: D 1001 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8070 (mm) REVERT: D 1005 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6910 (t80) REVERT: D 1013 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7408 (t80) outliers start: 85 outliers final: 54 residues processed: 271 average time/residue: 1.4275 time to fit residues: 502.4345 Evaluate side-chains 296 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 222 time to evaluate : 3.350 ------------------------------------------------------------------------------- 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 303 CYS 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 712 PHE 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 955 ILE Chi-restraints excluded: chain A residue 965 LEU 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 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 196 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 712 PHE 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 968 ASN 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 B residue 1082 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 326 CYS Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 712 PHE 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 968 ASN 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 196 VAL Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 692 ASN 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 968 ASN 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 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 217 optimal weight: 8.9990 chunk 349 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 366 optimal weight: 20.0000 chunk 337 optimal weight: 1.9990 chunk 291 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 225 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 29604 Z= 0.392 Angle : 0.584 8.799 40516 Z= 0.308 Chirality : 0.039 0.150 4740 Planarity : 0.004 0.051 4944 Dihedral : 7.847 176.508 5140 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.12 % Allowed : 16.59 % Favored : 80.29 % 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: 1.15 (0.14), residues: 3636 helix: 2.02 (0.11), residues: 2440 sheet: -2.02 (0.41), residues: 188 loop : -1.93 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 682 HIS 0.002 0.001 HIS B 765 PHE 0.015 0.002 PHE D 870 TYR 0.019 0.002 TYR A1022 ARG 0.004 0.001 ARG B 816 ********************** 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 318 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 233 time to evaluate : 3.473 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: A 120 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8139 (mm) REVERT: A 615 GLU cc_start: 0.8621 (pp20) cc_final: 0.8321 (pp20) REVERT: A 859 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8351 (ttp) REVERT: A 965 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9225 (tp) REVERT: A 1001 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8054 (mm) REVERT: A 1005 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6928 (t80) REVERT: A 1013 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 120 LEU cc_start: 0.8942 (mt) cc_final: 0.8735 (mm) REVERT: B 859 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8420 (ttp) REVERT: B 965 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9227 (tp) REVERT: B 1001 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8055 (mm) REVERT: B 1005 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6926 (t80) REVERT: B 1013 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7501 (t80) REVERT: C 120 LEU cc_start: 0.8944 (mt) cc_final: 0.8737 (mm) REVERT: C 645 VAL cc_start: 0.8615 (t) cc_final: 0.8382 (m) REVERT: C 859 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8445 (ttp) REVERT: C 965 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9225 (tp) REVERT: C 1001 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8057 (mm) REVERT: C 1005 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6927 (t80) REVERT: C 1013 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7501 (t80) REVERT: D 120 LEU cc_start: 0.8948 (mt) cc_final: 0.8742 (mm) REVERT: D 859 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8424 (ttp) REVERT: D 965 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9225 (tp) REVERT: D 1001 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8056 (mm) REVERT: D 1005 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.6928 (t80) REVERT: D 1013 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7501 (t80) outliers start: 85 outliers final: 52 residues processed: 281 average time/residue: 1.4481 time to fit residues: 535.4405 Evaluate side-chains 297 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 224 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU 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 303 CYS 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 850 SER Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 965 LEU 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 1009 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1082 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 326 CYS Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 692 ASN 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 968 ASN 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 196 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 692 ASN 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 968 ASN 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 C residue 1082 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 326 CYS Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 712 PHE 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 968 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 269 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 292 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 300 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.147224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092164 restraints weight = 144765.257| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.41 r_work: 0.3159 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29604 Z= 0.235 Angle : 0.522 8.870 40516 Z= 0.276 Chirality : 0.036 0.133 4740 Planarity : 0.003 0.050 4944 Dihedral : 7.607 178.277 5140 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.42 % Allowed : 17.55 % 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: 1.38 (0.14), residues: 3636 helix: 2.22 (0.11), residues: 2440 sheet: -1.98 (0.41), residues: 188 loop : -1.90 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 682 HIS 0.001 0.000 HIS A 500 PHE 0.012 0.001 PHE C 870 TYR 0.021 0.001 TYR A 170 ARG 0.004 0.000 ARG A 688 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12561.81 seconds wall clock time: 216 minutes 16.18 seconds (12976.18 seconds total)