Starting phenix.real_space_refine on Fri Jan 17 10:43:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6d_44255/01_2025/9b6d_44255_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6d_44255/01_2025/9b6d_44255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6d_44255/01_2025/9b6d_44255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6d_44255/01_2025/9b6d_44255.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6d_44255/01_2025/9b6d_44255_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6d_44255/01_2025/9b6d_44255_trim.cif" } resolution = 3.3 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= 0.001 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 116 5.16 5 C 18908 2.51 5 N 4604 2.21 5 O 5036 1.98 5 H 25920 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 54584 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 13475 Classifications: {'peptide': 933} Link IDs: {'PTRANS': 23, 'TRANS': 909} Chain breaks: 9 Unresolved non-hydrogen bonds: 637 Unresolved non-hydrogen angles: 784 Unresolved non-hydrogen dihedrals: 528 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 372 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 171 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Restraints were copied for chains: C, B, D Time building chain proxies: 35.97, per 1000 atoms: 0.66 Number of scatterers: 54584 At special positions: 0 Unit cell: (155.1, 155.1, 158.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 O 5036 8.00 N 4604 7.00 C 18908 6.00 H 25920 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=2.09 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 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: 10.94 Conformation dependent library (CDL) restraints added in 3.6 seconds 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7112 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 4 sheets defined 72.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.977A pdb=" N PHE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.515A pdb=" N TYR A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.933A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 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: 3.530A pdb=" N ILE A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 4.447A pdb=" N GLU A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.798A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 457 through 469 removed outlier: 4.488A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.731A pdb=" N THR A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.594A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.611A 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 586 through 603 removed outlier: 3.685A pdb=" N LEU A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.655A pdb=" N ALA A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.521A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.897A pdb=" N GLY A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 731 removed outlier: 3.549A pdb=" N PHE A 730 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 731 " --> pdb=" O TYR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 759 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: 3.516A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 841 removed outlier: 3.798A pdb=" N LEU A 825 " --> pdb=" O ASN A 821 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 847 removed outlier: 4.092A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 859 removed outlier: 3.581A pdb=" N MET A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 862 No H-bonds generated for 'chain 'A' and resid 860 through 862' Processing helix chain 'A' and resid 863 through 890 removed outlier: 3.722A pdb=" N VAL A 867 " --> pdb=" O MET A 863 " (cutoff:3.500A) 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: 3.841A pdb=" N THR A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) Proline residue: A 958 - end of helix removed outlier: 3.770A pdb=" N ILE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1008 removed outlier: 5.052A pdb=" N GLU A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 993 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1027 removed outlier: 4.477A pdb=" N VAL A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A1022 " --> pdb=" O PHE A1018 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A1025 " --> pdb=" O PHE A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1073 Processing helix chain 'A' and resid 1076 through 1104 removed outlier: 3.905A pdb=" N HIS A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.860A pdb=" N LYS A1097 " --> pdb=" O LYS A1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.514A pdb=" N TYR B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.932A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 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: 3.530A pdb=" N ILE B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 420 removed outlier: 4.447A pdb=" N GLU B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.799A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.488A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 533 removed outlier: 3.732A pdb=" N THR B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.595A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.610A 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 586 through 603 removed outlier: 3.685A pdb=" N LEU B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.655A pdb=" N ALA B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.521A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.899A pdb=" N GLY B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 731 removed outlier: 3.549A pdb=" N PHE B 730 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 731 " --> pdb=" O TYR B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 759 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: 3.516A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 841 removed outlier: 3.798A pdb=" N LEU B 825 " --> pdb=" O ASN B 821 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 847 removed outlier: 4.092A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 859 removed outlier: 3.581A pdb=" N MET B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 862 No H-bonds generated for 'chain 'B' and resid 860 through 862' Processing helix chain 'B' and resid 863 through 890 removed outlier: 3.723A pdb=" N VAL B 867 " --> pdb=" O MET B 863 " (cutoff:3.500A) 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: 3.841A pdb=" N THR B 956 " --> pdb=" O PRO B 952 " (cutoff:3.500A) Proline residue: B 958 - end of helix removed outlier: 3.769A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1008 removed outlier: 5.052A pdb=" N GLU B 988 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 989 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 993 " --> pdb=" O ASN B 989 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B1008 " --> pdb=" O GLU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1027 removed outlier: 4.477A pdb=" N VAL B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B1020 " --> pdb=" O VAL B1016 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B1022 " --> pdb=" O PHE B1018 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B1024 " --> pdb=" O TYR B1020 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B1025 " --> pdb=" O PHE B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1073 Processing helix chain 'B' and resid 1076 through 1104 removed outlier: 3.904A pdb=" N HIS B1080 " --> pdb=" O GLU B1076 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B1094 " --> pdb=" O ASN B1090 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.860A pdb=" N LYS B1097 " --> pdb=" O LYS B1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.516A pdb=" N TYR C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.932A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 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: 3.530A pdb=" N ILE C 374 " --> pdb=" O PRO C 370 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.447A pdb=" N GLU C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 removed outlier: 3.798A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 447 Processing helix chain 'C' and resid 457 through 469 removed outlier: 4.488A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 533 removed outlier: 3.731A pdb=" N THR C 522 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.594A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.611A 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 586 through 603 removed outlier: 3.685A pdb=" N LEU C 601 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.655A pdb=" N ALA C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.521A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.897A pdb=" N GLY C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 731 removed outlier: 3.549A pdb=" N PHE C 730 " --> pdb=" O TYR C 726 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 731 " --> pdb=" O TYR C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 759 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: 3.516A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 841 removed outlier: 3.798A pdb=" N LEU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 841 " --> pdb=" O ILE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 847 removed outlier: 4.091A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 859 removed outlier: 3.580A pdb=" N MET C 859 " --> pdb=" O PRO C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 862 No H-bonds generated for 'chain 'C' and resid 860 through 862' Processing helix chain 'C' and resid 863 through 890 removed outlier: 3.722A pdb=" N VAL C 867 " --> pdb=" O MET C 863 " (cutoff:3.500A) 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: 3.842A pdb=" N THR C 956 " --> pdb=" O PRO C 952 " (cutoff:3.500A) Proline residue: C 958 - end of helix removed outlier: 3.769A pdb=" N ILE C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1008 removed outlier: 5.052A pdb=" N GLU C 988 " --> pdb=" O GLY C 984 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN C 989 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 993 " --> pdb=" O ASN C 989 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C1008 " --> pdb=" O GLU C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1027 removed outlier: 4.478A pdb=" N VAL C1017 " --> pdb=" O PHE C1013 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE C1018 " --> pdb=" O PRO C1014 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C1020 " --> pdb=" O VAL C1016 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C1022 " --> pdb=" O PHE C1018 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL C1025 " --> pdb=" O PHE C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1073 Processing helix chain 'C' and resid 1076 through 1104 removed outlier: 3.905A pdb=" N HIS C1080 " --> pdb=" O GLU C1076 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C1094 " --> pdb=" O ASN C1090 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.860A pdb=" N LYS C1097 " --> pdb=" O LYS C1093 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 274 through 288 removed outlier: 3.515A pdb=" N TYR D 284 " --> pdb=" O GLN D 280 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.933A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 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: 3.529A pdb=" N ILE D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 420 removed outlier: 4.447A pdb=" N GLU D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 436 removed outlier: 3.798A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 447 Processing helix chain 'D' and resid 457 through 469 removed outlier: 4.488A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 533 removed outlier: 3.731A pdb=" N THR D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.594A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.611A 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 586 through 603 removed outlier: 3.685A pdb=" N LEU D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.655A pdb=" N ALA D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.522A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.897A pdb=" N GLY D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 731 removed outlier: 3.549A pdb=" N PHE D 730 " --> pdb=" O TYR D 726 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 731 " --> pdb=" O TYR D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 759 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: 3.516A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 841 removed outlier: 3.798A pdb=" N LEU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 841 " --> pdb=" O ILE D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 847 removed outlier: 4.092A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 859 removed outlier: 3.580A pdb=" N MET D 859 " --> pdb=" O PRO D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 862 No H-bonds generated for 'chain 'D' and resid 860 through 862' Processing helix chain 'D' and resid 863 through 890 removed outlier: 3.723A pdb=" N VAL D 867 " --> pdb=" O MET D 863 " (cutoff:3.500A) 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: 3.842A pdb=" N THR D 956 " --> pdb=" O PRO D 952 " (cutoff:3.500A) Proline residue: D 958 - end of helix removed outlier: 3.770A pdb=" N ILE D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 1008 removed outlier: 5.051A pdb=" N GLU D 988 " --> pdb=" O GLY D 984 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN D 989 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL D 993 " --> pdb=" O ASN D 989 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG D1008 " --> pdb=" O GLU D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1027 removed outlier: 4.477A pdb=" N VAL D1017 " --> pdb=" O PHE D1013 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE D1018 " --> pdb=" O PRO D1014 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D1020 " --> pdb=" O VAL D1016 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR D1022 " --> pdb=" O PHE D1018 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D1024 " --> pdb=" O TYR D1020 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL D1025 " --> pdb=" O PHE D1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1073 Processing helix chain 'D' and resid 1076 through 1104 removed outlier: 3.905A pdb=" N HIS D1080 " --> pdb=" O GLU D1076 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D1094 " --> pdb=" O ASN D1090 " (cutoff:3.500A) removed outlier: 3.956A 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: 3.860A pdb=" N LYS D1097 " --> pdb=" O LYS D1093 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.531A pdb=" N LEU A 118 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ALA A 216 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.531A pdb=" N LEU B 118 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ALA B 216 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.530A pdb=" N LEU C 118 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ALA C 216 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 120 removed outlier: 3.531A pdb=" N LEU D 118 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N ALA D 216 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) 1812 hydrogen bonds defined for protein. 5364 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: 18.65 Time building geometry restraints manager: 13.43 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: 25884 1.03 - 1.23: 123 1.23 - 1.42: 12305 1.42 - 1.62: 16800 1.62 - 1.81: 180 Bond restraints: 55292 Sorted by residual: bond pdb=" CAY Y01 D1204 " pdb=" OAW Y01 D1204 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CAY Y01 C1204 " pdb=" OAW Y01 C1204 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CAY Y01 A1204 " pdb=" OAW Y01 A1204 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" CAY Y01 B1204 " pdb=" OAW Y01 B1204 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.43e+01 bond pdb=" CAY Y01 A1202 " pdb=" OAW Y01 A1202 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 55287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 98251 2.62 - 5.24: 673 5.24 - 7.86: 100 7.86 - 10.48: 34 10.48 - 13.10: 26 Bond angle restraints: 99084 Sorted by residual: angle pdb=" CAT Y01 C1201 " pdb=" CBH Y01 C1201 " pdb=" CBF Y01 C1201 " ideal model delta sigma weight residual 108.46 95.36 13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CAT Y01 D1201 " pdb=" CBH Y01 D1201 " pdb=" CBF Y01 D1201 " ideal model delta sigma weight residual 108.46 95.37 13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CAT Y01 B1201 " pdb=" CBH Y01 B1201 " pdb=" CBF Y01 B1201 " ideal model delta sigma weight residual 108.46 95.37 13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CAT Y01 A1201 " pdb=" CBH Y01 A1201 " pdb=" CBF Y01 A1201 " ideal model delta sigma weight residual 108.46 95.37 13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CAT Y01 D1204 " pdb=" CBH Y01 D1204 " pdb=" CBF Y01 D1204 " ideal model delta sigma weight residual 108.46 95.55 12.91 3.00e+00 1.11e-01 1.85e+01 ... (remaining 99079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 25523 17.19 - 34.37: 1364 34.37 - 51.56: 438 51.56 - 68.74: 141 68.74 - 85.93: 12 Dihedral angle restraints: 27478 sinusoidal: 14174 harmonic: 13304 Sorted by residual: dihedral pdb=" CA GLY C 913 " pdb=" C GLY C 913 " pdb=" N GLN C 914 " pdb=" CA GLN C 914 " ideal model delta harmonic sigma weight residual 180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLY A 913 " pdb=" C GLY A 913 " pdb=" N GLN A 914 " pdb=" CA GLN A 914 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLY B 913 " pdb=" C GLY B 913 " pdb=" N GLN B 914 " pdb=" CA GLN B 914 " ideal model delta harmonic sigma weight residual 180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 27475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4358 0.076 - 0.152: 304 0.152 - 0.229: 18 0.229 - 0.305: 36 0.305 - 0.381: 48 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CBH Y01 C1205 " pdb=" CAT Y01 C1205 " pdb=" CAZ Y01 C1205 " pdb=" CBF Y01 C1205 " both_signs ideal model delta sigma weight residual False -2.85 -3.23 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CBH Y01 A1202 " pdb=" CAT Y01 A1202 " pdb=" CAZ Y01 A1202 " pdb=" CBF Y01 A1202 " both_signs ideal model delta sigma weight residual False -2.85 -3.23 0.38 2.00e-01 2.50e+01 3.61e+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 -3.23 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 4761 not shown) Planarity restraints: 8532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 304 " -0.010 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" N ALA D 305 " 0.032 2.00e-02 2.50e+03 pdb=" CA ALA D 305 " -0.008 2.00e-02 2.50e+03 pdb=" H ALA D 305 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 304 " -0.010 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" N ALA C 305 " 0.032 2.00e-02 2.50e+03 pdb=" CA ALA C 305 " -0.008 2.00e-02 2.50e+03 pdb=" H ALA C 305 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 304 " -0.010 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" N ALA B 305 " 0.032 2.00e-02 2.50e+03 pdb=" CA ALA B 305 " -0.008 2.00e-02 2.50e+03 pdb=" H ALA B 305 " -0.015 2.00e-02 2.50e+03 ... (remaining 8529 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 729 2.10 - 2.72: 86448 2.72 - 3.35: 147823 3.35 - 3.97: 170495 3.97 - 4.60: 279921 Nonbonded interactions: 685416 Sorted by model distance: nonbonded pdb=" OE1 GLU D1051 " pdb=" H GLU D1051 " model vdw 1.472 2.450 nonbonded pdb=" OE1 GLU C1051 " pdb=" H GLU C1051 " model vdw 1.472 2.450 nonbonded pdb=" OE1 GLU A1051 " pdb=" H GLU A1051 " model vdw 1.472 2.450 nonbonded pdb=" OE1 GLU B1051 " pdb=" H GLU B1051 " model vdw 1.473 2.450 nonbonded pdb=" O PRO C 855 " pdb="HD21 ASN C 990 " model vdw 1.494 2.450 ... (remaining 685411 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.760 Extract box with map and model: 1.510 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 103.770 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 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:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 0.099 29372 Z= 0.341 Angle : 0.824 13.097 40208 Z= 0.362 Chirality : 0.058 0.381 4764 Planarity : 0.003 0.045 4936 Dihedral : 12.333 85.928 10796 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.49 % Allowed : 12.14 % Favored : 87.37 % 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: 1.86 (0.14), residues: 3652 helix: 2.40 (0.11), residues: 2412 sheet: 0.13 (0.42), residues: 168 loop : -1.42 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 693 HIS 0.002 0.001 HIS C 389 PHE 0.021 0.002 PHE A 49 TYR 0.017 0.001 TYR A1022 ARG 0.006 0.000 ARG D 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 315 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 302 time to evaluate : 3.217 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 outliers start: 13 outliers final: 1 residues processed: 310 average time/residue: 0.7013 time to fit residues: 343.8035 Evaluate side-chains 248 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 930 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 0.0370 chunk 337 optimal weight: 0.7980 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN B 280 GLN C 280 GLN D 642 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.155469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105792 restraints weight = 132306.297| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.22 r_work: 0.3177 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29372 Z= 0.276 Angle : 0.541 9.782 40208 Z= 0.295 Chirality : 0.036 0.241 4764 Planarity : 0.004 0.065 4936 Dihedral : 7.095 59.941 5329 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.24 % Allowed : 12.03 % Favored : 86.73 % 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: 1.98 (0.14), residues: 3652 helix: 2.48 (0.10), residues: 2456 sheet: 0.02 (0.40), residues: 168 loop : -1.47 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 693 HIS 0.007 0.001 HIS D 389 PHE 0.018 0.002 PHE C 872 TYR 0.017 0.001 TYR A1022 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 912 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8692 (p90) REVERT: A 1020 TYR cc_start: 0.8206 (m-10) cc_final: 0.6239 (t80) REVERT: B 698 CYS cc_start: 0.8483 (t) cc_final: 0.8272 (m) REVERT: B 912 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8721 (p90) REVERT: C 189 MET cc_start: 0.7410 (mtm) cc_final: 0.7016 (mtm) REVERT: C 728 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7263 (p) REVERT: D 728 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7384 (p) REVERT: D 788 MET cc_start: 0.7445 (mmt) cc_final: 0.7055 (ttp) REVERT: D 912 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8681 (p90) outliers start: 33 outliers final: 19 residues processed: 305 average time/residue: 0.7137 time to fit residues: 342.1322 Evaluate side-chains 281 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 306 optimal weight: 9.9990 chunk 360 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 233 optimal weight: 0.5980 chunk 245 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 333 optimal weight: 6.9990 chunk 250 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN C 280 GLN C 642 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.155658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105797 restraints weight = 133010.764| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.37 r_work: 0.3155 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 29372 Z= 0.191 Angle : 0.467 14.652 40208 Z= 0.256 Chirality : 0.035 0.255 4764 Planarity : 0.003 0.057 4936 Dihedral : 6.548 59.248 5329 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.20 % Allowed : 11.99 % Favored : 86.80 % 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: 2.18 (0.14), residues: 3652 helix: 2.63 (0.10), residues: 2456 sheet: 0.56 (0.42), residues: 148 loop : -1.47 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 693 HIS 0.004 0.000 HIS D 389 PHE 0.018 0.001 PHE C 487 TYR 0.013 0.001 TYR B1022 ARG 0.003 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 299 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 698 CYS cc_start: 0.8466 (t) cc_final: 0.8262 (m) REVERT: A 912 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8698 (p90) REVERT: A 1016 VAL cc_start: 0.7969 (p) cc_final: 0.7762 (m) REVERT: A 1020 TYR cc_start: 0.8227 (m-10) cc_final: 0.6365 (t80) REVERT: B 912 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8725 (p90) REVERT: B 1020 TYR cc_start: 0.8232 (m-10) cc_final: 0.6323 (t80) REVERT: C 728 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7481 (p) REVERT: D 728 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7368 (p) REVERT: D 788 MET cc_start: 0.7408 (mmt) cc_final: 0.6956 (ttm) REVERT: D 912 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8656 (p90) outliers start: 32 outliers final: 18 residues processed: 288 average time/residue: 0.7484 time to fit residues: 338.1543 Evaluate side-chains 280 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 139 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 255 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 204 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102684 restraints weight = 132820.359| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.35 r_work: 0.3096 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29372 Z= 0.225 Angle : 0.476 6.144 40208 Z= 0.260 Chirality : 0.036 0.172 4764 Planarity : 0.003 0.055 4936 Dihedral : 6.329 59.641 5329 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.24 % Allowed : 11.84 % Favored : 86.92 % 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: 2.29 (0.14), residues: 3652 helix: 2.77 (0.10), residues: 2428 sheet: 0.58 (0.42), residues: 148 loop : -1.45 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 693 HIS 0.005 0.001 HIS D 389 PHE 0.016 0.001 PHE C 870 TYR 0.012 0.001 TYR C1022 ARG 0.003 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 317 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 912 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8672 (p90) REVERT: A 1020 TYR cc_start: 0.8306 (m-10) cc_final: 0.6423 (t80) REVERT: B 859 MET cc_start: 0.8737 (ptm) cc_final: 0.8200 (ttp) REVERT: B 912 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8635 (p90) REVERT: C 493 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7746 (mm) REVERT: C 912 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8708 (p90) REVERT: D 698 CYS cc_start: 0.8463 (t) cc_final: 0.8200 (m) REVERT: D 788 MET cc_start: 0.7389 (mmt) cc_final: 0.7041 (ttm) REVERT: D 912 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8589 (p90) outliers start: 33 outliers final: 22 residues processed: 304 average time/residue: 0.7638 time to fit residues: 367.1841 Evaluate side-chains 286 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1007 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 106 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 270 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN B 968 ASN D 968 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.155847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102840 restraints weight = 133623.509| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.29 r_work: 0.3228 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29372 Z= 0.263 Angle : 0.488 8.114 40208 Z= 0.268 Chirality : 0.036 0.153 4764 Planarity : 0.004 0.060 4936 Dihedral : 6.407 59.967 5329 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.58 % Allowed : 13.12 % Favored : 85.30 % 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: 2.14 (0.14), residues: 3652 helix: 2.66 (0.10), residues: 2432 sheet: 0.60 (0.43), residues: 148 loop : -1.54 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 693 HIS 0.004 0.001 HIS D 389 PHE 0.020 0.001 PHE C 487 TYR 0.012 0.001 TYR D1022 ARG 0.003 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 TRP cc_start: 0.4991 (t-100) cc_final: 0.4779 (t-100) REVERT: A 912 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8796 (p90) REVERT: A 1020 TYR cc_start: 0.8287 (m-10) cc_final: 0.6552 (t80) REVERT: A 1069 THR cc_start: 0.8179 (m) cc_final: 0.7918 (p) REVERT: B 859 MET cc_start: 0.8996 (ptm) cc_final: 0.8481 (ttp) REVERT: B 912 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8818 (p90) REVERT: B 1069 THR cc_start: 0.8224 (m) cc_final: 0.7968 (p) REVERT: C 493 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7765 (mm) REVERT: C 698 CYS cc_start: 0.8508 (t) cc_final: 0.8141 (m) REVERT: C 912 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8760 (p90) REVERT: D 698 CYS cc_start: 0.8467 (t) cc_final: 0.8197 (m) REVERT: D 788 MET cc_start: 0.7379 (mmt) cc_final: 0.7005 (ttm) REVERT: D 859 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8504 (ttp) REVERT: D 912 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8731 (p90) outliers start: 42 outliers final: 21 residues processed: 297 average time/residue: 0.7393 time to fit residues: 344.2281 Evaluate side-chains 280 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1007 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 36 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 335 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.155558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102677 restraints weight = 133905.618| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.31 r_work: 0.3227 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29372 Z= 0.230 Angle : 0.475 6.925 40208 Z= 0.260 Chirality : 0.035 0.167 4764 Planarity : 0.003 0.061 4936 Dihedral : 6.330 59.889 5329 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.28 % Allowed : 14.06 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.07 (0.14), residues: 3652 helix: 2.61 (0.10), residues: 2456 sheet: 0.71 (0.44), residues: 148 loop : -1.72 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 525 HIS 0.004 0.001 HIS D 389 PHE 0.017 0.001 PHE A 487 TYR 0.013 0.001 TYR D 787 ARG 0.002 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 293 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 TRP cc_start: 0.4982 (t-100) cc_final: 0.4781 (t-100) REVERT: A 859 MET cc_start: 0.9012 (ptm) cc_final: 0.8555 (ttp) REVERT: A 912 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8825 (p90) REVERT: A 1005 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6569 (t80) REVERT: A 1069 THR cc_start: 0.8198 (m) cc_final: 0.7944 (p) REVERT: B 859 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8536 (ttp) REVERT: B 912 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8818 (p90) REVERT: B 1069 THR cc_start: 0.8256 (m) cc_final: 0.7992 (p) REVERT: C 493 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7850 (mm) REVERT: C 698 CYS cc_start: 0.8535 (t) cc_final: 0.8200 (m) REVERT: C 859 MET cc_start: 0.8945 (ptm) cc_final: 0.8527 (ttp) REVERT: C 912 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8698 (p90) REVERT: D 698 CYS cc_start: 0.8428 (t) cc_final: 0.8168 (m) REVERT: D 788 MET cc_start: 0.7373 (mmt) cc_final: 0.6971 (ttm) REVERT: D 859 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8546 (ttp) REVERT: D 912 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8726 (p90) outliers start: 34 outliers final: 23 residues processed: 276 average time/residue: 0.7520 time to fit residues: 327.2127 Evaluate side-chains 284 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1007 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 341 optimal weight: 1.9990 chunk 348 optimal weight: 0.9980 chunk 278 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 309 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 973 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.155117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102160 restraints weight = 133940.227| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.30 r_work: 0.3215 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29372 Z= 0.247 Angle : 0.479 7.474 40208 Z= 0.264 Chirality : 0.036 0.166 4764 Planarity : 0.003 0.057 4936 Dihedral : 6.311 58.875 5329 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.28 % Allowed : 13.98 % Favored : 84.74 % 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: 1.99 (0.14), residues: 3652 helix: 2.58 (0.10), residues: 2448 sheet: 0.75 (0.44), residues: 148 loop : -1.83 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 525 HIS 0.003 0.001 HIS D 389 PHE 0.018 0.001 PHE C 487 TYR 0.012 0.001 TYR C1022 ARG 0.003 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 TRP cc_start: 0.4969 (t-100) cc_final: 0.4765 (t-100) REVERT: A 859 MET cc_start: 0.9010 (ptm) cc_final: 0.8543 (ttp) REVERT: A 912 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8784 (p90) REVERT: A 1005 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6625 (t80) REVERT: A 1069 THR cc_start: 0.8237 (m) cc_final: 0.8000 (p) REVERT: B 859 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8583 (ttp) REVERT: B 912 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8810 (p90) REVERT: B 1069 THR cc_start: 0.8289 (m) cc_final: 0.8043 (p) REVERT: C 493 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7894 (mm) REVERT: C 698 CYS cc_start: 0.8451 (t) cc_final: 0.8169 (m) REVERT: C 859 MET cc_start: 0.8947 (ptm) cc_final: 0.8532 (ttp) REVERT: C 863 MET cc_start: 0.8550 (mtt) cc_final: 0.8066 (mtt) REVERT: C 912 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8686 (p90) REVERT: C 1001 LEU cc_start: 0.9019 (tp) cc_final: 0.8243 (mt) REVERT: D 698 CYS cc_start: 0.8428 (t) cc_final: 0.8171 (m) REVERT: D 788 MET cc_start: 0.7401 (mmt) cc_final: 0.7001 (ttm) REVERT: D 859 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8580 (ttp) REVERT: D 912 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8734 (p90) REVERT: D 1001 LEU cc_start: 0.9025 (tp) cc_final: 0.8243 (mt) outliers start: 34 outliers final: 26 residues processed: 271 average time/residue: 0.7721 time to fit residues: 330.3699 Evaluate side-chains 281 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1007 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 10 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 256 optimal weight: 0.2980 chunk 303 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 358 optimal weight: 0.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN B 973 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.153992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101166 restraints weight = 133918.290| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.57 r_work: 0.3178 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29372 Z= 0.278 Angle : 0.498 6.012 40208 Z= 0.273 Chirality : 0.036 0.151 4764 Planarity : 0.004 0.064 4936 Dihedral : 6.369 58.038 5329 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.69 % Allowed : 13.68 % Favored : 84.62 % 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: 1.88 (0.14), residues: 3652 helix: 2.50 (0.10), residues: 2448 sheet: 0.82 (0.44), residues: 148 loop : -1.90 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 525 HIS 0.003 0.001 HIS D 389 PHE 0.017 0.001 PHE B 870 TYR 0.015 0.001 TYR D 787 ARG 0.003 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 306 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.9059 (ptm) cc_final: 0.8615 (ttp) REVERT: A 912 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8813 (p90) REVERT: A 1001 LEU cc_start: 0.8979 (tp) cc_final: 0.8199 (mt) REVERT: A 1005 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6683 (t80) REVERT: A 1069 THR cc_start: 0.8289 (m) cc_final: 0.8039 (p) REVERT: B 859 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8646 (ttp) REVERT: B 912 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8814 (p90) REVERT: B 1001 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8207 (mt) REVERT: B 1069 THR cc_start: 0.8299 (m) cc_final: 0.8039 (p) REVERT: C 698 CYS cc_start: 0.8573 (t) cc_final: 0.8228 (m) REVERT: C 859 MET cc_start: 0.9004 (ptm) cc_final: 0.8605 (ttp) REVERT: C 863 MET cc_start: 0.8653 (mtt) cc_final: 0.8204 (mtt) REVERT: C 912 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8699 (p90) REVERT: C 1001 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8217 (mt) REVERT: C 1069 THR cc_start: 0.8136 (m) cc_final: 0.7874 (p) REVERT: D 698 CYS cc_start: 0.8462 (t) cc_final: 0.8209 (m) REVERT: D 859 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8654 (ttp) REVERT: D 912 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8769 (p90) REVERT: D 1001 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8249 (mt) REVERT: D 1069 THR cc_start: 0.8298 (m) cc_final: 0.8034 (p) outliers start: 45 outliers final: 26 residues processed: 282 average time/residue: 0.7244 time to fit residues: 320.7885 Evaluate side-chains 290 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 850 SER Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1007 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 320 optimal weight: 0.1980 chunk 250 optimal weight: 0.1980 chunk 333 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 231 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN D 973 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.156318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104624 restraints weight = 133648.755| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.56 r_work: 0.3224 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29372 Z= 0.143 Angle : 0.447 6.879 40208 Z= 0.246 Chirality : 0.035 0.148 4764 Planarity : 0.003 0.060 4936 Dihedral : 6.123 59.059 5329 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.24 % Allowed : 14.10 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.14), residues: 3652 helix: 2.66 (0.10), residues: 2452 sheet: 0.93 (0.44), residues: 148 loop : -1.76 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 525 HIS 0.003 0.000 HIS D 389 PHE 0.017 0.001 PHE C 487 TYR 0.013 0.001 TYR C1022 ARG 0.003 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 295 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8973 (ptm) cc_final: 0.8559 (ttp) REVERT: A 912 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8779 (p90) REVERT: A 1001 LEU cc_start: 0.8897 (tp) cc_final: 0.8150 (mt) REVERT: A 1005 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6648 (t80) REVERT: A 1069 THR cc_start: 0.8292 (m) cc_final: 0.8034 (p) REVERT: B 859 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8584 (ttp) REVERT: B 912 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8760 (p90) REVERT: B 1001 LEU cc_start: 0.8848 (tp) cc_final: 0.8081 (mt) REVERT: B 1069 THR cc_start: 0.8278 (m) cc_final: 0.8026 (p) REVERT: C 698 CYS cc_start: 0.8307 (t) cc_final: 0.7974 (m) REVERT: C 859 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8573 (ttp) REVERT: C 863 MET cc_start: 0.8584 (mtt) cc_final: 0.8104 (mtt) REVERT: C 912 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8645 (p90) REVERT: C 1001 LEU cc_start: 0.9012 (tp) cc_final: 0.8182 (mt) REVERT: D 698 CYS cc_start: 0.8394 (t) cc_final: 0.8167 (m) REVERT: D 788 MET cc_start: 0.7376 (mmt) cc_final: 0.6987 (ttm) REVERT: D 859 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8604 (ttp) REVERT: D 912 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8689 (p90) REVERT: D 1001 LEU cc_start: 0.8935 (tp) cc_final: 0.8175 (mt) REVERT: D 1069 THR cc_start: 0.8356 (m) cc_final: 0.8104 (p) outliers start: 33 outliers final: 24 residues processed: 275 average time/residue: 0.7061 time to fit residues: 308.6956 Evaluate side-chains 286 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 758 MET Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 930 THR Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1007 ASN Chi-restraints excluded: chain D residue 1016 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 27 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 80 optimal weight: 0.0570 chunk 191 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 369 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 272 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.153722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100713 restraints weight = 134380.307| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.26 r_work: 0.3198 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29372 Z= 0.322 Angle : 0.507 6.553 40208 Z= 0.277 Chirality : 0.036 0.138 4764 Planarity : 0.004 0.064 4936 Dihedral : 6.276 59.875 5329 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.32 % Allowed : 14.10 % Favored : 84.59 % 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: 1.93 (0.14), residues: 3652 helix: 2.54 (0.10), residues: 2448 sheet: 0.93 (0.44), residues: 148 loop : -1.89 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 525 HIS 0.003 0.001 HIS A 818 PHE 0.018 0.002 PHE C 870 TYR 0.012 0.001 TYR A 506 ARG 0.003 0.000 ARG D 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 50 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 THR 134 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue LYS 140 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 THR 184 is missing expected H atoms. Skipping. Residue TYR 186 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 VAL 220 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 LEU 250 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue LEU 362 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 LYS 382 is missing expected H atoms. Skipping. Residue LYS 395 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 THR 503 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue TYR 516 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LYS 585 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 LEU 639 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue TYR 924 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 1066 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 291 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8586 (ttp) REVERT: A 912 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8796 (p90) REVERT: A 1001 LEU cc_start: 0.8968 (tp) cc_final: 0.8196 (mt) REVERT: A 1005 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6686 (t80) REVERT: A 1069 THR cc_start: 0.8398 (m) cc_final: 0.8153 (p) REVERT: B 859 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8630 (ttp) REVERT: B 912 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8790 (p90) REVERT: B 1001 LEU cc_start: 0.8983 (tp) cc_final: 0.8204 (mt) REVERT: B 1069 THR cc_start: 0.8392 (m) cc_final: 0.8156 (p) REVERT: C 698 CYS cc_start: 0.8560 (t) cc_final: 0.8238 (m) REVERT: C 859 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8617 (ttp) REVERT: C 863 MET cc_start: 0.8647 (mtt) cc_final: 0.8194 (mtt) REVERT: C 912 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8675 (p90) REVERT: C 1001 LEU cc_start: 0.9053 (tp) cc_final: 0.8217 (mt) REVERT: C 1069 THR cc_start: 0.8184 (m) cc_final: 0.7909 (p) REVERT: D 698 CYS cc_start: 0.8445 (t) cc_final: 0.8200 (m) REVERT: D 788 MET cc_start: 0.7417 (mmt) cc_final: 0.7020 (ttm) REVERT: D 859 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8628 (ttp) REVERT: D 912 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8660 (p90) REVERT: D 1001 LEU cc_start: 0.9056 (tp) cc_final: 0.8168 (mt) REVERT: D 1069 THR cc_start: 0.8322 (m) cc_final: 0.8059 (p) outliers start: 35 outliers final: 24 residues processed: 270 average time/residue: 0.7964 time to fit residues: 343.8234 Evaluate side-chains 285 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 930 THR Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 758 MET Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 930 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 758 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 930 THR Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain C residue 1016 VAL Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 758 MET Chi-restraints excluded: chain D residue 859 MET Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 930 THR Chi-restraints excluded: chain D residue 1007 ASN Chi-restraints excluded: chain D residue 1016 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 126 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 346 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.154174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101799 restraints weight = 134376.872| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.47 r_work: 0.3185 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29372 Z= 0.238 Angle : 0.478 6.215 40208 Z= 0.263 Chirality : 0.035 0.139 4764 Planarity : 0.003 0.066 4936 Dihedral : 6.224 59.857 5329 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.43 % Allowed : 13.98 % Favored : 84.59 % 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: 1.94 (0.14), residues: 3652 helix: 2.54 (0.10), residues: 2448 sheet: 0.96 (0.44), residues: 148 loop : -1.88 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 525 HIS 0.003 0.001 HIS D 389 PHE 0.015 0.001 PHE C 487 TYR 0.012 0.001 TYR C1022 ARG 0.003 0.000 ARG D 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25671.61 seconds wall clock time: 437 minutes 23.05 seconds (26243.05 seconds total)