Starting phenix.real_space_refine on Sun Jun 29 00:20:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc4_39922/06_2025/8zc4_39922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc4_39922/06_2025/8zc4_39922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zc4_39922/06_2025/8zc4_39922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc4_39922/06_2025/8zc4_39922.map" model { file = "/net/cci-nas-00/data/ceres_data/8zc4_39922/06_2025/8zc4_39922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc4_39922/06_2025/8zc4_39922.cif" } resolution = 3.95 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= 0.034 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 21546 2.51 5 N 5560 2.21 5 O 6590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33840 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7790 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "B" Number of atoms: 7790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7790 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "C" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7778 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "G" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "N" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "Q" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 19.75, per 1000 atoms: 0.58 Number of scatterers: 33840 At special positions: 0 Unit cell: (154.88, 211.2, 247.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 6590 8.00 N 5560 7.00 C 21546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 145 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 145 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 204 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 103 " - pdb=" SG CYS Q 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 154 " - pdb=" SG CYS Q 210 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 154 " - pdb=" SG CYS R 210 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1098 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 10.29 Conformation dependent library (CDL) restraints added in 5.6 seconds 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8002 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 76 sheets defined 17.1% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.095A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.933A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.614A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.748A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.768A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.726A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.606A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.188A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.984A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.535A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.729A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 removed outlier: 3.874A pdb=" N ALA B 419 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP B 420 " --> pdb=" O ASN B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 420' Processing helix chain 'B' and resid 502 through 505 removed outlier: 3.589A pdb=" N HIS B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.839A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.559A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.762A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.519A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.428A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.687A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.768A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.876A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.709A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.615A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.730A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.991A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.570A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.441A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 4.490A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'M' and resid 132 through 138 removed outlier: 3.749A pdb=" N ALA M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 197 Processing helix chain 'N' and resid 132 through 138 removed outlier: 3.640A pdb=" N ALA N 138 " --> pdb=" O GLU N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 199 removed outlier: 3.553A pdb=" N HIS N 199 " --> pdb=" O GLN N 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.687A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 172 No H-bonds generated for 'chain 'Q' and resid 170 through 172' Processing helix chain 'R' and resid 106 through 111 removed outlier: 3.826A pdb=" N GLN R 109 " --> pdb=" O ASN R 106 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG R 110 " --> pdb=" O SER R 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP R 111 " --> pdb=" O CYS R 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 106 through 111' Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing helix chain 'R' and resid 199 through 203 removed outlier: 3.582A pdb=" N LEU R 203 " --> pdb=" O SER R 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.364A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.724A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.122A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.236A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.664A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.650A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.431A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 722 through 727 removed outlier: 3.602A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.880A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.245A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 578 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.728A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.759A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.081A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.100A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 543 removed outlier: 4.014A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.158A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AC9, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.601A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.202A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.709A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.524A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.738A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.823A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.582A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 224 through 228 removed outlier: 5.234A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.053A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.364A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.154A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.716A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.665A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.594A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.728A pdb=" N THR G 108 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY G 12 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 18 through 23 removed outlier: 4.097A pdb=" N VAL G 18 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE G 76 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 20 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER G 66 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 45 through 49 removed outlier: 4.958A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP G 93 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY G 98 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.500A pdb=" N SER G 148 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR G 127 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 141 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS G 145 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP G 149 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.500A pdb=" N SER G 148 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR G 127 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL G 144 " --> pdb=" O PHE G 129 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 141 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS G 145 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP G 149 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR G 183 " --> pdb=" O ASP G 149 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA G 184 " --> pdb=" O SER G 176 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 176 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 157 through 160 removed outlier: 4.199A pdb=" N VAL G 206 " --> pdb=" O VAL G 213 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 213 " --> pdb=" O VAL G 206 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.511A pdb=" N CYS H 22 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 46 through 50 removed outlier: 4.640A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 46 through 50 removed outlier: 4.640A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 150 through 159 removed outlier: 3.503A pdb=" N SER H 194 " --> pdb=" O CYS H 154 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP H 158 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 164 through 168 removed outlier: 3.750A pdb=" N THR H 165 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN H 213 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS H 210 " --> pdb=" O LYS H 223 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.534A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.534A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP M 93 " --> pdb=" O GLY M 98 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY M 98 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG5, first strand: chain 'M' and resid 125 through 129 removed outlier: 3.802A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP M 149 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR M 183 " --> pdb=" O ASP M 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA M 184 " --> pdb=" O SER M 176 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 157 through 160 removed outlier: 3.775A pdb=" N TYR M 202 " --> pdb=" O VAL M 217 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS M 204 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS M 215 " --> pdb=" O CYS M 204 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.662A pdb=" N THR N 108 " --> pdb=" O ALA N 10 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 17 through 23 Processing sheet with id=AG9, first strand: chain 'N' and resid 46 through 49 removed outlier: 3.791A pdb=" N GLN N 38 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.513A pdb=" N SER N 125 " --> pdb=" O SER N 148 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER N 148 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU N 146 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL N 144 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA N 141 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS N 145 " --> pdb=" O SER N 187 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER N 187 " --> pdb=" O CYS N 145 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.513A pdb=" N SER N 125 " --> pdb=" O SER N 148 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER N 148 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU N 146 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL N 144 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 147 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR N 183 " --> pdb=" O ASP N 149 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 157 through 160 removed outlier: 3.897A pdb=" N ALA N 158 " --> pdb=" O GLN N 205 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN N 205 " --> pdb=" O ALA N 158 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS N 160 " --> pdb=" O SER N 203 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER N 203 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR N 202 " --> pdb=" O VAL N 217 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 17 through 18 Processing sheet with id=AH5, first strand: chain 'Q' and resid 45 through 47 removed outlier: 3.908A pdb=" N GLU Q 46 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG Q 38 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL Q 93 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 150 through 156 removed outlier: 3.538A pdb=" N CYS Q 154 " --> pdb=" O SER Q 194 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER Q 194 " --> pdb=" O CYS Q 154 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU Q 192 " --> pdb=" O VAL Q 156 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER Q 193 " --> pdb=" O PHE Q 180 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL Q 195 " --> pdb=" O HIS Q 178 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N HIS Q 178 " --> pdb=" O VAL Q 195 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 165 through 168 removed outlier: 4.244A pdb=" N THR Q 165 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN Q 213 " --> pdb=" O THR Q 165 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 6 through 7 removed outlier: 3.701A pdb=" N SER R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR R 69 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.628A pdb=" N LYS R 12 " --> pdb=" O THR R 124 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 121 " --> pdb=" O TYR R 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA R 92 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.628A pdb=" N LYS R 12 " --> pdb=" O THR R 124 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 121 " --> pdb=" O TYR R 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA R 92 " --> pdb=" O VAL R 123 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 134 through 136 removed outlier: 3.694A pdb=" N VAL R 198 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 152 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR R 190 " --> pdb=" O ASP R 158 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 134 through 136 removed outlier: 3.694A pdb=" N VAL R 198 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 152 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR R 190 " --> pdb=" O ASP R 158 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER R 191 " --> pdb=" O VAL R 183 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 165 through 168 removed outlier: 4.168A pdb=" N VAL R 212 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL R 221 " --> pdb=" O VAL R 212 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS R 214 " --> pdb=" O THR R 219 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR R 219 " --> pdb=" O HIS R 214 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 2859 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: 18.86 Time building geometry restraints manager: 11.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10658 1.34 - 1.47: 8784 1.47 - 1.60: 15019 1.60 - 1.72: 0 1.72 - 1.85: 180 Bond restraints: 34641 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.41e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.99e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" CA GLN B 755 " pdb=" C GLN B 755 " ideal model delta sigma weight residual 1.522 1.491 0.030 1.43e-02 4.89e+03 4.52e+00 bond pdb=" CA ASP C1139 " pdb=" C ASP C1139 " ideal model delta sigma weight residual 1.526 1.502 0.024 1.25e-02 6.40e+03 3.55e+00 ... (remaining 34636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 45928 2.00 - 4.00: 1052 4.00 - 6.00: 129 6.00 - 8.00: 46 8.00 - 10.00: 11 Bond angle restraints: 47166 Sorted by residual: angle pdb=" N ASP C1118 " pdb=" CA ASP C1118 " pdb=" C ASP C1118 " ideal model delta sigma weight residual 113.02 103.36 9.66 1.49e+00 4.50e-01 4.21e+01 angle pdb=" N THR R 124 " pdb=" CA THR R 124 " pdb=" C THR R 124 " ideal model delta sigma weight residual 109.24 118.23 -8.99 1.51e+00 4.39e-01 3.54e+01 angle pdb=" N ASN C1119 " pdb=" CA ASN C1119 " pdb=" C ASN C1119 " ideal model delta sigma weight residual 113.89 105.55 8.34 1.58e+00 4.01e-01 2.79e+01 angle pdb=" N GLN B 755 " pdb=" CA GLN B 755 " pdb=" C GLN B 755 " ideal model delta sigma weight residual 112.87 107.51 5.36 1.20e+00 6.94e-01 2.00e+01 angle pdb=" C ASP C1139 " pdb=" N PRO C1140 " pdb=" CA PRO C1140 " ideal model delta sigma weight residual 120.31 115.95 4.36 9.80e-01 1.04e+00 1.98e+01 ... (remaining 47161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 19199 17.93 - 35.86: 1669 35.86 - 53.80: 299 53.80 - 71.73: 68 71.73 - 89.66: 38 Dihedral angle restraints: 21273 sinusoidal: 8841 harmonic: 12432 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -172.80 86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.05 -81.95 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.87 -80.13 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 21270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4363 0.059 - 0.119: 1005 0.119 - 0.178: 99 0.178 - 0.238: 5 0.238 - 0.297: 5 Chirality restraints: 5477 Sorted by residual: chirality pdb=" CB ILE B 101 " pdb=" CA ILE B 101 " pdb=" CG1 ILE B 101 " pdb=" CG2 ILE B 101 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE A 410 " pdb=" CA ILE A 410 " pdb=" CG1 ILE A 410 " pdb=" CG2 ILE A 410 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 5474 not shown) Planarity restraints: 6037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 90 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C VAL C 90 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL C 90 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR C 91 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.057 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO C 987 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.054 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO B 987 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.045 5.00e-02 4.00e+02 ... (remaining 6034 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4212 2.76 - 3.29: 30009 3.29 - 3.83: 54154 3.83 - 4.36: 57843 4.36 - 4.90: 105108 Nonbonded interactions: 251326 Sorted by model distance: nonbonded pdb=" OG1 THR A 912 " pdb=" OE1 GLN A1106 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR M 35 " pdb=" O ARG Q 110 " model vdw 2.287 3.040 nonbonded pdb=" O PRO B 85 " pdb=" OH TYR B 269 " model vdw 2.288 3.040 ... (remaining 251321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1307)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1147 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'Q' selection = chain 'R' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.810 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: 0.020 Extract box with map and model: 1.360 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 83.030 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.460 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: 0.020 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 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 : 0.004 0.046 34740 Z= 0.178 Angle : 0.716 10.701 47412 Z= 0.364 Chirality : 0.049 0.297 5477 Planarity : 0.006 0.085 6001 Dihedral : 13.867 89.660 13118 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.57 (0.12), residues: 4193 helix: 0.22 (0.20), residues: 639 sheet: -0.11 (0.17), residues: 947 loop : -1.83 (0.11), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 47 HIS 0.005 0.001 HIS A1064 PHE 0.031 0.001 PHE Q 29 TYR 0.024 0.001 TYR C 489 ARG 0.005 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 36) link_NAG-ASN : angle 2.10197 ( 108) link_BETA1-4 : bond 0.00570 ( 12) link_BETA1-4 : angle 2.08019 ( 36) hydrogen bonds : bond 0.24051 ( 1021) hydrogen bonds : angle 9.02905 ( 2859) SS BOND : bond 0.00390 ( 51) SS BOND : angle 1.46661 ( 102) covalent geometry : bond 0.00351 (34641) covalent geometry : angle 0.70540 (47166) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 5.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7199 (tp-100) cc_final: 0.6861 (pm20) REVERT: A 533 LEU cc_start: 0.7145 (mm) cc_final: 0.6912 (mm) REVERT: A 1029 MET cc_start: 0.9319 (tpp) cc_final: 0.9081 (tpp) REVERT: A 1141 LEU cc_start: 0.8324 (mm) cc_final: 0.8085 (mm) REVERT: B 269 TYR cc_start: 0.8052 (m-80) cc_final: 0.7777 (m-80) REVERT: B 1017 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 135 PHE cc_start: 0.5785 (m-80) cc_final: 0.5518 (m-80) REVERT: C 697 MET cc_start: 0.8278 (tpp) cc_final: 0.7900 (mmt) REVERT: C 823 PHE cc_start: 0.7896 (t80) cc_final: 0.7631 (t80) REVERT: C 1029 MET cc_start: 0.9124 (tpp) cc_final: 0.8835 (tpp) outliers start: 1 outliers final: 1 residues processed: 272 average time/residue: 0.5809 time to fit residues: 275.2075 Evaluate side-chains 183 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 6.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 30.0000 chunk 322 optimal weight: 30.0000 chunk 179 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 333 optimal weight: 40.0000 chunk 129 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 386 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 907 ASN A1010 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 271 GLN B 505 HIS B 755 GLN B 926 GLN B 955 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 505 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN R 39 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.204778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.191222 restraints weight = 61903.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.188955 restraints weight = 84280.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.187207 restraints weight = 93293.976| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 34740 Z= 0.374 Angle : 0.790 12.083 47412 Z= 0.404 Chirality : 0.050 0.284 5477 Planarity : 0.006 0.083 6001 Dihedral : 6.078 54.726 5573 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.13 % Allowed : 9.23 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.66 (0.12), residues: 4193 helix: 0.02 (0.19), residues: 666 sheet: -0.32 (0.17), residues: 970 loop : -1.81 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Q 47 HIS 0.006 0.001 HIS A1048 PHE 0.032 0.003 PHE C 92 TYR 0.024 0.002 TYR C1067 ARG 0.010 0.001 ARG Q 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 36) link_NAG-ASN : angle 2.16690 ( 108) link_BETA1-4 : bond 0.00375 ( 12) link_BETA1-4 : angle 1.37996 ( 36) hydrogen bonds : bond 0.06458 ( 1021) hydrogen bonds : angle 6.69159 ( 2859) SS BOND : bond 0.00760 ( 51) SS BOND : angle 1.77984 ( 102) covalent geometry : bond 0.00891 (34641) covalent geometry : angle 0.77949 (47166) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7316 (tp-100) cc_final: 0.6984 (pm20) REVERT: A 227 VAL cc_start: 0.8269 (m) cc_final: 0.7957 (t) REVERT: A 533 LEU cc_start: 0.6760 (mm) cc_final: 0.6557 (mm) REVERT: B 816 SER cc_start: 0.8423 (p) cc_final: 0.7993 (m) REVERT: C 508 TYR cc_start: 0.8180 (m-80) cc_final: 0.7589 (m-80) REVERT: C 823 PHE cc_start: 0.8214 (t80) cc_final: 0.7995 (t80) REVERT: Q 31 ASP cc_start: 0.7836 (p0) cc_final: 0.7464 (p0) REVERT: Q 32 TYR cc_start: 0.8406 (m-80) cc_final: 0.8151 (m-10) outliers start: 42 outliers final: 31 residues processed: 239 average time/residue: 0.5055 time to fit residues: 205.3644 Evaluate side-chains 202 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain R residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 286 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 312 optimal weight: 7.9990 chunk 320 optimal weight: 40.0000 chunk 317 optimal weight: 40.0000 chunk 128 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 357 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 563 GLN B 196 ASN B 474 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 394 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN R 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.208806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.194039 restraints weight = 62170.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.192320 restraints weight = 88560.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.190623 restraints weight = 92475.686| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34740 Z= 0.182 Angle : 0.599 11.343 47412 Z= 0.302 Chirality : 0.045 0.246 5477 Planarity : 0.005 0.068 6001 Dihedral : 5.539 57.965 5573 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.48 % Allowed : 12.32 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.42 (0.13), residues: 4193 helix: 0.77 (0.21), residues: 653 sheet: -0.36 (0.17), residues: 994 loop : -1.73 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Q 113 HIS 0.005 0.001 HIS Q 35 PHE 0.021 0.002 PHE C 92 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 36) link_NAG-ASN : angle 1.88195 ( 108) link_BETA1-4 : bond 0.00317 ( 12) link_BETA1-4 : angle 1.35588 ( 36) hydrogen bonds : bond 0.05060 ( 1021) hydrogen bonds : angle 5.97485 ( 2859) SS BOND : bond 0.00375 ( 51) SS BOND : angle 1.36228 ( 102) covalent geometry : bond 0.00429 (34641) covalent geometry : angle 0.58887 (47166) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7243 (tp-100) cc_final: 0.6884 (pm20) REVERT: A 227 VAL cc_start: 0.8103 (m) cc_final: 0.7800 (t) REVERT: A 533 LEU cc_start: 0.6770 (mm) cc_final: 0.6547 (mm) REVERT: A 1029 MET cc_start: 0.8648 (ttm) cc_final: 0.8233 (ttm) REVERT: C 508 TYR cc_start: 0.8073 (m-80) cc_final: 0.7556 (m-80) REVERT: C 823 PHE cc_start: 0.8094 (t80) cc_final: 0.7884 (t80) REVERT: C 878 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8323 (mm) REVERT: C 904 TYR cc_start: 0.8125 (m-80) cc_final: 0.7512 (m-10) REVERT: Q 31 ASP cc_start: 0.7901 (p0) cc_final: 0.7549 (p0) REVERT: Q 32 TYR cc_start: 0.8229 (m-80) cc_final: 0.8024 (m-10) outliers start: 55 outliers final: 38 residues processed: 238 average time/residue: 0.4292 time to fit residues: 175.4029 Evaluate side-chains 207 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain R residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 245 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 376 optimal weight: 30.0000 chunk 287 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 128 optimal weight: 0.0040 chunk 166 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 755 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.209367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.194653 restraints weight = 61902.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.193300 restraints weight = 89093.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.191978 restraints weight = 88652.481| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34740 Z= 0.159 Angle : 0.575 15.666 47412 Z= 0.287 Chirality : 0.044 0.248 5477 Planarity : 0.004 0.081 6001 Dihedral : 5.168 59.458 5573 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.26 % Allowed : 13.50 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.28 (0.13), residues: 4193 helix: 1.08 (0.21), residues: 647 sheet: -0.39 (0.16), residues: 1027 loop : -1.64 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Q 113 HIS 0.005 0.001 HIS G 99 PHE 0.019 0.001 PHE C 92 TYR 0.024 0.001 TYR C 904 ARG 0.004 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 36) link_NAG-ASN : angle 1.82602 ( 108) link_BETA1-4 : bond 0.00294 ( 12) link_BETA1-4 : angle 1.35356 ( 36) hydrogen bonds : bond 0.04536 ( 1021) hydrogen bonds : angle 5.60637 ( 2859) SS BOND : bond 0.00384 ( 51) SS BOND : angle 1.20808 ( 102) covalent geometry : bond 0.00374 (34641) covalent geometry : angle 0.56570 (47166) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 187 time to evaluate : 4.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7946 (tp) REVERT: A 533 LEU cc_start: 0.6762 (mm) cc_final: 0.6546 (mm) REVERT: B 759 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6711 (t80) REVERT: C 118 LEU cc_start: 0.7032 (tt) cc_final: 0.6130 (mp) REVERT: C 508 TYR cc_start: 0.8047 (m-80) cc_final: 0.7569 (m-80) REVERT: C 523 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8159 (t) REVERT: C 697 MET cc_start: 0.8531 (tpp) cc_final: 0.8247 (tpt) REVERT: C 731 MET cc_start: 0.8060 (ptt) cc_final: 0.7690 (ptt) REVERT: C 823 PHE cc_start: 0.8105 (t80) cc_final: 0.7852 (t80) REVERT: C 878 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8235 (mm) REVERT: C 1029 MET cc_start: 0.9262 (tpp) cc_final: 0.9007 (tpp) REVERT: H 81 MET cc_start: 0.1206 (mmm) cc_final: 0.0747 (mmm) REVERT: Q 31 ASP cc_start: 0.7874 (p0) cc_final: 0.7492 (p0) REVERT: Q 32 TYR cc_start: 0.8253 (m-80) cc_final: 0.8033 (m-80) REVERT: Q 39 GLN cc_start: 0.1978 (tp40) cc_final: 0.1492 (tp40) outliers start: 84 outliers final: 60 residues processed: 261 average time/residue: 0.4480 time to fit residues: 202.2346 Evaluate side-chains 245 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 181 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 390 optimal weight: 20.0000 chunk 319 optimal weight: 0.0970 chunk 307 optimal weight: 40.0000 chunk 194 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 352 optimal weight: 40.0000 chunk 226 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 920 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.208935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.194867 restraints weight = 61997.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.192722 restraints weight = 76663.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.190640 restraints weight = 92569.127| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34740 Z= 0.174 Angle : 0.588 14.827 47412 Z= 0.294 Chirality : 0.045 0.248 5477 Planarity : 0.004 0.070 6001 Dihedral : 5.103 58.033 5573 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.77 % Allowed : 14.01 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.26 (0.13), residues: 4193 helix: 1.14 (0.21), residues: 642 sheet: -0.39 (0.16), residues: 1042 loop : -1.63 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Q 113 HIS 0.012 0.001 HIS G 99 PHE 0.018 0.001 PHE C 92 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 36) link_NAG-ASN : angle 1.89531 ( 108) link_BETA1-4 : bond 0.00301 ( 12) link_BETA1-4 : angle 1.38319 ( 36) hydrogen bonds : bond 0.04522 ( 1021) hydrogen bonds : angle 5.48166 ( 2859) SS BOND : bond 0.00372 ( 51) SS BOND : angle 1.78376 ( 102) covalent geometry : bond 0.00413 (34641) covalent geometry : angle 0.57578 (47166) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 187 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7161 (tp-100) cc_final: 0.6921 (pm20) REVERT: A 235 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7939 (tp) REVERT: A 533 LEU cc_start: 0.6795 (mm) cc_final: 0.6545 (mm) REVERT: A 1029 MET cc_start: 0.8499 (ttm) cc_final: 0.8240 (ttm) REVERT: A 1031 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: B 759 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6817 (t80) REVERT: C 508 TYR cc_start: 0.8066 (m-80) cc_final: 0.7634 (m-80) REVERT: C 523 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8118 (t) REVERT: C 731 MET cc_start: 0.8044 (ptt) cc_final: 0.7668 (ptt) REVERT: C 823 PHE cc_start: 0.8129 (t80) cc_final: 0.7861 (t80) REVERT: C 878 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (mm) REVERT: C 1029 MET cc_start: 0.9252 (tpp) cc_final: 0.9035 (tpp) REVERT: G 92 TRP cc_start: 0.2393 (t-100) cc_final: 0.2003 (m-90) REVERT: H 81 MET cc_start: 0.1028 (mmm) cc_final: 0.0606 (mmm) REVERT: Q 31 ASP cc_start: 0.7892 (p0) cc_final: 0.7510 (p0) REVERT: Q 32 TYR cc_start: 0.8329 (m-80) cc_final: 0.8107 (m-80) outliers start: 103 outliers final: 77 residues processed: 276 average time/residue: 0.4207 time to fit residues: 201.7516 Evaluate side-chains 256 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 174 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 117 TRP Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 186 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 268 optimal weight: 0.2980 chunk 114 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 353 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.211118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.197336 restraints weight = 61727.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.195116 restraints weight = 75342.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.193074 restraints weight = 90781.143| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34740 Z= 0.116 Angle : 0.540 12.221 47412 Z= 0.269 Chirality : 0.043 0.239 5477 Planarity : 0.004 0.065 6001 Dihedral : 4.775 51.961 5572 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.47 % Allowed : 15.09 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.10 (0.13), residues: 4193 helix: 1.40 (0.21), residues: 644 sheet: -0.31 (0.16), residues: 1033 loop : -1.56 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP Q 113 HIS 0.004 0.000 HIS B1048 PHE 0.015 0.001 PHE C 86 TYR 0.029 0.001 TYR M 88 ARG 0.003 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 36) link_NAG-ASN : angle 1.74097 ( 108) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.39002 ( 36) hydrogen bonds : bond 0.04028 ( 1021) hydrogen bonds : angle 5.21564 ( 2859) SS BOND : bond 0.00400 ( 51) SS BOND : angle 1.18844 ( 102) covalent geometry : bond 0.00268 (34641) covalent geometry : angle 0.53075 (47166) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 205 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 LEU cc_start: 0.6763 (mm) cc_final: 0.6512 (mm) REVERT: A 756 TYR cc_start: 0.7908 (m-80) cc_final: 0.7633 (m-80) REVERT: A 1031 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: B 759 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6724 (t80) REVERT: C 508 TYR cc_start: 0.7982 (m-80) cc_final: 0.7556 (m-80) REVERT: C 523 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8248 (t) REVERT: C 697 MET cc_start: 0.8343 (tpp) cc_final: 0.8026 (tpt) REVERT: C 731 MET cc_start: 0.8039 (ptt) cc_final: 0.7756 (ptt) REVERT: C 823 PHE cc_start: 0.8027 (t80) cc_final: 0.7768 (t80) REVERT: C 878 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8142 (mm) REVERT: C 881 THR cc_start: 0.8693 (t) cc_final: 0.6956 (p) REVERT: C 1029 MET cc_start: 0.9258 (tpp) cc_final: 0.9019 (tpp) REVERT: H 81 MET cc_start: 0.1033 (mmm) cc_final: 0.0719 (mmm) REVERT: Q 31 ASP cc_start: 0.7854 (p0) cc_final: 0.7508 (p0) outliers start: 92 outliers final: 61 residues processed: 284 average time/residue: 0.4079 time to fit residues: 201.2304 Evaluate side-chains 250 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 185 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 324 optimal weight: 20.0000 chunk 27 optimal weight: 40.0000 chunk 94 optimal weight: 2.9990 chunk 342 optimal weight: 0.0870 chunk 144 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 345 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1106 GLN B 196 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.212842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.199431 restraints weight = 62009.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.197161 restraints weight = 73965.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.194650 restraints weight = 78201.369| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34740 Z= 0.099 Angle : 0.534 12.396 47412 Z= 0.265 Chirality : 0.043 0.232 5477 Planarity : 0.004 0.063 6001 Dihedral : 4.525 49.856 5572 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.02 % Allowed : 16.22 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4193 helix: 1.58 (0.22), residues: 644 sheet: -0.22 (0.16), residues: 1023 loop : -1.49 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP Q 113 HIS 0.004 0.001 HIS Q 35 PHE 0.017 0.001 PHE M 63 TYR 0.032 0.001 TYR M 88 ARG 0.007 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 36) link_NAG-ASN : angle 1.66431 ( 108) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 1.40150 ( 36) hydrogen bonds : bond 0.03705 ( 1021) hydrogen bonds : angle 5.00890 ( 2859) SS BOND : bond 0.00341 ( 51) SS BOND : angle 1.26906 ( 102) covalent geometry : bond 0.00224 (34641) covalent geometry : angle 0.52421 (47166) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 196 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 LEU cc_start: 0.6808 (mm) cc_final: 0.6543 (mm) REVERT: A 574 ASP cc_start: 0.7810 (p0) cc_final: 0.7542 (p0) REVERT: A 756 TYR cc_start: 0.7781 (m-80) cc_final: 0.7565 (m-80) REVERT: A 1031 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: B 759 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6526 (t80) REVERT: C 508 TYR cc_start: 0.7909 (m-80) cc_final: 0.7516 (m-80) REVERT: C 523 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8230 (t) REVERT: C 823 PHE cc_start: 0.7934 (t80) cc_final: 0.7615 (t80) REVERT: C 878 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8259 (mm) REVERT: C 881 THR cc_start: 0.8621 (t) cc_final: 0.6845 (p) REVERT: C 1029 MET cc_start: 0.9331 (tpp) cc_final: 0.9071 (tpp) REVERT: H 81 MET cc_start: 0.1121 (mmm) cc_final: 0.0823 (mmm) REVERT: N 61 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6848 (mt-10) outliers start: 75 outliers final: 58 residues processed: 262 average time/residue: 0.4281 time to fit residues: 193.9501 Evaluate side-chains 241 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 283 optimal weight: 0.6980 chunk 373 optimal weight: 40.0000 chunk 225 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 318 optimal weight: 30.0000 chunk 290 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 386 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.209132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.194364 restraints weight = 61855.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.193484 restraints weight = 90049.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.192035 restraints weight = 85359.018| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34740 Z= 0.185 Angle : 0.590 12.241 47412 Z= 0.295 Chirality : 0.045 0.243 5477 Planarity : 0.004 0.063 6001 Dihedral : 4.731 45.741 5572 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.66 % Allowed : 16.27 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.11 (0.13), residues: 4193 helix: 1.29 (0.21), residues: 644 sheet: -0.38 (0.16), residues: 1063 loop : -1.50 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Q 36 HIS 0.004 0.001 HIS Q 35 PHE 0.021 0.002 PHE C 92 TYR 0.021 0.001 TYR M 88 ARG 0.005 0.000 ARG N 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 36) link_NAG-ASN : angle 1.75376 ( 108) link_BETA1-4 : bond 0.00273 ( 12) link_BETA1-4 : angle 1.38887 ( 36) hydrogen bonds : bond 0.04386 ( 1021) hydrogen bonds : angle 5.17053 ( 2859) SS BOND : bond 0.00420 ( 51) SS BOND : angle 1.41591 ( 102) covalent geometry : bond 0.00440 (34641) covalent geometry : angle 0.58091 (47166) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 185 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7373 (t) REVERT: A 533 LEU cc_start: 0.6694 (mm) cc_final: 0.6423 (mm) REVERT: A 756 TYR cc_start: 0.8008 (m-80) cc_final: 0.7796 (m-80) REVERT: A 1031 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: B 759 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6717 (t80) REVERT: C 158 ARG cc_start: 0.5577 (mtt180) cc_final: 0.5247 (mtt180) REVERT: C 508 TYR cc_start: 0.8022 (m-80) cc_final: 0.7641 (m-80) REVERT: C 523 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8420 (t) REVERT: C 823 PHE cc_start: 0.8058 (t80) cc_final: 0.7757 (t80) REVERT: C 878 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8274 (mm) REVERT: C 1029 MET cc_start: 0.9245 (tpp) cc_final: 0.9012 (tpp) REVERT: H 81 MET cc_start: 0.1164 (mmm) cc_final: 0.0852 (mmm) outliers start: 99 outliers final: 86 residues processed: 276 average time/residue: 0.3961 time to fit residues: 189.6317 Evaluate side-chains 266 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 175 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain Q residue 117 TRP Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 147 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 423 optimal weight: 0.0770 chunk 420 optimal weight: 50.0000 chunk 53 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 346 optimal weight: 7.9990 chunk 118 optimal weight: 0.0970 chunk 163 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.212211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.198697 restraints weight = 62059.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.196395 restraints weight = 73482.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.194042 restraints weight = 81407.617| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34740 Z= 0.106 Angle : 0.541 13.328 47412 Z= 0.269 Chirality : 0.043 0.230 5477 Planarity : 0.004 0.062 6001 Dihedral : 4.504 48.877 5572 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.10 % Allowed : 17.24 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4193 helix: 1.61 (0.21), residues: 644 sheet: -0.22 (0.16), residues: 1034 loop : -1.46 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP Q 113 HIS 0.004 0.001 HIS G 99 PHE 0.017 0.001 PHE M 63 TYR 0.034 0.001 TYR M 88 ARG 0.007 0.000 ARG N 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 36) link_NAG-ASN : angle 1.64432 ( 108) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 1.40406 ( 36) hydrogen bonds : bond 0.03764 ( 1021) hydrogen bonds : angle 4.94567 ( 2859) SS BOND : bond 0.00345 ( 51) SS BOND : angle 1.23832 ( 102) covalent geometry : bond 0.00243 (34641) covalent geometry : angle 0.53216 (47166) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 186 time to evaluate : 4.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7351 (t) REVERT: A 533 LEU cc_start: 0.6820 (mm) cc_final: 0.6550 (mm) REVERT: A 756 TYR cc_start: 0.7804 (m-80) cc_final: 0.7594 (m-80) REVERT: A 1031 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: B 759 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6734 (t80) REVERT: C 118 LEU cc_start: 0.7690 (tt) cc_final: 0.7130 (pp) REVERT: C 158 ARG cc_start: 0.5513 (mtt180) cc_final: 0.5185 (mtt180) REVERT: C 508 TYR cc_start: 0.7904 (m-80) cc_final: 0.7519 (m-80) REVERT: C 523 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8314 (t) REVERT: C 697 MET cc_start: 0.8300 (tpp) cc_final: 0.7873 (tpp) REVERT: C 823 PHE cc_start: 0.7936 (t80) cc_final: 0.7604 (t80) REVERT: C 878 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8263 (mm) REVERT: C 881 THR cc_start: 0.8608 (t) cc_final: 0.6828 (p) REVERT: C 1029 MET cc_start: 0.9305 (tpp) cc_final: 0.9075 (tpp) REVERT: H 81 MET cc_start: 0.1067 (mmm) cc_final: 0.0799 (mmm) REVERT: N 61 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7244 (mt-10) outliers start: 78 outliers final: 63 residues processed: 256 average time/residue: 0.5037 time to fit residues: 222.1853 Evaluate side-chains 247 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 7.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain Q residue 117 TRP Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 26 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 419 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 346 optimal weight: 9.9990 chunk 390 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 381 optimal weight: 0.1980 chunk 171 optimal weight: 0.6980 chunk 243 optimal weight: 0.0870 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.210062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.195446 restraints weight = 61845.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.193699 restraints weight = 88147.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.192374 restraints weight = 91978.330| |-----------------------------------------------------------------------------| r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34740 Z= 0.160 Angle : 0.575 16.332 47412 Z= 0.285 Chirality : 0.044 0.330 5477 Planarity : 0.004 0.063 6001 Dihedral : 4.589 46.841 5572 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.26 % Allowed : 17.24 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.01 (0.13), residues: 4193 helix: 1.47 (0.21), residues: 644 sheet: -0.31 (0.16), residues: 1069 loop : -1.48 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP Q 113 HIS 0.004 0.001 HIS G 99 PHE 0.021 0.001 PHE R 136 TYR 0.024 0.001 TYR M 88 ARG 0.006 0.000 ARG N 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 36) link_NAG-ASN : angle 1.69487 ( 108) link_BETA1-4 : bond 0.00299 ( 12) link_BETA1-4 : angle 1.38182 ( 36) hydrogen bonds : bond 0.04103 ( 1021) hydrogen bonds : angle 5.02602 ( 2859) SS BOND : bond 0.00366 ( 51) SS BOND : angle 1.31255 ( 102) covalent geometry : bond 0.00380 (34641) covalent geometry : angle 0.56646 (47166) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8386 Ramachandran restraints generated. 4193 Oldfield, 0 Emsley, 4193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 179 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.7766 (OUTLIER) cc_final: 0.7463 (t) REVERT: A 533 LEU cc_start: 0.6761 (mm) cc_final: 0.6502 (mm) REVERT: A 1031 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: B 759 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6713 (t80) REVERT: C 118 LEU cc_start: 0.7799 (tt) cc_final: 0.7173 (pp) REVERT: C 158 ARG cc_start: 0.5469 (mtt180) cc_final: 0.5201 (mtt180) REVERT: C 508 TYR cc_start: 0.7981 (m-80) cc_final: 0.7558 (m-80) REVERT: C 523 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8422 (t) REVERT: C 823 PHE cc_start: 0.8024 (t80) cc_final: 0.7718 (t80) REVERT: C 878 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8304 (mm) REVERT: C 1029 MET cc_start: 0.9321 (tpp) cc_final: 0.9091 (tpp) REVERT: H 81 MET cc_start: 0.0983 (mmm) cc_final: 0.0709 (mmm) outliers start: 84 outliers final: 77 residues processed: 255 average time/residue: 0.4308 time to fit residues: 189.4031 Evaluate side-chains 256 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 174 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain Q residue 117 TRP Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 190 optimal weight: 4.9990 chunk 276 optimal weight: 0.0670 chunk 410 optimal weight: 6.9990 chunk 300 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 66 optimal weight: 0.0040 chunk 99 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 overall best weight: 1.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.209353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.194727 restraints weight = 61986.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.193225 restraints weight = 87628.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.191711 restraints weight = 87275.706| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34740 Z= 0.175 Angle : 0.590 19.163 47412 Z= 0.293 Chirality : 0.045 0.280 5477 Planarity : 0.004 0.063 6001 Dihedral : 4.709 45.648 5572 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.42 % Allowed : 17.32 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.06 (0.13), residues: 4193 helix: 1.37 (0.21), residues: 644 sheet: -0.31 (0.16), residues: 1047 loop : -1.50 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP Q 113 HIS 0.003 0.001 HIS G 99 PHE 0.022 0.001 PHE C 456 TYR 0.018 0.001 TYR C 501 ARG 0.012 0.000 ARG M 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 36) link_NAG-ASN : angle 1.73907 ( 108) link_BETA1-4 : bond 0.00296 ( 12) link_BETA1-4 : angle 1.40027 ( 36) hydrogen bonds : bond 0.04302 ( 1021) hydrogen bonds : angle 5.07865 ( 2859) SS BOND : bond 0.00380 ( 51) SS BOND : angle 1.31155 ( 102) covalent geometry : bond 0.00416 (34641) covalent geometry : angle 0.58114 (47166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9773.67 seconds wall clock time: 178 minutes 38.99 seconds (10718.99 seconds total)