Starting phenix.real_space_refine on Fri May 30 15:12:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc4_39922/05_2025/8zc4_39922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc4_39922/05_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_39922/05_2025/8zc4_39922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc4_39922/05_2025/8zc4_39922.map" model { file = "/net/cci-nas-00/data/ceres_data/8zc4_39922/05_2025/8zc4_39922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc4_39922/05_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 19.84, per 1000 atoms: 0.59 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: 9.08 Conformation dependent library (CDL) restraints added in 4.5 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: 5.55 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: 16.49 Time building geometry restraints manager: 10.41 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 79.700 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.210 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.100 ------------------------------------------------------------------------------- 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 : 3.691 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: 0.4297 time to fit residues: 195.9629 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 : 3.280 ------------------------------------------------------------------------------- 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 = 61903.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.188955 restraints weight = 84279.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.187207 restraints weight = 93289.219| |-----------------------------------------------------------------------------| 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 : 3.599 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: 0.6556 (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: 0.4262 time to fit residues: 172.6215 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 : 3.585 ------------------------------------------------------------------------------- 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: 1.9990 chunk 312 optimal weight: 7.9990 chunk 320 optimal weight: 40.0000 chunk 317 optimal weight: 40.0000 chunk 128 optimal weight: 8.9990 chunk 367 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 357 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 563 GLN A 907 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.209808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.195243 restraints weight = 62179.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.193714 restraints weight = 86231.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.192148 restraints weight = 86233.879| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34740 Z= 0.153 Angle : 0.580 11.145 47412 Z= 0.293 Chirality : 0.044 0.245 5477 Planarity : 0.004 0.069 6001 Dihedral : 5.453 58.747 5573 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.29 % Allowed : 12.16 % Favored : 86.55 % 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: -1.35 (0.13), residues: 4193 helix: 0.91 (0.21), residues: 647 sheet: -0.32 (0.17), residues: 986 loop : -1.70 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 113 HIS 0.004 0.001 HIS Q 35 PHE 0.019 0.001 PHE C 92 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 36) link_NAG-ASN : angle 1.84068 ( 108) link_BETA1-4 : bond 0.00332 ( 12) link_BETA1-4 : angle 1.35279 ( 36) hydrogen bonds : bond 0.04919 ( 1021) hydrogen bonds : angle 5.92492 ( 2859) SS BOND : bond 0.00354 ( 51) SS BOND : angle 1.31712 ( 102) covalent geometry : bond 0.00357 (34641) covalent geometry : angle 0.57031 (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 242 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7206 (tp-100) cc_final: 0.6839 (pm20) REVERT: A 227 VAL cc_start: 0.8091 (m) cc_final: 0.7808 (t) REVERT: A 533 LEU cc_start: 0.6750 (mm) cc_final: 0.6534 (mm) REVERT: A 1029 MET cc_start: 0.8598 (ttm) cc_final: 0.8175 (ttm) REVERT: C 508 TYR cc_start: 0.8048 (m-80) cc_final: 0.7573 (m-80) REVERT: C 823 PHE cc_start: 0.8079 (t80) cc_final: 0.7804 (t80) REVERT: C 878 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8264 (mm) REVERT: C 904 TYR cc_start: 0.8087 (m-80) cc_final: 0.7613 (m-10) REVERT: Q 31 ASP cc_start: 0.7880 (p0) cc_final: 0.7519 (p0) REVERT: Q 32 TYR cc_start: 0.8152 (m-80) cc_final: 0.7943 (m-10) outliers start: 48 outliers final: 33 residues processed: 237 average time/residue: 0.4233 time to fit residues: 170.2463 Evaluate side-chains 207 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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 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 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 441 LEU Chi-restraints excluded: chain C residue 524 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 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 G residue 99 HIS 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: 3.9990 chunk 78 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 227 optimal weight: 0.0070 chunk 376 optimal weight: 7.9990 chunk 287 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 128 optimal weight: 0.0770 chunk 166 optimal weight: 2.9990 chunk 379 optimal weight: 20.0000 overall best weight: 0.7958 ------------------------------------------------------------------------------- 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 B 196 ASN B 755 GLN B 965 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.211985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.197413 restraints weight = 61922.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.195316 restraints weight = 88295.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.194418 restraints weight = 82575.496| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34740 Z= 0.109 Angle : 0.539 15.344 47412 Z= 0.268 Chirality : 0.043 0.244 5477 Planarity : 0.004 0.080 6001 Dihedral : 4.905 57.447 5573 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.80 % Allowed : 13.29 % Favored : 84.91 % 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: 1.33 (0.21), residues: 648 sheet: -0.18 (0.17), residues: 1000 loop : -1.61 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Q 113 HIS 0.003 0.000 HIS Q 35 PHE 0.016 0.001 PHE A 643 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 36) link_NAG-ASN : angle 1.71555 ( 108) link_BETA1-4 : bond 0.00366 ( 12) link_BETA1-4 : angle 1.36712 ( 36) hydrogen bonds : bond 0.04130 ( 1021) hydrogen bonds : angle 5.43713 ( 2859) SS BOND : bond 0.00477 ( 51) SS BOND : angle 1.07928 ( 102) covalent geometry : bond 0.00247 (34641) covalent geometry : angle 0.52996 (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: 67 poor density : 204 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 LEU cc_start: 0.6727 (mm) cc_final: 0.6495 (mm) REVERT: A 1029 MET cc_start: 0.8381 (ttm) cc_final: 0.8007 (ttm) REVERT: A 1031 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: B 759 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6768 (t80) REVERT: C 118 LEU cc_start: 0.6796 (tt) cc_final: 0.6033 (mt) REVERT: C 508 TYR cc_start: 0.7945 (m-80) cc_final: 0.7479 (m-80) REVERT: C 697 MET cc_start: 0.8549 (tpp) cc_final: 0.8125 (mmt) REVERT: C 823 PHE cc_start: 0.8038 (t80) cc_final: 0.7742 (t80) REVERT: C 878 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8288 (mm) REVERT: G 92 TRP cc_start: 0.2661 (t-100) cc_final: 0.1950 (t-100) REVERT: H 81 MET cc_start: 0.1178 (mmm) cc_final: 0.0747 (mmm) REVERT: Q 31 ASP cc_start: 0.7834 (p0) cc_final: 0.7475 (p0) REVERT: Q 32 TYR cc_start: 0.7996 (m-80) cc_final: 0.7784 (m-80) REVERT: Q 39 GLN cc_start: 0.2067 (tp40) cc_final: 0.1620 (tp40) outliers start: 67 outliers final: 43 residues processed: 261 average time/residue: 0.4114 time to fit residues: 183.7174 Evaluate side-chains 235 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 3.341 ------------------------------------------------------------------------------- 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 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 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 A residue 1141 LEU Chi-restraints excluded: chain B residue 109 THR 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 759 PHE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR 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 1030 SER 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 708 SER 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 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1106 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 390 optimal weight: 20.0000 chunk 319 optimal weight: 0.6980 chunk 307 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 352 optimal weight: 40.0000 chunk 226 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 317 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.209168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.195143 restraints weight = 62031.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.193062 restraints weight = 76739.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.190939 restraints weight = 94297.182| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34740 Z= 0.184 Angle : 0.593 13.668 47412 Z= 0.296 Chirality : 0.045 0.248 5477 Planarity : 0.004 0.071 6001 Dihedral : 4.975 54.706 5573 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.31 % Allowed : 14.04 % Favored : 83.65 % 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: -1.20 (0.13), residues: 4193 helix: 1.19 (0.21), residues: 643 sheet: -0.34 (0.16), residues: 1042 loop : -1.60 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Q 113 HIS 0.004 0.001 HIS G 99 PHE 0.022 0.001 PHE C 92 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG R 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 36) link_NAG-ASN : angle 1.85255 ( 108) link_BETA1-4 : bond 0.00277 ( 12) link_BETA1-4 : angle 1.36385 ( 36) hydrogen bonds : bond 0.04537 ( 1021) hydrogen bonds : angle 5.44613 ( 2859) SS BOND : bond 0.00380 ( 51) SS BOND : angle 1.84587 ( 102) covalent geometry : bond 0.00437 (34641) covalent geometry : angle 0.58025 (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 277 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 191 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7067 (tp-100) cc_final: 0.6814 (pm20) REVERT: A 533 LEU cc_start: 0.6775 (mm) cc_final: 0.6530 (mm) REVERT: A 1029 MET cc_start: 0.8498 (ttm) cc_final: 0.8250 (ttm) REVERT: B 759 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6663 (t80) REVERT: C 508 TYR cc_start: 0.8064 (m-80) cc_final: 0.7593 (m-80) REVERT: C 523 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8087 (t) REVERT: C 823 PHE cc_start: 0.8110 (t80) cc_final: 0.7869 (t80) REVERT: C 878 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8235 (mm) REVERT: G 92 TRP cc_start: 0.2559 (t-100) cc_final: 0.1949 (t-100) REVERT: H 81 MET cc_start: 0.1028 (mmm) cc_final: 0.0615 (mmm) REVERT: Q 31 ASP cc_start: 0.7897 (p0) cc_final: 0.7539 (p0) outliers start: 86 outliers final: 65 residues processed: 267 average time/residue: 0.4192 time to fit residues: 192.5834 Evaluate side-chains 249 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 931 ILE 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 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 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 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 1027 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 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 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 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 H residue 70 MET Chi-restraints excluded: chain H residue 124 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 186 optimal weight: 0.8980 chunk 247 optimal weight: 0.9990 chunk 268 optimal weight: 0.1980 chunk 114 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 353 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 365 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 B 196 ASN B 920 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.211524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.196921 restraints weight = 61756.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.195023 restraints weight = 88989.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.193864 restraints weight = 89565.300| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1959 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= 0.114 Angle : 0.535 10.942 47412 Z= 0.267 Chirality : 0.043 0.236 5477 Planarity : 0.004 0.065 6001 Dihedral : 4.689 48.329 5572 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.26 % Allowed : 14.82 % Favored : 82.92 % 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: -1.05 (0.13), residues: 4193 helix: 1.45 (0.21), residues: 644 sheet: -0.27 (0.16), residues: 1022 loop : -1.53 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP Q 113 HIS 0.003 0.000 HIS B1048 PHE 0.014 0.001 PHE B 456 TYR 0.023 0.001 TYR M 88 ARG 0.003 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 36) link_NAG-ASN : angle 1.71367 ( 108) link_BETA1-4 : bond 0.00336 ( 12) link_BETA1-4 : angle 1.37508 ( 36) hydrogen bonds : bond 0.03999 ( 1021) hydrogen bonds : angle 5.20095 ( 2859) SS BOND : bond 0.00375 ( 51) SS BOND : angle 1.26780 ( 102) covalent geometry : bond 0.00263 (34641) covalent geometry : angle 0.52494 (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 284 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 200 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 LEU cc_start: 0.6655 (mm) cc_final: 0.6414 (mm) REVERT: A 907 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8845 (t0) REVERT: A 1031 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: B 759 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6788 (t80) REVERT: C 508 TYR cc_start: 0.7983 (m-80) cc_final: 0.7503 (m-80) REVERT: C 697 MET cc_start: 0.8287 (tpp) cc_final: 0.7972 (tpt) REVERT: C 823 PHE cc_start: 0.8019 (t80) cc_final: 0.7761 (t80) REVERT: C 878 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8171 (mm) REVERT: G 92 TRP cc_start: 0.2461 (t-100) cc_final: 0.1976 (t-100) REVERT: H 81 MET cc_start: 0.1052 (mmm) cc_final: 0.0747 (mmm) outliers start: 84 outliers final: 62 residues processed: 273 average time/residue: 0.4237 time to fit residues: 201.6841 Evaluate side-chains 246 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 THR 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 907 ASN 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 1051 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 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 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 819 GLU 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 1027 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 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 511 VAL 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 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 882 ILE 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 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 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 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 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 324 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 342 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 345 optimal weight: 9.9990 chunk 60 optimal weight: 0.0070 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.0770 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A1106 GLN B 196 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.212675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.199302 restraints weight = 62110.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.196902 restraints weight = 74000.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.194492 restraints weight = 86548.744| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34740 Z= 0.099 Angle : 0.528 12.462 47412 Z= 0.262 Chirality : 0.043 0.234 5477 Planarity : 0.004 0.064 6001 Dihedral : 4.481 49.491 5572 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.75 % Allowed : 15.73 % Favored : 82.52 % 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: -0.95 (0.13), residues: 4193 helix: 1.61 (0.21), residues: 644 sheet: -0.21 (0.16), residues: 1026 loop : -1.48 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP Q 113 HIS 0.004 0.000 HIS Q 35 PHE 0.019 0.001 PHE C 541 TYR 0.027 0.001 TYR M 88 ARG 0.002 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 36) link_NAG-ASN : angle 1.64850 ( 108) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 1.39279 ( 36) hydrogen bonds : bond 0.03744 ( 1021) hydrogen bonds : angle 5.05283 ( 2859) SS BOND : bond 0.00444 ( 51) SS BOND : angle 1.06516 ( 102) covalent geometry : bond 0.00224 (34641) covalent geometry : angle 0.51943 (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 263 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7255 (tp-100) cc_final: 0.6992 (pm20) REVERT: A 533 LEU cc_start: 0.6822 (mm) cc_final: 0.6573 (mm) REVERT: A 1031 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: B 759 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6590 (t80) REVERT: C 508 TYR cc_start: 0.7916 (m-80) cc_final: 0.7491 (m-80) REVERT: C 697 MET cc_start: 0.8291 (tpp) cc_final: 0.7980 (tpt) REVERT: C 823 PHE cc_start: 0.7907 (t80) cc_final: 0.7641 (t80) REVERT: C 878 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8323 (mm) REVERT: G 92 TRP cc_start: 0.2389 (t-100) cc_final: 0.1993 (t-100) REVERT: H 81 MET cc_start: 0.1138 (mmm) cc_final: 0.0830 (mmm) outliers start: 65 outliers final: 53 residues processed: 256 average time/residue: 0.4213 time to fit residues: 184.1613 Evaluate side-chains 241 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 931 ILE 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 320 VAL 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 887 THR 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 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 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 511 VAL 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 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 H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 51 ILE 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: 0.9990 chunk 373 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 318 optimal weight: 30.0000 chunk 290 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 386 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1054 GLN ** 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** ** 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 = 0.4628 r_free = 0.4628 target = 0.207981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.193130 restraints weight = 61846.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.191798 restraints weight = 91474.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.190567 restraints weight = 90430.908| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34740 Z= 0.221 Angle : 0.623 13.343 47412 Z= 0.312 Chirality : 0.046 0.248 5477 Planarity : 0.004 0.064 6001 Dihedral : 4.862 44.442 5572 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.53 % Allowed : 15.52 % Favored : 81.95 % 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: -1.18 (0.13), residues: 4193 helix: 1.16 (0.21), residues: 644 sheet: -0.40 (0.16), residues: 1056 loop : -1.54 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP Q 113 HIS 0.003 0.001 HIS Q 35 PHE 0.023 0.002 PHE C 92 TYR 0.020 0.001 TYR Q 32 ARG 0.006 0.000 ARG R 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 36) link_NAG-ASN : angle 1.82038 ( 108) link_BETA1-4 : bond 0.00269 ( 12) link_BETA1-4 : angle 1.41176 ( 36) hydrogen bonds : bond 0.04730 ( 1021) hydrogen bonds : angle 5.31430 ( 2859) SS BOND : bond 0.00468 ( 51) SS BOND : angle 1.46763 ( 102) covalent geometry : bond 0.00530 (34641) covalent geometry : angle 0.61315 (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 282 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 188 time to evaluate : 4.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 LEU cc_start: 0.6742 (mm) cc_final: 0.6497 (mm) REVERT: A 1031 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: B 759 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6750 (t80) REVERT: C 508 TYR cc_start: 0.8088 (m-80) cc_final: 0.7594 (m-80) REVERT: C 523 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8418 (t) REVERT: C 823 PHE cc_start: 0.8106 (t80) cc_final: 0.7825 (t80) REVERT: C 878 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8174 (mm) REVERT: G 92 TRP cc_start: 0.2473 (t-100) cc_final: 0.2020 (t-100) REVERT: H 81 MET cc_start: 0.1067 (mmm) cc_final: 0.0761 (mmm) REVERT: M 88 TYR cc_start: 0.4809 (m-80) cc_final: 0.4582 (m-10) REVERT: Q 31 ASP cc_start: 0.7763 (p0) cc_final: 0.7483 (p0) outliers start: 94 outliers final: 77 residues processed: 274 average time/residue: 0.3945 time to fit residues: 186.7451 Evaluate side-chains 259 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 549 THR 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 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 109 THR 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 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 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 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 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 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 320 VAL Chi-restraints excluded: chain C residue 392 PHE 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 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 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 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 34 VAL Chi-restraints excluded: chain N residue 38 GLN 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 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: 4.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 423 optimal weight: 3.9990 chunk 420 optimal weight: 50.0000 chunk 53 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 346 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 920 GLN ** 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 = 0.4636 r_free = 0.4636 target = 0.208699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.194667 restraints weight = 62065.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.192816 restraints weight = 77417.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.190276 restraints weight = 81528.098| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34740 Z= 0.184 Angle : 0.594 14.587 47412 Z= 0.296 Chirality : 0.045 0.243 5477 Planarity : 0.004 0.063 6001 Dihedral : 4.844 45.172 5572 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.66 % Allowed : 15.92 % Favored : 81.41 % 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: -1.15 (0.13), residues: 4193 helix: 1.22 (0.21), residues: 644 sheet: -0.35 (0.16), residues: 1044 loop : -1.55 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP Q 113 HIS 0.003 0.001 HIS Q 35 PHE 0.020 0.001 PHE C 92 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG N 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 36) link_NAG-ASN : angle 1.79087 ( 108) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 1.39887 ( 36) hydrogen bonds : bond 0.04447 ( 1021) hydrogen bonds : angle 5.22092 ( 2859) SS BOND : bond 0.00375 ( 51) SS BOND : angle 1.36788 ( 102) covalent geometry : bond 0.00439 (34641) covalent geometry : angle 0.58460 (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 281 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 182 time to evaluate : 3.644 Fit side-chains revert: symmetry clash REVERT: A 533 LEU cc_start: 0.6753 (mm) cc_final: 0.6505 (mm) REVERT: A 756 TYR cc_start: 0.8000 (m-80) cc_final: 0.7751 (m-80) REVERT: A 1031 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: B 458 LYS cc_start: 0.7689 (mptt) cc_final: 0.7475 (mptt) REVERT: B 759 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6731 (t80) REVERT: C 158 ARG cc_start: 0.5598 (mtt180) cc_final: 0.5252 (mtt180) REVERT: C 508 TYR cc_start: 0.8053 (m-80) cc_final: 0.7557 (m-80) REVERT: C 523 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8582 (t) REVERT: C 823 PHE cc_start: 0.8084 (t80) cc_final: 0.7812 (t80) REVERT: C 878 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8251 (mm) REVERT: C 902 MET cc_start: 0.8814 (tpp) cc_final: 0.8522 (tpt) REVERT: G 92 TRP cc_start: 0.2489 (t-100) cc_final: 0.2017 (t-100) REVERT: H 81 MET cc_start: 0.1058 (mmm) cc_final: 0.0756 (mmm) REVERT: Q 31 ASP cc_start: 0.7698 (p0) cc_final: 0.7495 (p0) outliers start: 99 outliers final: 86 residues processed: 272 average time/residue: 0.4336 time to fit residues: 201.6711 Evaluate side-chains 265 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 175 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 549 THR 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 901 GLN Chi-restraints excluded: chain A residue 906 PHE 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 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 109 THR 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 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 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 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 882 ILE 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 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 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 34 VAL Chi-restraints excluded: chain N residue 38 GLN 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 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 26 optimal weight: 8.9990 chunk 178 optimal weight: 0.3980 chunk 419 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 390 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.205967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.192524 restraints weight = 61667.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.190307 restraints weight = 81728.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.188096 restraints weight = 97641.410| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 34740 Z= 0.257 Angle : 0.666 17.893 47412 Z= 0.334 Chirality : 0.047 0.254 5477 Planarity : 0.005 0.063 6001 Dihedral : 5.144 43.177 5572 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.74 % Allowed : 16.03 % Favored : 81.23 % 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: -1.34 (0.13), residues: 4193 helix: 0.79 (0.20), residues: 656 sheet: -0.45 (0.16), residues: 1047 loop : -1.62 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP Q 36 HIS 0.006 0.001 HIS Q 35 PHE 0.026 0.002 PHE C 497 TYR 0.030 0.002 TYR C 501 ARG 0.007 0.001 ARG R 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 36) link_NAG-ASN : angle 1.93443 ( 108) link_BETA1-4 : bond 0.00259 ( 12) link_BETA1-4 : angle 1.43217 ( 36) hydrogen bonds : bond 0.04987 ( 1021) hydrogen bonds : angle 5.41433 ( 2859) SS BOND : bond 0.00441 ( 51) SS BOND : angle 1.59696 ( 102) covalent geometry : bond 0.00614 (34641) covalent geometry : angle 0.65620 (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 279 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 177 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7514 (t) REVERT: A 533 LEU cc_start: 0.6770 (mm) cc_final: 0.6511 (mm) REVERT: A 1031 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: B 759 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6710 (t80) REVERT: C 158 ARG cc_start: 0.5713 (mtt180) cc_final: 0.5324 (mtt180) REVERT: C 508 TYR cc_start: 0.8101 (m-80) cc_final: 0.7549 (m-80) REVERT: C 523 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8694 (t) REVERT: C 697 MET cc_start: 0.8470 (tpp) cc_final: 0.8158 (tpp) REVERT: C 823 PHE cc_start: 0.8129 (t80) cc_final: 0.7804 (t80) REVERT: C 878 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8283 (mm) REVERT: C 902 MET cc_start: 0.8829 (tpp) cc_final: 0.8548 (tpt) REVERT: G 92 TRP cc_start: 0.2491 (t-100) cc_final: 0.2009 (t-100) REVERT: H 81 MET cc_start: 0.1101 (mmm) cc_final: 0.0800 (mmm) outliers start: 102 outliers final: 91 residues processed: 269 average time/residue: 0.4114 time to fit residues: 191.3338 Evaluate side-chains 269 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 173 time to evaluate : 3.613 ------------------------------------------------------------------------------- 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 549 THR Chi-restraints excluded: chain A residue 574 ASP 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 901 GLN 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 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1077 THR 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 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 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 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 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 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 931 ILE 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 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 N residue 34 VAL Chi-restraints excluded: chain N residue 38 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 190 optimal weight: 0.0010 chunk 276 optimal weight: 1.9990 chunk 410 optimal weight: 8.9990 chunk 300 optimal weight: 20.0000 chunk 281 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 50 optimal weight: 0.0970 chunk 218 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.4674 r_free = 0.4674 target = 0.212414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.198968 restraints weight = 62087.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.196629 restraints weight = 73164.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.194287 restraints weight = 79787.634| |-----------------------------------------------------------------------------| r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34740 Z= 0.099 Angle : 0.559 17.268 47412 Z= 0.276 Chirality : 0.043 0.236 5477 Planarity : 0.004 0.062 6001 Dihedral : 4.600 49.127 5572 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.51 % Allowed : 17.35 % Favored : 81.15 % 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: -0.98 (0.13), residues: 4193 helix: 1.60 (0.21), residues: 644 sheet: -0.31 (0.16), residues: 1072 loop : -1.48 (0.12), residues: 2477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP Q 36 HIS 0.005 0.001 HIS B1048 PHE 0.020 0.001 PHE Q 64 TYR 0.023 0.001 TYR M 88 ARG 0.004 0.000 ARG R 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 36) link_NAG-ASN : angle 1.71037 ( 108) link_BETA1-4 : bond 0.00419 ( 12) link_BETA1-4 : angle 1.47845 ( 36) hydrogen bonds : bond 0.03741 ( 1021) hydrogen bonds : angle 4.94489 ( 2859) SS BOND : bond 0.00316 ( 51) SS BOND : angle 1.17658 ( 102) covalent geometry : bond 0.00221 (34641) covalent geometry : angle 0.55063 (47166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8295.12 seconds wall clock time: 147 minutes 53.02 seconds (8873.02 seconds total)