Starting phenix.real_space_refine on Tue Aug 26 05:14:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc4_39922/08_2025/8zc4_39922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc4_39922/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zc4_39922/08_2025/8zc4_39922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc4_39922/08_2025/8zc4_39922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zc4_39922/08_2025/8zc4_39922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc4_39922/08_2025/8zc4_39922.map" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.31, per 1000 atoms: 0.22 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.08 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: 7.01 Time building geometry restraints manager: 3.66 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 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1307)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.460 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- 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 : 4.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG C 498 TYR 0.024 0.001 TYR C 489 PHE 0.031 0.001 PHE Q 29 TRP 0.041 0.002 TRP H 47 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00351 (34641) covalent geometry : angle 0.70540 (47166) SS BOND : bond 0.00390 ( 51) SS BOND : angle 1.46661 ( 102) hydrogen bonds : bond 0.24051 ( 1021) hydrogen bonds : angle 9.02905 ( 2859) link_BETA1-4 : bond 0.00570 ( 12) link_BETA1-4 : angle 2.08019 ( 36) link_NAG-ASN : bond 0.00672 ( 36) link_NAG-ASN : angle 2.10197 ( 108) *********************** 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 : 1.102 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: 0.9082 (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: 0.7776 (m-80) REVERT: B 1017 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7685 (tm-30) 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: 0.7632 (t80) REVERT: C 1029 MET cc_start: 0.9124 (tpp) cc_final: 0.8838 (tpp) outliers start: 1 outliers final: 1 residues processed: 272 average time/residue: 0.1896 time to fit residues: 86.3151 Evaluate side-chains 181 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 493 GLN B 196 ASN B 755 GLN B 926 GLN B 955 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 30 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.211930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.197351 restraints weight = 62450.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.196098 restraints weight = 94813.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.194668 restraints weight = 85371.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.193885 restraints weight = 94868.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.193335 restraints weight = 94125.703| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34740 Z= 0.179 Angle : 0.604 11.049 47412 Z= 0.305 Chirality : 0.045 0.277 5477 Planarity : 0.005 0.080 6001 Dihedral : 5.520 58.708 5573 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.70 % Allowed : 6.97 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.13), residues: 4193 helix: 0.86 (0.21), residues: 648 sheet: -0.11 (0.17), residues: 990 loop : -1.67 (0.11), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 98 TYR 0.021 0.001 TYR C1067 PHE 0.021 0.002 PHE B 377 TRP 0.023 0.001 TRP Q 113 HIS 0.006 0.001 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00417 (34641) covalent geometry : angle 0.59469 (47166) SS BOND : bond 0.00487 ( 51) SS BOND : angle 1.35940 ( 102) hydrogen bonds : bond 0.05002 ( 1021) hydrogen bonds : angle 6.37225 ( 2859) link_BETA1-4 : bond 0.00285 ( 12) link_BETA1-4 : angle 1.24353 ( 36) link_NAG-ASN : bond 0.00301 ( 36) link_NAG-ASN : angle 1.78522 ( 108) *********************** 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 240 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8342 (t) cc_final: 0.8098 (t) REVERT: A 533 LEU cc_start: 0.6607 (mm) cc_final: 0.6369 (mm) REVERT: A 1029 MET cc_start: 0.9067 (tpp) cc_final: 0.8600 (ttm) REVERT: B 816 SER cc_start: 0.8552 (p) cc_final: 0.8224 (p) REVERT: B 819 GLU cc_start: 0.7736 (pt0) cc_final: 0.7476 (pt0) REVERT: B 1017 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 508 TYR cc_start: 0.7973 (m-80) cc_final: 0.7406 (m-80) REVERT: C 697 MET cc_start: 0.8437 (tpp) cc_final: 0.8176 (mmt) REVERT: C 750 SER cc_start: 0.7343 (p) cc_final: 0.7124 (p) REVERT: C 823 PHE cc_start: 0.7984 (t80) cc_final: 0.7735 (t80) REVERT: Q 31 ASP cc_start: 0.7798 (p0) cc_final: 0.7439 (p0) REVERT: Q 32 TYR cc_start: 0.7881 (m-80) cc_final: 0.7645 (m-10) REVERT: Q 39 GLN cc_start: 0.2206 (tp40) cc_final: 0.1603 (tp40) outliers start: 26 outliers final: 19 residues processed: 235 average time/residue: 0.1697 time to fit residues: 67.9040 Evaluate side-chains 199 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 298 GLU 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 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1037 SER 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 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 125 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 55 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 0.2980 chunk 281 optimal weight: 8.9990 chunk 300 optimal weight: 40.0000 chunk 3 optimal weight: 0.9990 chunk 386 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 474 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.214074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.198887 restraints weight = 62428.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.197018 restraints weight = 88123.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.195825 restraints weight = 85575.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.194955 restraints weight = 94060.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.194150 restraints weight = 96402.737| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34740 Z= 0.113 Angle : 0.539 15.115 47412 Z= 0.269 Chirality : 0.043 0.233 5477 Planarity : 0.004 0.080 6001 Dihedral : 4.999 56.618 5573 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.83 % Allowed : 10.11 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.13), residues: 4193 helix: 1.32 (0.21), residues: 648 sheet: -0.04 (0.17), residues: 971 loop : -1.57 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE C 201 TRP 0.029 0.001 TRP Q 113 HIS 0.004 0.000 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00255 (34641) covalent geometry : angle 0.53080 (47166) SS BOND : bond 0.00315 ( 51) SS BOND : angle 1.10845 ( 102) hydrogen bonds : bond 0.04325 ( 1021) hydrogen bonds : angle 5.74413 ( 2859) link_BETA1-4 : bond 0.00379 ( 12) link_BETA1-4 : angle 1.34648 ( 36) link_NAG-ASN : bond 0.00265 ( 36) link_NAG-ASN : angle 1.65301 ( 108) *********************** 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 233 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7348 (tp-100) cc_final: 0.6911 (pm20) REVERT: A 533 LEU cc_start: 0.6659 (mm) cc_final: 0.6414 (mm) REVERT: A 574 ASP cc_start: 0.7788 (p0) cc_final: 0.7474 (p0) REVERT: A 1029 MET cc_start: 0.8889 (tpp) cc_final: 0.8454 (ttm) REVERT: B 759 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6359 (t80) REVERT: B 816 SER cc_start: 0.8427 (p) cc_final: 0.8171 (p) REVERT: B 1017 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7386 (tm-30) REVERT: C 394 ASN cc_start: 0.6786 (m110) cc_final: 0.6548 (m-40) REVERT: C 508 TYR cc_start: 0.7921 (m-80) cc_final: 0.7408 (m-80) REVERT: C 823 PHE cc_start: 0.7965 (t80) cc_final: 0.7726 (t80) REVERT: Q 31 ASP cc_start: 0.7856 (p0) cc_final: 0.7340 (p0) REVERT: Q 32 TYR cc_start: 0.7877 (m-80) cc_final: 0.7573 (m-10) outliers start: 31 outliers final: 22 residues processed: 226 average time/residue: 0.1962 time to fit residues: 75.3157 Evaluate side-chains 199 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1104 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 759 PHE 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 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 882 ILE 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 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain R residue 54 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 30 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 304 optimal weight: 50.0000 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 174 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 A1010 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 271 GLN B 755 GLN B1054 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN R 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.206439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.193059 restraints weight = 61736.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.190939 restraints weight = 79964.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.188940 restraints weight = 98652.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.187931 restraints weight = 112283.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.186800 restraints weight = 111540.633| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 34740 Z= 0.271 Angle : 0.675 12.713 47412 Z= 0.341 Chirality : 0.047 0.297 5477 Planarity : 0.005 0.069 6001 Dihedral : 5.304 54.834 5573 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.99 % Allowed : 12.21 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.13), residues: 4193 helix: 0.78 (0.21), residues: 648 sheet: -0.40 (0.16), residues: 1023 loop : -1.62 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 98 TYR 0.020 0.002 TYR C1067 PHE 0.029 0.002 PHE C 92 TRP 0.029 0.002 TRP Q 113 HIS 0.006 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00643 (34641) covalent geometry : angle 0.66565 (47166) SS BOND : bond 0.00793 ( 51) SS BOND : angle 1.57461 ( 102) hydrogen bonds : bond 0.05377 ( 1021) hydrogen bonds : angle 5.84687 ( 2859) link_BETA1-4 : bond 0.00310 ( 12) link_BETA1-4 : angle 1.37685 ( 36) link_NAG-ASN : bond 0.00383 ( 36) link_NAG-ASN : angle 1.93665 ( 108) *********************** 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 261 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 187 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7332 (tp-100) cc_final: 0.6991 (pm20) REVERT: A 227 VAL cc_start: 0.8197 (m) cc_final: 0.7881 (t) REVERT: A 1029 MET cc_start: 0.9145 (tpp) cc_final: 0.8680 (ttm) REVERT: B 759 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6790 (t80) REVERT: C 118 LEU cc_start: 0.6929 (tt) cc_final: 0.5924 (mp) REVERT: C 508 TYR cc_start: 0.8095 (m-80) cc_final: 0.7660 (m-80) REVERT: C 523 THR cc_start: 0.8570 (p) cc_final: 0.8225 (t) REVERT: C 697 MET cc_start: 0.8507 (tpp) cc_final: 0.8266 (tpt) REVERT: C 823 PHE cc_start: 0.8152 (t80) cc_final: 0.7901 (t80) REVERT: C 878 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8401 (mm) REVERT: C 1029 MET cc_start: 0.9224 (tpp) cc_final: 0.8894 (tpp) REVERT: G 92 TRP cc_start: 0.2477 (t-100) cc_final: 0.1619 (t-100) REVERT: H 81 MET cc_start: 0.0971 (mmm) cc_final: 0.0538 (mmm) REVERT: Q 31 ASP cc_start: 0.7886 (p0) cc_final: 0.7468 (p0) REVERT: Q 32 TYR cc_start: 0.8242 (m-80) cc_final: 0.7991 (m-10) outliers start: 74 outliers final: 51 residues processed: 252 average time/residue: 0.1828 time to fit residues: 79.3788 Evaluate side-chains 223 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 770 ILE 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 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 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE 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 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 781 VAL 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 B residue 1061 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 950 ASP 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 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 N residue 38 GLN Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 260 optimal weight: 8.9990 chunk 173 optimal weight: 0.6980 chunk 324 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 190 optimal weight: 0.0570 chunk 246 optimal weight: 3.9990 chunk 409 optimal weight: 2.9990 chunk 42 optimal weight: 50.0000 chunk 2 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.209798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.195113 restraints weight = 61955.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.193412 restraints weight = 88280.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.191962 restraints weight = 91413.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.191246 restraints weight = 104341.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.190113 restraints weight = 101980.458| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34740 Z= 0.158 Angle : 0.570 11.410 47412 Z= 0.286 Chirality : 0.044 0.242 5477 Planarity : 0.004 0.063 6001 Dihedral : 4.992 47.671 5573 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.02 % Allowed : 13.74 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.13), residues: 4193 helix: 1.17 (0.21), residues: 642 sheet: -0.35 (0.16), residues: 1043 loop : -1.56 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 328 TYR 0.017 0.001 TYR C1067 PHE 0.017 0.001 PHE C 92 TRP 0.030 0.001 TRP Q 113 HIS 0.003 0.001 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00373 (34641) covalent geometry : angle 0.56000 (47166) SS BOND : bond 0.00365 ( 51) SS BOND : angle 1.49851 ( 102) hydrogen bonds : bond 0.04457 ( 1021) hydrogen bonds : angle 5.45934 ( 2859) link_BETA1-4 : bond 0.00313 ( 12) link_BETA1-4 : angle 1.36000 ( 36) link_NAG-ASN : bond 0.00256 ( 36) link_NAG-ASN : angle 1.76199 ( 108) *********************** 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 262 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 187 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7230 (tp-100) cc_final: 0.6891 (pm20) REVERT: A 227 VAL cc_start: 0.8070 (m) cc_final: 0.7770 (t) REVERT: A 1029 MET cc_start: 0.8898 (tpp) cc_final: 0.8466 (ttm) REVERT: B 759 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6734 (t80) REVERT: C 118 LEU cc_start: 0.6960 (tt) cc_final: 0.5970 (mp) REVERT: C 508 TYR cc_start: 0.8020 (m-80) cc_final: 0.7500 (m-80) REVERT: C 523 THR cc_start: 0.8634 (p) cc_final: 0.8263 (t) REVERT: C 823 PHE cc_start: 0.8091 (t80) cc_final: 0.7796 (t80) REVERT: C 878 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8324 (mm) REVERT: G 92 TRP cc_start: 0.2475 (t-100) cc_final: 0.1912 (t-100) REVERT: H 81 MET cc_start: 0.0959 (mmm) cc_final: 0.0526 (mmm) REVERT: Q 31 ASP cc_start: 0.7879 (p0) cc_final: 0.7490 (p0) REVERT: Q 32 TYR cc_start: 0.8241 (m-80) cc_final: 0.8014 (m-80) outliers start: 75 outliers final: 50 residues processed: 248 average time/residue: 0.1706 time to fit residues: 73.4811 Evaluate side-chains 229 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 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 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 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 781 VAL Chi-restraints excluded: chain B residue 819 GLU 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 C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 950 ASP 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 H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 70 MET 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 228 optimal weight: 0.8980 chunk 399 optimal weight: 30.0000 chunk 29 optimal weight: 0.2980 chunk 171 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 316 optimal weight: 40.0000 chunk 108 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 196 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 644 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.211944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.197474 restraints weight = 61659.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.195857 restraints weight = 88644.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.194729 restraints weight = 90036.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.193810 restraints weight = 98773.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.193049 restraints weight = 96176.221| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34740 Z= 0.109 Angle : 0.538 11.187 47412 Z= 0.268 Chirality : 0.043 0.235 5477 Planarity : 0.004 0.061 6001 Dihedral : 4.643 48.553 5572 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.91 % Allowed : 14.58 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.13), residues: 4193 helix: 1.50 (0.21), residues: 643 sheet: -0.21 (0.16), residues: 1019 loop : -1.51 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 328 TYR 0.027 0.001 TYR M 88 PHE 0.014 0.001 PHE C 92 TRP 0.037 0.001 TRP Q 113 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00250 (34641) covalent geometry : angle 0.52662 (47166) SS BOND : bond 0.00379 ( 51) SS BOND : angle 1.50521 ( 102) hydrogen bonds : bond 0.03932 ( 1021) hydrogen bonds : angle 5.19027 ( 2859) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 1.37961 ( 36) link_NAG-ASN : bond 0.00230 ( 36) link_NAG-ASN : angle 1.77705 ( 108) *********************** 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 269 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 198 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 907 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8850 (t0) REVERT: A 1029 MET cc_start: 0.8904 (tpp) cc_final: 0.8463 (ttm) REVERT: B 759 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6564 (t80) REVERT: C 118 LEU cc_start: 0.6941 (tt) cc_final: 0.5980 (mp) REVERT: C 508 TYR cc_start: 0.7958 (m-80) cc_final: 0.7506 (m-80) REVERT: C 523 THR cc_start: 0.8653 (p) cc_final: 0.8159 (t) REVERT: C 697 MET cc_start: 0.8330 (tpp) cc_final: 0.8027 (tpt) REVERT: C 823 PHE cc_start: 0.7994 (t80) cc_final: 0.7716 (t80) REVERT: C 878 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8219 (mm) REVERT: C 902 MET cc_start: 0.8195 (tpt) cc_final: 0.7991 (tpp) REVERT: G 92 TRP cc_start: 0.2436 (t-100) cc_final: 0.2013 (t-100) REVERT: H 81 MET cc_start: 0.0883 (mmm) cc_final: 0.0577 (mmm) REVERT: Q 31 ASP cc_start: 0.7836 (p0) cc_final: 0.7482 (p0) outliers start: 71 outliers final: 49 residues processed: 258 average time/residue: 0.1783 time to fit residues: 79.3550 Evaluate side-chains 230 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN 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 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 649 CYS 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 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 C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 169 GLU 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 615 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 915 VAL Chi-restraints excluded: chain C residue 950 ASP 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 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 54 ASP 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 315 optimal weight: 50.0000 chunk 119 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 397 optimal weight: 9.9990 chunk 4 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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 ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.208120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.193967 restraints weight = 62276.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.191887 restraints weight = 77158.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.189665 restraints weight = 91847.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.188945 restraints weight = 118015.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.187953 restraints weight = 107411.928| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34740 Z= 0.225 Angle : 0.615 11.871 47412 Z= 0.309 Chirality : 0.045 0.246 5477 Planarity : 0.004 0.088 6001 Dihedral : 4.901 44.792 5572 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.37 % Allowed : 14.95 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.13), residues: 4193 helix: 1.14 (0.21), residues: 644 sheet: -0.43 (0.16), residues: 1051 loop : -1.54 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 110 TYR 0.020 0.001 TYR C 200 PHE 0.025 0.002 PHE C 92 TRP 0.038 0.002 TRP Q 113 HIS 0.003 0.001 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00538 (34641) covalent geometry : angle 0.60530 (47166) SS BOND : bond 0.00493 ( 51) SS BOND : angle 1.47461 ( 102) hydrogen bonds : bond 0.04673 ( 1021) hydrogen bonds : angle 5.37882 ( 2859) link_BETA1-4 : bond 0.00266 ( 12) link_BETA1-4 : angle 1.39291 ( 36) link_NAG-ASN : bond 0.00315 ( 36) link_NAG-ASN : angle 1.84080 ( 108) *********************** 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 267 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 179 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9044 (tpp) cc_final: 0.8650 (ttm) REVERT: B 759 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6762 (t80) REVERT: C 118 LEU cc_start: 0.7264 (tt) cc_final: 0.6235 (mp) REVERT: C 508 TYR cc_start: 0.8100 (m-80) cc_final: 0.7604 (m-80) REVERT: C 523 THR cc_start: 0.8675 (p) cc_final: 0.8330 (t) REVERT: C 823 PHE cc_start: 0.8173 (t80) cc_final: 0.7913 (t80) REVERT: C 878 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8194 (mm) REVERT: H 81 MET cc_start: 0.0783 (mmm) cc_final: 0.0472 (mmm) REVERT: M 47 LEU cc_start: 0.7504 (tt) cc_final: 0.7118 (tt) outliers start: 88 outliers final: 70 residues processed: 257 average time/residue: 0.1776 time to fit residues: 78.7320 Evaluate side-chains 247 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR 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 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 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 433 VAL 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 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 950 ASP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain Q residue 117 TRP Chi-restraints excluded: chain Q residue 123 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 416 optimal weight: 9.9990 chunk 360 optimal weight: 30.0000 chunk 255 optimal weight: 3.9990 chunk 392 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 165 optimal weight: 0.0010 chunk 153 optimal weight: 0.3980 chunk 175 optimal weight: 0.0980 chunk 286 optimal weight: 0.6980 chunk 313 optimal weight: 40.0000 chunk 203 optimal weight: 0.0770 overall best weight: 0.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 920 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.196152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.170955 restraints weight = 59268.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.171603 restraints weight = 148908.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.171435 restraints weight = 90386.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.171112 restraints weight = 63394.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.171543 restraints weight = 53221.202| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34740 Z= 0.092 Angle : 0.533 11.280 47412 Z= 0.266 Chirality : 0.043 0.226 5477 Planarity : 0.004 0.078 6001 Dihedral : 4.451 50.327 5572 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.51 % Allowed : 16.00 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.13), residues: 4193 helix: 1.66 (0.21), residues: 644 sheet: -0.19 (0.16), residues: 1015 loop : -1.46 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.017 0.001 TYR C1067 PHE 0.015 0.001 PHE B 456 TRP 0.043 0.001 TRP Q 113 HIS 0.004 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00201 (34641) covalent geometry : angle 0.52423 (47166) SS BOND : bond 0.00327 ( 51) SS BOND : angle 1.07058 ( 102) hydrogen bonds : bond 0.03639 ( 1021) hydrogen bonds : angle 4.94031 ( 2859) link_BETA1-4 : bond 0.00434 ( 12) link_BETA1-4 : angle 1.43848 ( 36) link_NAG-ASN : bond 0.00272 ( 36) link_NAG-ASN : angle 1.64932 ( 108) *********************** 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 259 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8830 (tpp) cc_final: 0.8400 (ttm) REVERT: B 759 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6724 (t80) REVERT: C 508 TYR cc_start: 0.7932 (m-80) cc_final: 0.7393 (m-80) REVERT: C 523 THR cc_start: 0.8521 (p) cc_final: 0.8224 (t) REVERT: C 823 PHE cc_start: 0.7956 (t80) cc_final: 0.7644 (t80) REVERT: C 878 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7943 (mm) REVERT: C 881 THR cc_start: 0.8593 (t) cc_final: 0.6822 (p) REVERT: C 906 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8497 (m-10) REVERT: H 81 MET cc_start: 0.0211 (mmm) cc_final: -0.0028 (mmm) REVERT: M 47 LEU cc_start: 0.7771 (tt) cc_final: 0.7410 (tt) REVERT: M 88 TYR cc_start: 0.4753 (m-10) cc_final: 0.4530 (m-10) REVERT: R 87 ARG cc_start: 0.4910 (mmp80) cc_final: 0.4628 (mmp80) outliers start: 56 outliers final: 37 residues processed: 250 average time/residue: 0.1818 time to fit residues: 78.3435 Evaluate side-chains 226 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 906 PHE 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 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 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1030 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 878 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1104 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 M residue 59 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 70 MET 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 205 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 402 optimal weight: 4.9990 chunk 405 optimal weight: 0.9980 chunk 397 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 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 = 0.4672 r_free = 0.4672 target = 0.212164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.198747 restraints weight = 61938.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.196468 restraints weight = 74508.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.193875 restraints weight = 82849.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.193688 restraints weight = 105563.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.192457 restraints weight = 96764.332| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34740 Z= 0.116 Angle : 0.535 11.904 47412 Z= 0.267 Chirality : 0.043 0.234 5477 Planarity : 0.004 0.076 6001 Dihedral : 4.395 48.758 5572 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.43 % Allowed : 16.27 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.13), residues: 4193 helix: 1.66 (0.21), residues: 644 sheet: -0.18 (0.16), residues: 1028 loop : -1.44 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 328 TYR 0.027 0.001 TYR Q 32 PHE 0.016 0.001 PHE A 275 TRP 0.059 0.002 TRP Q 36 HIS 0.003 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00271 (34641) covalent geometry : angle 0.52637 (47166) SS BOND : bond 0.00311 ( 51) SS BOND : angle 1.22120 ( 102) hydrogen bonds : bond 0.03752 ( 1021) hydrogen bonds : angle 4.90670 ( 2859) link_BETA1-4 : bond 0.00333 ( 12) link_BETA1-4 : angle 1.38239 ( 36) link_NAG-ASN : bond 0.00206 ( 36) link_NAG-ASN : angle 1.63997 ( 108) *********************** 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 237 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8938 (tpp) cc_final: 0.8466 (ttm) REVERT: B 759 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6777 (t80) REVERT: C 158 ARG cc_start: 0.5778 (mtt180) cc_final: 0.5450 (mtt180) REVERT: C 508 TYR cc_start: 0.7945 (m-80) cc_final: 0.7508 (m-80) REVERT: C 523 THR cc_start: 0.8547 (p) cc_final: 0.8310 (t) REVERT: C 823 PHE cc_start: 0.8001 (t80) cc_final: 0.7681 (t80) REVERT: C 878 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8086 (mm) REVERT: C 881 THR cc_start: 0.8617 (t) cc_final: 0.6903 (p) REVERT: H 81 MET cc_start: 0.0852 (mmm) cc_final: 0.0563 (mmm) REVERT: M 88 TYR cc_start: 0.4353 (m-10) cc_final: 0.4059 (m-10) outliers start: 53 outliers final: 44 residues processed: 230 average time/residue: 0.1893 time to fit residues: 74.8354 Evaluate side-chains 226 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE 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 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1030 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 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 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 961 THR 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 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 126 VAL Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 365 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 409 optimal weight: 9.9990 chunk 377 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 421 optimal weight: 50.0000 chunk 208 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 856 ASN A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 920 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.204582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.190357 restraints weight = 62116.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.188923 restraints weight = 95248.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.187986 restraints weight = 86300.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.187408 restraints weight = 99641.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.186810 restraints weight = 105718.585| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 34740 Z= 0.331 Angle : 0.731 12.089 47412 Z= 0.369 Chirality : 0.049 0.259 5477 Planarity : 0.005 0.078 6001 Dihedral : 5.312 43.148 5572 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.67 % Allowed : 16.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.13), residues: 4193 helix: 0.62 (0.20), residues: 656 sheet: -0.43 (0.16), residues: 1026 loop : -1.62 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 110 TYR 0.026 0.002 TYR C 917 PHE 0.034 0.003 PHE C 92 TRP 0.042 0.003 TRP Q 113 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00790 (34641) covalent geometry : angle 0.72036 (47166) SS BOND : bond 0.00518 ( 51) SS BOND : angle 1.72375 ( 102) hydrogen bonds : bond 0.05584 ( 1021) hydrogen bonds : angle 5.59961 ( 2859) link_BETA1-4 : bond 0.00301 ( 12) link_BETA1-4 : angle 1.51201 ( 36) link_NAG-ASN : bond 0.00501 ( 36) link_NAG-ASN : angle 2.02547 ( 108) ********************** 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 239 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9175 (tpp) cc_final: 0.8835 (ttm) REVERT: B 759 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6752 (t80) REVERT: C 158 ARG cc_start: 0.5780 (mtt180) cc_final: 0.5380 (mtt180) REVERT: C 508 TYR cc_start: 0.8148 (m-80) cc_final: 0.7661 (m-80) REVERT: C 697 MET cc_start: 0.8314 (tpp) cc_final: 0.7998 (tpp) REVERT: C 823 PHE cc_start: 0.8156 (t80) cc_final: 0.7896 (t80) REVERT: C 878 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8351 (mm) REVERT: H 81 MET cc_start: 0.1075 (mmm) cc_final: 0.0767 (mmm) outliers start: 62 outliers final: 51 residues processed: 232 average time/residue: 0.1900 time to fit residues: 74.8381 Evaluate side-chains 227 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 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 B residue 109 THR 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 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 981 LEU 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 392 PHE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 500 THR 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 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 961 THR 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 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 126 VAL Chi-restraints excluded: chain R residue 54 ASP Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 277 optimal weight: 0.9980 chunk 378 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 352 optimal weight: 20.0000 chunk 410 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 382 optimal weight: 1.9990 chunk 319 optimal weight: 10.0000 chunk 262 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 196 ASN B 920 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 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 = 0.4659 r_free = 0.4659 target = 0.210983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.197178 restraints weight = 61824.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.195188 restraints weight = 76343.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.192634 restraints weight = 80298.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.192303 restraints weight = 105226.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.191244 restraints weight = 97226.107| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34740 Z= 0.116 Angle : 0.561 12.854 47412 Z= 0.279 Chirality : 0.044 0.237 5477 Planarity : 0.004 0.076 6001 Dihedral : 4.751 47.364 5572 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.43 % Allowed : 16.81 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.13), residues: 4193 helix: 1.44 (0.21), residues: 644 sheet: -0.35 (0.16), residues: 1043 loop : -1.52 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 87 TYR 0.042 0.001 TYR M 88 PHE 0.017 0.001 PHE Q 95 TRP 0.040 0.002 TRP Q 36 HIS 0.005 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00270 (34641) covalent geometry : angle 0.55166 (47166) SS BOND : bond 0.00343 ( 51) SS BOND : angle 1.20898 ( 102) hydrogen bonds : bond 0.04041 ( 1021) hydrogen bonds : angle 5.04525 ( 2859) link_BETA1-4 : bond 0.00310 ( 12) link_BETA1-4 : angle 1.43191 ( 36) link_NAG-ASN : bond 0.00250 ( 36) link_NAG-ASN : angle 1.74576 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4034.84 seconds wall clock time: 71 minutes 23.31 seconds (4283.31 seconds total)