Starting phenix.real_space_refine on Sun Jun 22 17:06:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bon_16144/06_2025/8bon_16144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bon_16144/06_2025/8bon_16144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bon_16144/06_2025/8bon_16144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bon_16144/06_2025/8bon_16144.map" model { file = "/net/cci-nas-00/data/ceres_data/8bon_16144/06_2025/8bon_16144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bon_16144/06_2025/8bon_16144.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 117 5.16 5 C 16509 2.51 5 N 4277 2.21 5 O 5027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 1.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25930 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 8304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8304 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 157 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 157 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 8298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1069, 8292 Classifications: {'peptide': 1069} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1011} Chain breaks: 4 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 1069, 8292 Classifications: {'peptide': 1069} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1011} Chain breaks: 4 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 8483 Chain: "C" Number of atoms: 8168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8168 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 56, 'TRANS': 996} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 157 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" 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: "H" 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: "M" 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: "N" 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: "Q" 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: "R" 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: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" 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: 21.02, per 1000 atoms: 0.81 Number of scatterers: 25930 At special positions: 0 Unit cell: (152.323, 160.992, 196.906, 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 117 16.00 O 5027 8.00 N 4277 7.00 C 16509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 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 C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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 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=9, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 282 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 17 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 17 " " NAG C1309 " - " ASN C 331 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1134 " Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.23 Conformation dependent library (CDL) restraints added in 4.5 seconds 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6076 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 46 sheets defined 24.1% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.595A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.101A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.506A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.621A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.647A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 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 758 through 783 removed outlier: 3.623A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.913A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.957A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.704A 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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.555A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.381A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.240A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.783A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.721A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.601A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.562A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.985A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.744A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.423A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.874A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.727A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.142A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.529A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.636A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 753 removed outlier: 3.554A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.534A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.530A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.315A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.650A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.822A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.770A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.549A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.370A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 30 current: chain 'B' and resid 78 through 79 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 186 through 195 removed outlier: 4.358A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.617A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 4.005A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.108A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.646A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.305A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.176A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.566A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.032A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.042A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.358A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.590A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.492A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 27 through 30 current: chain 'A' and resid 78 through 79 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 186 through 197 removed outlier: 4.367A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.519A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.880A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 3.568A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.323A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.068A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.054A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.604A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.000A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.845A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.238A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.238A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 6.332A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 171 current: chain 'C' and resid 258 through 259 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.656A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.472A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.728A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.559A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.621A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.345A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.708A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.929A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.363A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 919 hydrogen bonds defined for protein. 2576 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: 11.24 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4176 1.32 - 1.44: 7515 1.44 - 1.57: 14685 1.57 - 1.69: 1 1.69 - 1.82: 151 Bond restraints: 26528 Sorted by residual: bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.191 0.312 3.40e-02 8.65e+02 8.40e+01 bond pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.473 1.567 -0.094 1.40e-02 5.10e+03 4.49e+01 bond pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 1.469 1.410 0.059 1.28e-02 6.10e+03 2.10e+01 bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.709 -0.217 5.00e-02 4.00e+02 1.88e+01 bond pdb=" CD CCS D 17 " pdb=" CE CCS D 17 " ideal model delta sigma weight residual 1.548 1.499 0.049 2.00e-02 2.50e+03 6.09e+00 ... (remaining 26523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 36104 4.19 - 8.39: 25 8.39 - 12.58: 4 12.58 - 16.77: 2 16.77 - 20.96: 3 Bond angle restraints: 36138 Sorted by residual: angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 92.68 19.32 1.40e+00 5.10e-01 1.90e+02 angle pdb=" N PRO A 384 " pdb=" CD PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 103.20 87.19 16.01 1.50e+00 4.44e-01 1.14e+02 angle pdb=" SG CCS E 17 " pdb=" CD CCS E 17 " pdb=" CE CCS E 17 " ideal model delta sigma weight residual 117.40 138.36 -20.96 3.00e+00 1.11e-01 4.88e+01 angle pdb=" SG CCS F 17 " pdb=" CD CCS F 17 " pdb=" CE CCS F 17 " ideal model delta sigma weight residual 117.40 137.93 -20.53 3.00e+00 1.11e-01 4.68e+01 angle pdb=" CA PRO A 384 " pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 104.50 92.74 11.76 1.90e+00 2.77e-01 3.83e+01 ... (remaining 36133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14997 17.95 - 35.89: 1112 35.89 - 53.84: 216 53.84 - 71.79: 60 71.79 - 89.73: 22 Dihedral angle restraints: 16407 sinusoidal: 6961 harmonic: 9446 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.64 72.64 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.78 58.78 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 142.03 -49.03 1 1.00e+01 1.00e-02 3.31e+01 ... (remaining 16404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3615 0.063 - 0.126: 604 0.126 - 0.189: 13 0.189 - 0.252: 4 0.252 - 0.315: 2 Chirality restraints: 4238 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 4235 not shown) Planarity restraints: 4655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.112 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO A 384 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " 0.065 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO B 209 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 233 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C ILE A 233 " -0.048 2.00e-02 2.50e+03 pdb=" O ILE A 233 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 234 " 0.016 2.00e-02 2.50e+03 ... (remaining 4652 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 652 2.70 - 3.25: 24624 3.25 - 3.80: 39949 3.80 - 4.35: 53087 4.35 - 4.90: 90317 Nonbonded interactions: 208629 Sorted by model distance: nonbonded pdb=" O ILE A 233 " pdb=" N2 NAG A1303 " model vdw 2.145 3.120 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.208 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU C 298 " pdb=" OG SER C 316 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.216 3.040 ... (remaining 208624 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 14 through 69 or resid 76 through 183 or resid 188 through \ 209 or resid 219 through 247 or resid 251 through 308 or (resid 309 and (name N \ or name CA or name C or name O or name CB )) or resid 310 through 492 or resid \ 494 through 528 or (resid 529 and (name N or name CA or name C or name O or name \ CB )) or resid 530 through 553 or (resid 554 and (name N or name CA or name C o \ r name O or name CB )) or resid 555 through 793 or (resid 794 and (name N or nam \ e CA or name C or name O or name CB )) or resid 795 or (resid 796 and (name N or \ name CA or name C or name O or name CB )) or resid 797 through 1141 or (resid 1 \ 142 and (name N or name CA or name C or name O or name CB )) or resid 1143 throu \ gh 1144 or (resid 1145 through 1146 and (name N or name CA or name C or name O o \ r name CB )) or resid 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 69 or resid 76 through 183 or resid 188 through \ 209 or resid 219 through 247 or resid 251 through 492 or resid 494 through 581 \ or (resid 582 through 583 and (name N or name CA or name C or name O or name CB \ )) or resid 584 through 585 or (resid 586 and (name N or name CA or name C or na \ me O or name CB )) or resid 587 through 613 or (resid 614 and (name N or name CA \ or name C or name O or name CB )) or resid 615 through 618 or (resid 619 and (n \ ame N or name CA or name C or name O or name CB )) or resid 620 through 676 or r \ esid 690 through 744 or (resid 745 and (name N or name CA or name C or name O or \ name CB )) or resid 746 through 920 or (resid 921 and (name N or name CA or nam \ e C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name N \ or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (res \ id 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 t \ hrough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 457 or (resid 458 and (name N or name CA or nam \ e C or name O or name CB )) or resid 459 through 492 or resid 494 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 613 or (resid 614 and (name N or name CA o \ r name C or name O or name CB )) or resid 615 through 618 or (resid 619 and (nam \ e N or name CA or name C or name O or name CB )) or resid 620 through 676 or res \ id 690 through 744 or (resid 745 and (name N or name CA or name C or name O or n \ ame CB )) or resid 746 through 920 or (resid 921 and (name N or name CA or name \ C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name N o \ r name CA or name C or name O or name CB )) or resid 1074 through 1117 or (resid \ 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 thr \ ough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O \ or name CB )) or resid 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 70.240 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.180 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.312 26625 Z= 0.238 Angle : 0.585 20.964 36361 Z= 0.285 Chirality : 0.044 0.315 4238 Planarity : 0.004 0.150 4621 Dihedral : 13.294 89.735 10208 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3199 helix: 1.35 (0.21), residues: 648 sheet: 0.60 (0.20), residues: 724 loop : -0.56 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.026 0.001 PHE A 168 TYR 0.013 0.001 TYR B1067 ARG 0.004 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 34) link_NAG-ASN : angle 2.50875 ( 102) link_BETA1-4 : bond 0.00394 ( 13) link_BETA1-4 : angle 1.07967 ( 39) hydrogen bonds : bond 0.20775 ( 919) hydrogen bonds : angle 8.46895 ( 2576) SS BOND : bond 0.00320 ( 41) SS BOND : angle 1.12323 ( 82) covalent geometry : bond 0.00441 (26528) covalent geometry : angle 0.56785 (36138) Misc. bond : bond 0.08298 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 2.933 Fit side-chains REVERT: A 168 PHE cc_start: 0.6763 (t80) cc_final: 0.6542 (t80) REVERT: A 384 PRO cc_start: 0.6775 (Cg_exo) cc_final: 0.6361 (Cg_exo) REVERT: C 238 PHE cc_start: 0.7312 (p90) cc_final: 0.7051 (p90) REVERT: C 950 ASP cc_start: 0.7788 (m-30) cc_final: 0.7442 (m-30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3381 time to fit residues: 120.0712 Evaluate side-chains 167 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 129 optimal weight: 0.1980 chunk 251 optimal weight: 50.0000 chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 187 optimal weight: 0.6980 chunk 291 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.196308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163791 restraints weight = 36771.984| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.06 r_work: 0.3610 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26625 Z= 0.118 Angle : 0.540 11.802 36361 Z= 0.273 Chirality : 0.045 0.370 4238 Planarity : 0.004 0.074 4621 Dihedral : 6.597 59.093 4518 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.29 % Allowed : 4.40 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3199 helix: 1.94 (0.21), residues: 645 sheet: 0.58 (0.19), residues: 726 loop : -0.52 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.004 0.001 HIS C1083 PHE 0.027 0.001 PHE C 168 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 34) link_NAG-ASN : angle 2.59215 ( 102) link_BETA1-4 : bond 0.00442 ( 13) link_BETA1-4 : angle 1.11812 ( 39) hydrogen bonds : bond 0.04560 ( 919) hydrogen bonds : angle 6.12571 ( 2576) SS BOND : bond 0.00358 ( 41) SS BOND : angle 1.15228 ( 82) covalent geometry : bond 0.00263 (26528) covalent geometry : angle 0.51967 (36138) Misc. bond : bond 0.00360 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 2.918 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 189 average time/residue: 0.3636 time to fit residues: 114.9597 Evaluate side-chains 169 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 65 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 287 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 249 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 784 GLN B1125 ASN A 613 GLN A 955 ASN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.192572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160604 restraints weight = 37534.089| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.16 r_work: 0.3573 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 26625 Z= 0.281 Angle : 0.636 11.657 36361 Z= 0.320 Chirality : 0.049 0.366 4238 Planarity : 0.004 0.039 4621 Dihedral : 6.284 59.099 4518 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.89 % Allowed : 6.19 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3199 helix: 1.52 (0.21), residues: 644 sheet: 0.37 (0.19), residues: 722 loop : -0.71 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 886 HIS 0.009 0.001 HIS C1083 PHE 0.027 0.002 PHE A 559 TYR 0.024 0.002 TYR B1067 ARG 0.005 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 34) link_NAG-ASN : angle 2.80129 ( 102) link_BETA1-4 : bond 0.00288 ( 13) link_BETA1-4 : angle 1.35561 ( 39) hydrogen bonds : bond 0.05676 ( 919) hydrogen bonds : angle 5.95731 ( 2576) SS BOND : bond 0.00707 ( 41) SS BOND : angle 1.65895 ( 82) covalent geometry : bond 0.00692 (26528) covalent geometry : angle 0.61320 (36138) Misc. bond : bond 0.00365 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 2.813 Fit side-chains REVERT: B 784 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: B 869 MET cc_start: 0.9104 (mtt) cc_final: 0.8861 (mtt) REVERT: C 950 ASP cc_start: 0.8504 (m-30) cc_final: 0.8301 (m-30) outliers start: 25 outliers final: 21 residues processed: 194 average time/residue: 0.3425 time to fit residues: 110.5244 Evaluate side-chains 188 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 215 optimal weight: 30.0000 chunk 82 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN ** A 762 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 = 0.4194 r_free = 0.4194 target = 0.194429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152497 restraints weight = 35559.292| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 4.55 r_work: 0.3126 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26625 Z= 0.153 Angle : 0.554 11.359 36361 Z= 0.277 Chirality : 0.045 0.379 4238 Planarity : 0.004 0.040 4621 Dihedral : 5.738 56.747 4518 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.86 % Allowed : 7.55 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3199 helix: 1.81 (0.21), residues: 645 sheet: 0.43 (0.19), residues: 720 loop : -0.66 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 886 HIS 0.004 0.001 HIS C1083 PHE 0.032 0.001 PHE A 238 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 34) link_NAG-ASN : angle 2.64535 ( 102) link_BETA1-4 : bond 0.00369 ( 13) link_BETA1-4 : angle 1.23568 ( 39) hydrogen bonds : bond 0.04508 ( 919) hydrogen bonds : angle 5.61584 ( 2576) SS BOND : bond 0.00447 ( 41) SS BOND : angle 1.31096 ( 82) covalent geometry : bond 0.00367 (26528) covalent geometry : angle 0.53268 (36138) Misc. bond : bond 0.00346 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 2.662 Fit side-chains REVERT: C 984 LEU cc_start: 0.8504 (mp) cc_final: 0.8264 (mp) outliers start: 24 outliers final: 22 residues processed: 191 average time/residue: 0.3468 time to fit residues: 110.5645 Evaluate side-chains 186 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 226 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 690 GLN A 87 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.193094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163179 restraints weight = 48727.529| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.16 r_work: 0.3573 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26625 Z= 0.216 Angle : 0.594 11.282 36361 Z= 0.297 Chirality : 0.047 0.366 4238 Planarity : 0.004 0.040 4621 Dihedral : 5.577 59.860 4518 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.18 % Allowed : 8.59 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3199 helix: 1.61 (0.20), residues: 653 sheet: 0.34 (0.19), residues: 724 loop : -0.72 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 886 HIS 0.006 0.001 HIS B1064 PHE 0.027 0.002 PHE A 238 TYR 0.023 0.001 TYR B1067 ARG 0.007 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 34) link_NAG-ASN : angle 2.72175 ( 102) link_BETA1-4 : bond 0.00318 ( 13) link_BETA1-4 : angle 1.33667 ( 39) hydrogen bonds : bond 0.04966 ( 919) hydrogen bonds : angle 5.55609 ( 2576) SS BOND : bond 0.00585 ( 41) SS BOND : angle 1.48292 ( 82) covalent geometry : bond 0.00533 (26528) covalent geometry : angle 0.57212 (36138) Misc. bond : bond 0.00325 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 2.938 Fit side-chains REVERT: C 984 LEU cc_start: 0.8271 (mp) cc_final: 0.8066 (mp) outliers start: 33 outliers final: 27 residues processed: 192 average time/residue: 0.3472 time to fit residues: 110.7520 Evaluate side-chains 191 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 117 optimal weight: 6.9990 chunk 51 optimal weight: 0.0270 chunk 262 optimal weight: 50.0000 chunk 130 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 overall best weight: 2.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.192576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151518 restraints weight = 43070.526| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.50 r_work: 0.3396 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26625 Z= 0.249 Angle : 0.616 11.086 36361 Z= 0.308 Chirality : 0.048 0.372 4238 Planarity : 0.004 0.042 4621 Dihedral : 5.586 58.582 4518 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.43 % Allowed : 9.45 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3199 helix: 1.43 (0.20), residues: 653 sheet: 0.21 (0.19), residues: 742 loop : -0.75 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 PHE 0.026 0.002 PHE A 238 TYR 0.023 0.001 TYR B1067 ARG 0.007 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 34) link_NAG-ASN : angle 2.75046 ( 102) link_BETA1-4 : bond 0.00306 ( 13) link_BETA1-4 : angle 1.37169 ( 39) hydrogen bonds : bond 0.05124 ( 919) hydrogen bonds : angle 5.56215 ( 2576) SS BOND : bond 0.00638 ( 41) SS BOND : angle 1.65348 ( 82) covalent geometry : bond 0.00612 (26528) covalent geometry : angle 0.59358 (36138) Misc. bond : bond 0.00319 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 2.548 Fit side-chains REVERT: C 984 LEU cc_start: 0.8489 (mp) cc_final: 0.8272 (mp) outliers start: 40 outliers final: 31 residues processed: 197 average time/residue: 0.3268 time to fit residues: 107.0290 Evaluate side-chains 199 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 315 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 304 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 310 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN C 66 HIS C 540 ASN C 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.194493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164065 restraints weight = 43668.852| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.11 r_work: 0.3600 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26625 Z= 0.130 Angle : 0.545 11.635 36361 Z= 0.271 Chirality : 0.045 0.389 4238 Planarity : 0.004 0.041 4621 Dihedral : 5.245 57.933 4518 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.22 % Allowed : 9.84 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3199 helix: 1.83 (0.21), residues: 646 sheet: 0.25 (0.19), residues: 752 loop : -0.66 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 PHE 0.025 0.001 PHE A 238 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 34) link_NAG-ASN : angle 2.60399 ( 102) link_BETA1-4 : bond 0.00380 ( 13) link_BETA1-4 : angle 1.23167 ( 39) hydrogen bonds : bond 0.04209 ( 919) hydrogen bonds : angle 5.35159 ( 2576) SS BOND : bond 0.00381 ( 41) SS BOND : angle 1.30930 ( 82) covalent geometry : bond 0.00307 (26528) covalent geometry : angle 0.52322 (36138) Misc. bond : bond 0.00326 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 2.584 Fit side-chains REVERT: B 902 MET cc_start: 0.9090 (tpt) cc_final: 0.8862 (tpt) outliers start: 34 outliers final: 27 residues processed: 197 average time/residue: 0.3453 time to fit residues: 113.7287 Evaluate side-chains 193 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.193167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161105 restraints weight = 35106.932| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.07 r_work: 0.3573 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26625 Z= 0.212 Angle : 0.594 11.480 36361 Z= 0.296 Chirality : 0.047 0.378 4238 Planarity : 0.004 0.041 4621 Dihedral : 5.313 56.972 4518 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.43 % Allowed : 10.06 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3199 helix: 1.63 (0.21), residues: 654 sheet: 0.18 (0.19), residues: 753 loop : -0.70 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.006 0.001 HIS B1064 PHE 0.028 0.001 PHE A 238 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 34) link_NAG-ASN : angle 2.69004 ( 102) link_BETA1-4 : bond 0.00328 ( 13) link_BETA1-4 : angle 1.32654 ( 39) hydrogen bonds : bond 0.04826 ( 919) hydrogen bonds : angle 5.41966 ( 2576) SS BOND : bond 0.00570 ( 41) SS BOND : angle 1.52800 ( 82) covalent geometry : bond 0.00521 (26528) covalent geometry : angle 0.57240 (36138) Misc. bond : bond 0.00312 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 4.256 Fit side-chains REVERT: B 869 MET cc_start: 0.9042 (mtt) cc_final: 0.8791 (mtt) REVERT: C 745 ASP cc_start: 0.7199 (t70) cc_final: 0.6993 (t0) outliers start: 40 outliers final: 32 residues processed: 196 average time/residue: 0.5247 time to fit residues: 176.5095 Evaluate side-chains 194 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 5.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 117 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 161 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 238 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.193800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.164322 restraints weight = 43532.432| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.00 r_work: 0.3611 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26625 Z= 0.172 Angle : 0.569 11.624 36361 Z= 0.283 Chirality : 0.046 0.384 4238 Planarity : 0.004 0.041 4621 Dihedral : 5.189 56.852 4518 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.25 % Allowed : 10.45 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3199 helix: 1.76 (0.21), residues: 646 sheet: 0.19 (0.19), residues: 738 loop : -0.68 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.027 0.001 PHE A 238 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 34) link_NAG-ASN : angle 2.62606 ( 102) link_BETA1-4 : bond 0.00362 ( 13) link_BETA1-4 : angle 1.26952 ( 39) hydrogen bonds : bond 0.04492 ( 919) hydrogen bonds : angle 5.34207 ( 2576) SS BOND : bond 0.00487 ( 41) SS BOND : angle 1.40874 ( 82) covalent geometry : bond 0.00420 (26528) covalent geometry : angle 0.54732 (36138) Misc. bond : bond 0.00318 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 2.615 Fit side-chains outliers start: 35 outliers final: 32 residues processed: 199 average time/residue: 0.3375 time to fit residues: 111.9883 Evaluate side-chains 198 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 222 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 294 optimal weight: 0.7980 chunk 249 optimal weight: 20.0000 chunk 192 optimal weight: 0.4980 chunk 304 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.193630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.158035 restraints weight = 35273.463| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.15 r_work: 0.3557 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26625 Z= 0.148 Angle : 0.559 11.749 36361 Z= 0.277 Chirality : 0.045 0.387 4238 Planarity : 0.004 0.048 4621 Dihedral : 5.040 56.771 4518 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.22 % Allowed : 10.52 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3199 helix: 1.84 (0.21), residues: 652 sheet: 0.19 (0.19), residues: 744 loop : -0.65 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS A1064 PHE 0.026 0.001 PHE A 238 TYR 0.018 0.001 TYR B1067 ARG 0.008 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 34) link_NAG-ASN : angle 2.58493 ( 102) link_BETA1-4 : bond 0.00380 ( 13) link_BETA1-4 : angle 1.24840 ( 39) hydrogen bonds : bond 0.04258 ( 919) hydrogen bonds : angle 5.26081 ( 2576) SS BOND : bond 0.00460 ( 41) SS BOND : angle 1.32838 ( 82) covalent geometry : bond 0.00357 (26528) covalent geometry : angle 0.53810 (36138) Misc. bond : bond 0.00317 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 2.526 Fit side-chains outliers start: 34 outliers final: 32 residues processed: 196 average time/residue: 0.3448 time to fit residues: 112.0802 Evaluate side-chains 198 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 277 optimal weight: 0.0770 chunk 63 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 43 optimal weight: 50.0000 chunk 16 optimal weight: 10.0000 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.194289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159252 restraints weight = 41498.373| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.17 r_work: 0.3558 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26625 Z= 0.135 Angle : 0.546 11.776 36361 Z= 0.271 Chirality : 0.045 0.387 4238 Planarity : 0.004 0.045 4621 Dihedral : 4.897 56.710 4518 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.18 % Allowed : 10.59 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3199 helix: 1.94 (0.21), residues: 646 sheet: 0.20 (0.19), residues: 736 loop : -0.60 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 PHE 0.025 0.001 PHE A 238 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 34) link_NAG-ASN : angle 2.55230 ( 102) link_BETA1-4 : bond 0.00384 ( 13) link_BETA1-4 : angle 1.22470 ( 39) hydrogen bonds : bond 0.04108 ( 919) hydrogen bonds : angle 5.19625 ( 2576) SS BOND : bond 0.00402 ( 41) SS BOND : angle 1.26470 ( 82) covalent geometry : bond 0.00323 (26528) covalent geometry : angle 0.52579 (36138) Misc. bond : bond 0.00316 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14660.07 seconds wall clock time: 253 minutes 59.74 seconds (15239.74 seconds total)