Starting phenix.real_space_refine on Thu Jun 26 10:23:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yr1_34042/06_2025/7yr1_34042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr1_34042/06_2025/7yr1_34042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yr1_34042/06_2025/7yr1_34042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr1_34042/06_2025/7yr1_34042.map" model { file = "/net/cci-nas-00/data/ceres_data/7yr1_34042/06_2025/7yr1_34042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr1_34042/06_2025/7yr1_34042.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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 135 5.16 5 C 19302 2.51 5 N 4926 2.21 5 O 5973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.98s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30336 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7993 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 791 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "B" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7993 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "F" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 791 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "C" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7993 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 791 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 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 Time building chain proxies: 18.92, per 1000 atoms: 0.62 Number of scatterers: 30336 At special positions: 0 Unit cell: (153.01, 158.36, 169.06, 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 135 16.00 O 5973 8.00 N 4926 7.00 C 19302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.01 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=2.02 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 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 H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=2.02 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 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 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=2.02 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 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG I 1 " - " ASN A 122 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 709 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN A1074 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 709 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 709 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C1074 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 8.35 Conformation dependent library (CDL) restraints added in 3.9 seconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7002 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 66 sheets defined 19.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.502A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.931A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.055A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.646A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 410' Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.908A pdb=" N THR A 415 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.274A pdb=" N LYS A 440 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 441 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.925A pdb=" N THR A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.573A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) 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 759 through 781 removed outlier: 3.636A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.505A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.658A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.585A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 941 removed outlier: 7.084A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.930A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.920A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.214A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.516A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.760A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.093A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.380A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 410' Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.924A pdb=" N THR B 415 " --> pdb=" O PRO B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.927A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.564A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) 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 759 through 781 removed outlier: 3.617A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.558A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 868 through 884 removed outlier: 3.659A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.610A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 7.065A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.935A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.946A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.275A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.518A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.932A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.084A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.634A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 410' Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.916A pdb=" N THR C 415 " --> pdb=" O PRO C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.260A pdb=" N LYS C 440 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 441 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.896A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.520A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.646A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 759 through 781 removed outlier: 3.629A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.596A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.687A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.609A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 7.037A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.990A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.930A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.252A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.653A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.356A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.256A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.542A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 319 removed outlier: 5.685A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.608A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.540A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.093A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 660 removed outlier: 4.238A pdb=" N TYR A 660 " --> pdb=" O THR A 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.566A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.203A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'A' and resid 1089 through 1090 removed outlier: 3.519A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.747A pdb=" N GLY H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N HIS H 33 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.747A pdb=" N GLY H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS H 95 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TRP H 118 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG H 97 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.587A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR L 49 " --> pdb=" O SER L 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.096A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.586A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.384A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.265A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.564A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 314 through 319 removed outlier: 5.664A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.615A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.525A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.097A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 659 through 660 removed outlier: 4.223A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 664 through 665 Processing sheet with id=AD7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD8, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD9, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.581A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AE3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.765A pdb=" N GLY D 10 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N HIS D 33 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.765A pdb=" N GLY D 10 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N CYS D 95 " --> pdb=" O TRP D 118 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TRP D 118 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG D 97 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.588A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR F 49 " --> pdb=" O SER F 53 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.122A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.662A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.324A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.344A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.529A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 314 through 319 removed outlier: 5.721A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 595 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.602A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.510A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.148A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 659 through 660 removed outlier: 4.221A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AG2, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AG3, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.558A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG5, first strand: chain 'C' and resid 1089 through 1090 removed outlier: 3.516A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.477A pdb=" N HIS E 33 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 50 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.416A pdb=" N CYS E 95 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TRP E 118 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG E 97 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AH2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.575A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 49 " --> pdb=" O SER G 53 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.095A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2433 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: 13.50 Time building geometry restraints manager: 9.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9507 1.34 - 1.46: 7947 1.46 - 1.58: 13395 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 31023 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.97e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 ... (remaining 31018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 39880 1.29 - 2.57: 1811 2.57 - 3.86: 422 3.86 - 5.14: 62 5.14 - 6.43: 38 Bond angle restraints: 42213 Sorted by residual: angle pdb=" N VAL A 615 " pdb=" CA VAL A 615 " pdb=" C VAL A 615 " ideal model delta sigma weight residual 113.53 108.78 4.75 9.80e-01 1.04e+00 2.35e+01 angle pdb=" N VAL C 615 " pdb=" CA VAL C 615 " pdb=" C VAL C 615 " ideal model delta sigma weight residual 113.47 108.84 4.63 1.01e+00 9.80e-01 2.10e+01 angle pdb=" N VAL B 615 " pdb=" CA VAL B 615 " pdb=" C VAL B 615 " ideal model delta sigma weight residual 113.10 109.76 3.34 9.70e-01 1.06e+00 1.19e+01 angle pdb=" CA GLY C 219 " pdb=" C GLY C 219 " pdb=" N PHE C 220 " ideal model delta sigma weight residual 114.65 117.54 -2.89 9.20e-01 1.18e+00 9.88e+00 angle pdb=" N SER B 605 " pdb=" CA SER B 605 " pdb=" C SER B 605 " ideal model delta sigma weight residual 108.24 112.26 -4.02 1.32e+00 5.74e-01 9.29e+00 ... (remaining 42208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 17988 22.04 - 44.09: 1182 44.09 - 66.13: 135 66.13 - 88.17: 80 88.17 - 110.22: 46 Dihedral angle restraints: 19431 sinusoidal: 8508 harmonic: 10923 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 23.71 69.29 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 24.33 68.67 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 25.16 67.84 1 1.00e+01 1.00e-02 5.98e+01 ... (remaining 19428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4019 0.054 - 0.109: 857 0.109 - 0.163: 122 0.163 - 0.218: 3 0.218 - 0.272: 12 Chirality restraints: 5013 Sorted by residual: chirality pdb=" C5 BMA c 3 " pdb=" C4 BMA c 3 " pdb=" C6 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5010 not shown) Planarity restraints: 5364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " 0.016 2.00e-02 2.50e+03 1.46e-02 3.74e+00 pdb=" CG PHE B 906 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO C 986 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 986 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.021 5.00e-02 4.00e+02 ... (remaining 5361 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 894 2.69 - 3.24: 29479 3.24 - 3.80: 43477 3.80 - 4.35: 54959 4.35 - 4.90: 94911 Nonbonded interactions: 223720 Sorted by model distance: nonbonded pdb=" O ALA C 520 " pdb=" NE2 GLN C 564 " model vdw 2.141 3.120 nonbonded pdb=" O ALA A 520 " pdb=" NE2 GLN A 564 " model vdw 2.147 3.120 nonbonded pdb=" O ALA B 520 " pdb=" NE2 GLN B 564 " model vdw 2.154 3.120 nonbonded pdb=" OE1 GLN G 6 " pdb=" OG1 THR G 102 " model vdw 2.169 3.040 nonbonded pdb=" OE1 GLN F 6 " pdb=" OG1 THR F 102 " model vdw 2.187 3.040 ... (remaining 223715 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'd' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 1.100 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 71.410 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31146 Z= 0.205 Angle : 0.677 8.256 42540 Z= 0.338 Chirality : 0.047 0.272 5013 Planarity : 0.004 0.052 5316 Dihedral : 15.636 110.216 12303 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3708 helix: 1.65 (0.22), residues: 615 sheet: -1.05 (0.17), residues: 966 loop : -2.08 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 633 HIS 0.002 0.001 HIS B1101 PHE 0.034 0.001 PHE B 906 TYR 0.014 0.001 TYR A 904 ARG 0.006 0.001 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 48) link_NAG-ASN : angle 2.43808 ( 144) link_BETA1-4 : bond 0.00478 ( 33) link_BETA1-4 : angle 1.31442 ( 99) hydrogen bonds : bond 0.16847 ( 901) hydrogen bonds : angle 6.52327 ( 2433) SS BOND : bond 0.00476 ( 42) SS BOND : angle 1.66778 ( 84) covalent geometry : bond 0.00446 (31023) covalent geometry : angle 0.65774 (42213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8823 (m-10) cc_final: 0.8410 (m-80) REVERT: H 88 GLU cc_start: 0.8632 (tp30) cc_final: 0.8376 (tp30) REVERT: H 115 MET cc_start: 0.6801 (mpp) cc_final: 0.6485 (mmp) REVERT: B 532 ASN cc_start: 0.8716 (t0) cc_final: 0.8510 (t0) REVERT: B 850 ILE cc_start: 0.8954 (mm) cc_final: 0.8743 (tp) REVERT: C 429 PHE cc_start: 0.8544 (t80) cc_final: 0.8270 (t80) REVERT: E 115 MET cc_start: 0.6815 (mpp) cc_final: 0.6162 (mmp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.4533 time to fit residues: 192.0471 Evaluate side-chains 204 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 291 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 337 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 926 GLN B 121 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 66 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.114526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.084997 restraints weight = 66729.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086099 restraints weight = 44150.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086861 restraints weight = 31857.496| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 31146 Z= 0.183 Angle : 0.635 8.380 42540 Z= 0.319 Chirality : 0.045 0.356 5013 Planarity : 0.004 0.041 5316 Dihedral : 9.842 69.576 5724 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.06 % Favored : 90.86 % Rotamer: Outliers : 1.05 % Allowed : 6.69 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3708 helix: 1.44 (0.22), residues: 636 sheet: -1.01 (0.17), residues: 1008 loop : -2.19 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 633 HIS 0.004 0.001 HIS A1048 PHE 0.016 0.001 PHE A1121 TYR 0.015 0.001 TYR E 111 ARG 0.007 0.001 ARG C 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 48) link_NAG-ASN : angle 2.37596 ( 144) link_BETA1-4 : bond 0.00592 ( 33) link_BETA1-4 : angle 1.86215 ( 99) hydrogen bonds : bond 0.04741 ( 901) hydrogen bonds : angle 5.43968 ( 2433) SS BOND : bond 0.00456 ( 42) SS BOND : angle 1.79842 ( 84) covalent geometry : bond 0.00437 (31023) covalent geometry : angle 0.61039 (42213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 3.047 Fit side-chains REVERT: A 177 MET cc_start: 0.7676 (mpp) cc_final: 0.7444 (mmm) REVERT: A 421 TYR cc_start: 0.5934 (m-10) cc_final: 0.5528 (m-10) REVERT: A 457 ARG cc_start: 0.5621 (tmt170) cc_final: 0.5002 (ttt180) REVERT: A 736 VAL cc_start: 0.9543 (t) cc_final: 0.9297 (p) REVERT: H 88 GLU cc_start: 0.8695 (tp30) cc_final: 0.8448 (tp30) REVERT: H 115 MET cc_start: 0.6989 (mpp) cc_final: 0.6716 (mtm) REVERT: B 421 TYR cc_start: 0.6031 (m-10) cc_final: 0.5776 (m-10) REVERT: B 850 ILE cc_start: 0.8981 (mm) cc_final: 0.8766 (tp) REVERT: C 421 TYR cc_start: 0.5990 (m-10) cc_final: 0.5789 (m-10) REVERT: C 532 ASN cc_start: 0.8714 (t0) cc_final: 0.8491 (t0) REVERT: E 115 MET cc_start: 0.7158 (mpp) cc_final: 0.6773 (mtm) outliers start: 34 outliers final: 28 residues processed: 244 average time/residue: 0.4091 time to fit residues: 161.4745 Evaluate side-chains 220 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 173 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 82 optimal weight: 0.0020 chunk 78 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 564 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 955 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 804 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.112454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082849 restraints weight = 67100.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083535 restraints weight = 45263.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084352 restraints weight = 33371.320| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 31146 Z= 0.232 Angle : 0.671 8.337 42540 Z= 0.338 Chirality : 0.046 0.330 5013 Planarity : 0.004 0.060 5316 Dihedral : 8.151 54.835 5724 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.57 % Favored : 89.35 % Rotamer: Outliers : 1.82 % Allowed : 10.47 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.14), residues: 3708 helix: 1.28 (0.22), residues: 633 sheet: -1.07 (0.17), residues: 999 loop : -2.31 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 102 HIS 0.008 0.001 HIS C 66 PHE 0.017 0.002 PHE C1089 TYR 0.017 0.002 TYR C 279 ARG 0.007 0.001 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 48) link_NAG-ASN : angle 2.60923 ( 144) link_BETA1-4 : bond 0.00463 ( 33) link_BETA1-4 : angle 1.91088 ( 99) hydrogen bonds : bond 0.05314 ( 901) hydrogen bonds : angle 5.51980 ( 2433) SS BOND : bond 0.00503 ( 42) SS BOND : angle 1.86045 ( 84) covalent geometry : bond 0.00560 (31023) covalent geometry : angle 0.64474 (42213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 209 time to evaluate : 4.083 Fit side-chains REVERT: A 421 TYR cc_start: 0.5967 (m-10) cc_final: 0.5530 (m-10) REVERT: H 88 GLU cc_start: 0.8709 (tp30) cc_final: 0.8463 (tp30) REVERT: B 532 ASN cc_start: 0.8547 (t0) cc_final: 0.8220 (t0) REVERT: B 850 ILE cc_start: 0.8915 (mm) cc_final: 0.8704 (tp) REVERT: F 79 GLN cc_start: 0.6413 (mm110) cc_final: 0.6145 (mt0) REVERT: C 532 ASN cc_start: 0.8673 (t0) cc_final: 0.8388 (t0) outliers start: 59 outliers final: 39 residues processed: 257 average time/residue: 0.4273 time to fit residues: 181.3484 Evaluate side-chains 221 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 295 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 277 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 221 optimal weight: 0.3980 chunk 270 optimal weight: 0.0670 overall best weight: 1.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084038 restraints weight = 67187.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085293 restraints weight = 42871.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085992 restraints weight = 31500.548| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31146 Z= 0.158 Angle : 0.606 8.373 42540 Z= 0.306 Chirality : 0.044 0.326 5013 Planarity : 0.004 0.041 5316 Dihedral : 6.753 52.999 5724 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.63 % Favored : 91.29 % Rotamer: Outliers : 2.06 % Allowed : 11.95 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3708 helix: 1.36 (0.22), residues: 636 sheet: -1.09 (0.17), residues: 969 loop : -2.21 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 102 HIS 0.005 0.001 HIS C 66 PHE 0.015 0.001 PHE A1121 TYR 0.014 0.001 TYR C 453 ARG 0.016 0.000 ARG H 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 48) link_NAG-ASN : angle 2.38431 ( 144) link_BETA1-4 : bond 0.00517 ( 33) link_BETA1-4 : angle 1.78362 ( 99) hydrogen bonds : bond 0.04421 ( 901) hydrogen bonds : angle 5.24461 ( 2433) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.72073 ( 84) covalent geometry : bond 0.00378 (31023) covalent geometry : angle 0.58113 (42213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 208 time to evaluate : 3.159 Fit side-chains REVERT: A 421 TYR cc_start: 0.5958 (m-10) cc_final: 0.5513 (m-10) REVERT: H 88 GLU cc_start: 0.8648 (tp30) cc_final: 0.8390 (tp30) REVERT: B 532 ASN cc_start: 0.8643 (t0) cc_final: 0.8231 (t0) REVERT: B 663 ASP cc_start: 0.8002 (m-30) cc_final: 0.7738 (m-30) REVERT: C 532 ASN cc_start: 0.8605 (t0) cc_final: 0.8303 (t0) REVERT: C 663 ASP cc_start: 0.7830 (m-30) cc_final: 0.7595 (m-30) REVERT: G 27 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7614 (mp10) outliers start: 67 outliers final: 52 residues processed: 265 average time/residue: 0.4104 time to fit residues: 177.4522 Evaluate side-chains 241 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 64 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 336 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 913 GLN H 39 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085442 restraints weight = 66703.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087483 restraints weight = 42206.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087728 restraints weight = 29860.448| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31146 Z= 0.120 Angle : 0.572 8.445 42540 Z= 0.289 Chirality : 0.044 0.323 5013 Planarity : 0.004 0.037 5316 Dihedral : 5.867 53.125 5724 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.47 % Favored : 91.45 % Rotamer: Outliers : 2.28 % Allowed : 12.78 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3708 helix: 1.57 (0.22), residues: 624 sheet: -1.08 (0.17), residues: 978 loop : -2.08 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 102 HIS 0.004 0.000 HIS C 66 PHE 0.014 0.001 PHE B1121 TYR 0.013 0.001 TYR A 453 ARG 0.006 0.000 ARG E 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 48) link_NAG-ASN : angle 2.25479 ( 144) link_BETA1-4 : bond 0.00511 ( 33) link_BETA1-4 : angle 1.55280 ( 99) hydrogen bonds : bond 0.03930 ( 901) hydrogen bonds : angle 5.04496 ( 2433) SS BOND : bond 0.00329 ( 42) SS BOND : angle 1.53957 ( 84) covalent geometry : bond 0.00278 (31023) covalent geometry : angle 0.54951 (42213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 210 time to evaluate : 4.067 Fit side-chains REVERT: A 663 ASP cc_start: 0.7909 (m-30) cc_final: 0.7708 (m-30) REVERT: H 88 GLU cc_start: 0.8642 (tp30) cc_final: 0.8372 (tp30) REVERT: L 27 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: B 429 PHE cc_start: 0.8412 (t80) cc_final: 0.7903 (t80) REVERT: B 532 ASN cc_start: 0.8641 (t0) cc_final: 0.8224 (t0) REVERT: B 663 ASP cc_start: 0.8001 (m-30) cc_final: 0.7744 (m-30) REVERT: F 27 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: C 532 ASN cc_start: 0.8608 (t0) cc_final: 0.8237 (t0) REVERT: C 633 TRP cc_start: 0.8130 (t60) cc_final: 0.7815 (t60) REVERT: C 663 ASP cc_start: 0.7853 (m-30) cc_final: 0.7618 (m-30) REVERT: E 64 LYS cc_start: 0.8722 (tttt) cc_final: 0.8044 (mtpt) REVERT: G 27 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7661 (mp10) outliers start: 74 outliers final: 56 residues processed: 274 average time/residue: 0.4560 time to fit residues: 205.3763 Evaluate side-chains 249 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 300 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 269 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083312 restraints weight = 67138.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.084394 restraints weight = 43856.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085435 restraints weight = 30747.351| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 31146 Z= 0.204 Angle : 0.625 8.314 42540 Z= 0.316 Chirality : 0.044 0.322 5013 Planarity : 0.004 0.038 5316 Dihedral : 5.966 57.602 5724 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.92 % Favored : 89.99 % Rotamer: Outliers : 2.46 % Allowed : 13.22 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3708 helix: 1.46 (0.22), residues: 615 sheet: -1.08 (0.17), residues: 969 loop : -2.21 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 102 HIS 0.004 0.001 HIS A1048 PHE 0.015 0.002 PHE C1121 TYR 0.015 0.001 TYR C 279 ARG 0.007 0.000 ARG E 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 48) link_NAG-ASN : angle 2.47434 ( 144) link_BETA1-4 : bond 0.00457 ( 33) link_BETA1-4 : angle 1.59253 ( 99) hydrogen bonds : bond 0.04676 ( 901) hydrogen bonds : angle 5.23333 ( 2433) SS BOND : bond 0.00502 ( 42) SS BOND : angle 1.69791 ( 84) covalent geometry : bond 0.00492 (31023) covalent geometry : angle 0.60100 (42213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 195 time to evaluate : 3.261 Fit side-chains REVERT: A 88 ASP cc_start: 0.8186 (m-30) cc_final: 0.7952 (m-30) REVERT: A 663 ASP cc_start: 0.7919 (m-30) cc_final: 0.7700 (m-30) REVERT: H 88 GLU cc_start: 0.8674 (tp30) cc_final: 0.8374 (tp30) REVERT: L 27 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: B 532 ASN cc_start: 0.8704 (t0) cc_final: 0.8332 (t0) REVERT: B 663 ASP cc_start: 0.7999 (m-30) cc_final: 0.7710 (m-30) REVERT: F 27 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: C 532 ASN cc_start: 0.8636 (t0) cc_final: 0.8386 (t0) REVERT: C 663 ASP cc_start: 0.7867 (m-30) cc_final: 0.7623 (m-30) REVERT: G 27 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7721 (mp10) outliers start: 80 outliers final: 68 residues processed: 264 average time/residue: 0.3887 time to fit residues: 170.0146 Evaluate side-chains 257 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 117 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 304 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 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 = 0.3742 r_free = 0.3742 target = 0.114105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084400 restraints weight = 66452.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.086443 restraints weight = 41294.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.086684 restraints weight = 29791.878| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 31146 Z= 0.140 Angle : 0.582 8.324 42540 Z= 0.294 Chirality : 0.043 0.318 5013 Planarity : 0.004 0.037 5316 Dihedral : 5.630 59.373 5724 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 2.46 % Allowed : 13.77 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3708 helix: 1.55 (0.22), residues: 615 sheet: -1.03 (0.17), residues: 957 loop : -2.15 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 102 HIS 0.004 0.000 HIS C 66 PHE 0.014 0.001 PHE B1121 TYR 0.015 0.001 TYR A 380 ARG 0.007 0.000 ARG E 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 48) link_NAG-ASN : angle 2.30331 ( 144) link_BETA1-4 : bond 0.00509 ( 33) link_BETA1-4 : angle 1.46361 ( 99) hydrogen bonds : bond 0.04111 ( 901) hydrogen bonds : angle 5.05043 ( 2433) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.69642 ( 84) covalent geometry : bond 0.00333 (31023) covalent geometry : angle 0.55923 (42213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 201 time to evaluate : 3.580 Fit side-chains REVERT: A 88 ASP cc_start: 0.8188 (m-30) cc_final: 0.7955 (m-30) REVERT: A 663 ASP cc_start: 0.7921 (m-30) cc_final: 0.7709 (m-30) REVERT: H 88 GLU cc_start: 0.8654 (tp30) cc_final: 0.8345 (tp30) REVERT: L 27 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: B 532 ASN cc_start: 0.8692 (t0) cc_final: 0.8334 (t0) REVERT: B 663 ASP cc_start: 0.7964 (m-30) cc_final: 0.7677 (m-30) REVERT: F 27 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: C 532 ASN cc_start: 0.8672 (t0) cc_final: 0.8418 (t0) REVERT: C 663 ASP cc_start: 0.7840 (m-30) cc_final: 0.7596 (m-30) REVERT: G 27 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7688 (mp10) outliers start: 80 outliers final: 70 residues processed: 266 average time/residue: 0.5393 time to fit residues: 237.5891 Evaluate side-chains 265 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 192 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 139 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 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 = 0.3769 r_free = 0.3769 target = 0.115853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085575 restraints weight = 66903.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088447 restraints weight = 40129.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088767 restraints weight = 26399.230| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31146 Z= 0.105 Angle : 0.555 8.454 42540 Z= 0.279 Chirality : 0.043 0.319 5013 Planarity : 0.003 0.037 5316 Dihedral : 5.107 55.731 5724 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.98 % Favored : 91.94 % Rotamer: Outliers : 2.16 % Allowed : 14.48 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3708 helix: 1.66 (0.23), residues: 618 sheet: -1.03 (0.18), residues: 897 loop : -2.06 (0.12), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 102 HIS 0.004 0.000 HIS C 66 PHE 0.013 0.001 PHE B1121 TYR 0.017 0.001 TYR B 365 ARG 0.005 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 48) link_NAG-ASN : angle 2.13576 ( 144) link_BETA1-4 : bond 0.00524 ( 33) link_BETA1-4 : angle 1.33651 ( 99) hydrogen bonds : bond 0.03552 ( 901) hydrogen bonds : angle 4.78991 ( 2433) SS BOND : bond 0.00323 ( 42) SS BOND : angle 1.54748 ( 84) covalent geometry : bond 0.00239 (31023) covalent geometry : angle 0.53464 (42213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 4.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8186 (m-30) cc_final: 0.7954 (m-30) REVERT: A 663 ASP cc_start: 0.7885 (m-30) cc_final: 0.7658 (m-30) REVERT: H 88 GLU cc_start: 0.8643 (tp30) cc_final: 0.8302 (tp30) REVERT: L 27 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: B 429 PHE cc_start: 0.8483 (t80) cc_final: 0.8121 (t80) REVERT: B 532 ASN cc_start: 0.8634 (t0) cc_final: 0.8292 (t0) REVERT: B 663 ASP cc_start: 0.7959 (m-30) cc_final: 0.7679 (m-30) REVERT: F 27 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: C 532 ASN cc_start: 0.8640 (t0) cc_final: 0.8323 (t0) REVERT: C 663 ASP cc_start: 0.7725 (m-30) cc_final: 0.7485 (m-30) REVERT: G 27 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7591 (mp10) outliers start: 70 outliers final: 57 residues processed: 270 average time/residue: 0.7463 time to fit residues: 340.4671 Evaluate side-chains 257 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 6.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 32 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 320 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 292 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.115163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084870 restraints weight = 66463.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088113 restraints weight = 39524.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088380 restraints weight = 25087.290| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31146 Z= 0.127 Angle : 0.569 8.445 42540 Z= 0.286 Chirality : 0.043 0.318 5013 Planarity : 0.004 0.037 5316 Dihedral : 5.074 48.944 5724 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.67 % Rotamer: Outliers : 2.03 % Allowed : 14.82 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3708 helix: 1.63 (0.22), residues: 618 sheet: -0.96 (0.17), residues: 954 loop : -2.06 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 633 HIS 0.003 0.000 HIS C 66 PHE 0.020 0.001 PHE C 392 TYR 0.014 0.001 TYR C 453 ARG 0.006 0.000 ARG G 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 48) link_NAG-ASN : angle 2.21241 ( 144) link_BETA1-4 : bond 0.00495 ( 33) link_BETA1-4 : angle 1.35601 ( 99) hydrogen bonds : bond 0.03802 ( 901) hydrogen bonds : angle 4.81425 ( 2433) SS BOND : bond 0.00354 ( 42) SS BOND : angle 1.57756 ( 84) covalent geometry : bond 0.00299 (31023) covalent geometry : angle 0.54769 (42213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 5.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8144 (m-30) cc_final: 0.7902 (m-30) REVERT: A 663 ASP cc_start: 0.7835 (m-30) cc_final: 0.7616 (m-30) REVERT: H 88 GLU cc_start: 0.8638 (tp30) cc_final: 0.8291 (tp30) REVERT: L 27 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: B 429 PHE cc_start: 0.8510 (t80) cc_final: 0.8249 (t80) REVERT: B 532 ASN cc_start: 0.8670 (t0) cc_final: 0.8335 (t0) REVERT: B 663 ASP cc_start: 0.7931 (m-30) cc_final: 0.7642 (m-30) REVERT: F 27 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7570 (mp10) REVERT: C 532 ASN cc_start: 0.8654 (t0) cc_final: 0.8414 (t0) REVERT: C 663 ASP cc_start: 0.7750 (m-30) cc_final: 0.7507 (m-30) REVERT: G 27 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7671 (mp10) outliers start: 66 outliers final: 61 residues processed: 253 average time/residue: 0.4502 time to fit residues: 187.7860 Evaluate side-chains 258 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 194 time to evaluate : 5.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 337 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 165 optimal weight: 20.0000 chunk 149 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086737 restraints weight = 66425.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088676 restraints weight = 42052.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088846 restraints weight = 30239.869| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31146 Z= 0.099 Angle : 0.550 8.486 42540 Z= 0.277 Chirality : 0.043 0.321 5013 Planarity : 0.003 0.037 5316 Dihedral : 4.791 40.749 5724 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 1.94 % Allowed : 14.94 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.14), residues: 3708 helix: 1.68 (0.22), residues: 618 sheet: -0.96 (0.18), residues: 897 loop : -2.00 (0.12), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 633 HIS 0.004 0.000 HIS C 66 PHE 0.015 0.001 PHE C 392 TYR 0.015 0.001 TYR C 453 ARG 0.010 0.000 ARG G 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 48) link_NAG-ASN : angle 2.08936 ( 144) link_BETA1-4 : bond 0.00527 ( 33) link_BETA1-4 : angle 1.27334 ( 99) hydrogen bonds : bond 0.03394 ( 901) hydrogen bonds : angle 4.65516 ( 2433) SS BOND : bond 0.00303 ( 42) SS BOND : angle 1.47073 ( 84) covalent geometry : bond 0.00224 (31023) covalent geometry : angle 0.53141 (42213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8182 (m-30) cc_final: 0.7949 (m-30) REVERT: A 663 ASP cc_start: 0.7835 (m-30) cc_final: 0.7608 (m-30) REVERT: H 88 GLU cc_start: 0.8653 (tp30) cc_final: 0.8304 (tp30) REVERT: L 27 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: B 429 PHE cc_start: 0.8557 (t80) cc_final: 0.8239 (t80) REVERT: B 532 ASN cc_start: 0.8595 (t0) cc_final: 0.8257 (t0) REVERT: B 663 ASP cc_start: 0.7984 (m-30) cc_final: 0.7711 (m-30) REVERT: F 27 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: C 532 ASN cc_start: 0.8590 (t0) cc_final: 0.8242 (t0) REVERT: C 663 ASP cc_start: 0.7605 (m-30) cc_final: 0.7374 (m-30) REVERT: G 27 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7584 (mp10) outliers start: 63 outliers final: 55 residues processed: 260 average time/residue: 0.5318 time to fit residues: 230.0526 Evaluate side-chains 260 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 152 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 222 optimal weight: 0.3980 chunk 124 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 314 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.116495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.087075 restraints weight = 66460.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088339 restraints weight = 42726.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089044 restraints weight = 32327.872| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31146 Z= 0.102 Angle : 0.547 8.525 42540 Z= 0.275 Chirality : 0.042 0.322 5013 Planarity : 0.003 0.037 5316 Dihedral : 4.659 33.350 5724 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.63 % Favored : 92.29 % Rotamer: Outliers : 1.91 % Allowed : 15.03 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3708 helix: 1.70 (0.22), residues: 618 sheet: -0.92 (0.18), residues: 897 loop : -1.98 (0.12), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 633 HIS 0.004 0.000 HIS C 66 PHE 0.013 0.001 PHE B1121 TYR 0.015 0.001 TYR C 453 ARG 0.008 0.000 ARG G 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 48) link_NAG-ASN : angle 2.10223 ( 144) link_BETA1-4 : bond 0.00512 ( 33) link_BETA1-4 : angle 1.26406 ( 99) hydrogen bonds : bond 0.03401 ( 901) hydrogen bonds : angle 4.61081 ( 2433) SS BOND : bond 0.00364 ( 42) SS BOND : angle 1.44225 ( 84) covalent geometry : bond 0.00235 (31023) covalent geometry : angle 0.52759 (42213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9331.34 seconds wall clock time: 172 minutes 9.19 seconds (10329.19 seconds total)